diff --git a/docs/sphinx-builddir/doctrees/algorithms.doctree b/docs/sphinx-builddir/doctrees/algorithms.doctree
index 6001b11..2bd2f27 100644
Binary files a/docs/sphinx-builddir/doctrees/algorithms.doctree and b/docs/sphinx-builddir/doctrees/algorithms.doctree differ
diff --git a/docs/sphinx-builddir/doctrees/environment.pickle b/docs/sphinx-builddir/doctrees/environment.pickle
index c40c51b..037c01d 100644
Binary files a/docs/sphinx-builddir/doctrees/environment.pickle and b/docs/sphinx-builddir/doctrees/environment.pickle differ
diff --git a/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.doctree b/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.doctree
index ad07e31..1eeb5e7 100644
Binary files a/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.doctree and b/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.doctree differ
diff --git a/docs/sphinx-builddir/html/_sources/algorithms.rst.txt b/docs/sphinx-builddir/html/_sources/algorithms.rst.txt
index 38f7060..4c7d25e 100644
--- a/docs/sphinx-builddir/html/_sources/algorithms.rst.txt
+++ b/docs/sphinx-builddir/html/_sources/algorithms.rst.txt
@@ -103,7 +103,7 @@ ChemPropHyperoptRegressor
     :members:
 
 
-ChemPropHyperoptRegressorPretrained
+ChemPropRegressorPretrained
 #########################
 ..  autoclass:: optunaz.config.optconfig.ChemPropRegressorPretrained
     :members:
diff --git a/docs/sphinx-builddir/html/algorithms.html b/docs/sphinx-builddir/html/algorithms.html
index ea71e91..4852e49 100644
--- a/docs/sphinx-builddir/html/algorithms.html
+++ b/docs/sphinx-builddir/html/algorithms.html
@@ -67,7 +67,7 @@
 <li class="toctree-l2"><a class="reference internal" href="#chempropclassifier">ChemPropClassifier</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#chemprophyperoptclassifier">ChemPropHyperoptClassifier</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#chemprophyperoptregressor">ChemPropHyperoptRegressor</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#chemprophyperoptregressorpretrained">ChemPropHyperoptRegressorPretrained</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#chempropregressorpretrained">ChemPropRegressorPretrained</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#calibratedclassifiercvwithva">CalibratedClassifierCVWithVA</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#mapie">Mapie</a></li>
 </ul>
@@ -853,8 +853,8 @@ <h2>ChemPropHyperoptRegressor<a class="headerlink" href="#chemprophyperoptregres
 </dd></dl>
 
 </section>
-<section id="chemprophyperoptregressorpretrained">
-<h2>ChemPropHyperoptRegressorPretrained<a class="headerlink" href="#chemprophyperoptregressorpretrained" title="Permalink to this heading"></a></h2>
+<section id="chempropregressorpretrained">
+<h2>ChemPropRegressorPretrained<a class="headerlink" href="#chempropregressorpretrained" title="Permalink to this heading"></a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="optunaz.config.optconfig.ChemPropRegressorPretrained">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">optunaz.config.optconfig.</span></span><span class="sig-name descname"><span class="pre">ChemPropRegressorPretrained</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameters</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/optunaz/config/optconfig.html#ChemPropRegressorPretrained"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#optunaz.config.optconfig.ChemPropRegressorPretrained" title="Permalink to this definition"></a></dt>
diff --git a/docs/sphinx-builddir/html/index.html b/docs/sphinx-builddir/html/index.html
index c44f20d..9f76572 100644
--- a/docs/sphinx-builddir/html/index.html
+++ b/docs/sphinx-builddir/html/index.html
@@ -161,7 +161,7 @@ <h1>Welcome to QSARtuna Documentation!<a class="headerlink" href="#welcome-to-qs
 <li class="toctree-l2"><a class="reference internal" href="algorithms.html#chempropclassifier">ChemPropClassifier</a></li>
 <li class="toctree-l2"><a class="reference internal" href="algorithms.html#chemprophyperoptclassifier">ChemPropHyperoptClassifier</a></li>
 <li class="toctree-l2"><a class="reference internal" href="algorithms.html#chemprophyperoptregressor">ChemPropHyperoptRegressor</a></li>
-<li class="toctree-l2"><a class="reference internal" href="algorithms.html#chemprophyperoptregressorpretrained">ChemPropHyperoptRegressorPretrained</a></li>
+<li class="toctree-l2"><a class="reference internal" href="algorithms.html#chempropregressorpretrained">ChemPropRegressorPretrained</a></li>
 <li class="toctree-l2"><a class="reference internal" href="algorithms.html#calibratedclassifiercvwithva">CalibratedClassifierCVWithVA</a></li>
 <li class="toctree-l2"><a class="reference internal" href="algorithms.html#mapie">Mapie</a></li>
 </ul>
diff --git a/docs/sphinx-builddir/html/objects.inv b/docs/sphinx-builddir/html/objects.inv
index a28761f..86e556b 100644
Binary files a/docs/sphinx-builddir/html/objects.inv and b/docs/sphinx-builddir/html/objects.inv differ
diff --git a/docs/sphinx-builddir/html/searchindex.js b/docs/sphinx-builddir/html/searchindex.js
index 7354c41..e597be2 100644
--- a/docs/sphinx-builddir/html/searchindex.js
+++ b/docs/sphinx-builddir/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["README", "algorithms", "deduplicator", "descriptors", "index", "modules", "notebooks/QSARtuna_Tutorial", "notebooks/preprocess_data", "optunaz", "optunaz.config", "optunaz.utils", "optunaz.utils.enums", "optunaz.utils.preprocessing", "splitters", "transform"], "filenames": ["README.md", "algorithms.rst", "deduplicator.rst", "descriptors.rst", "index.rst", "modules.rst", "notebooks/QSARtuna_Tutorial.ipynb", "notebooks/preprocess_data.ipynb", "optunaz.rst", "optunaz.config.rst", "optunaz.utils.rst", "optunaz.utils.enums.rst", "optunaz.utils.preprocessing.rst", "splitters.rst", "transform.rst"], "titles": ["QSARtuna \ud80c\udd9b: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ and QPTUNA)", "Available algorithms", "Available deduplicators", "Available descriptors", "Welcome to QSARtuna Documentation!", "optunaz", "QSARtuna CLI Tutorial", "Preprocessing data for QSARtuna", "optunaz package", "optunaz.config package", "optunaz.utils package", "optunaz.utils.enums package", "optunaz.utils.preprocessing package", "Available splitters", "Available transform"], "terms": {"build": [0, 4, 8, 9, 10, 11], "predict": [0, 1, 3, 5, 6, 7, 9, 10, 11], "compchem": 0, "develop": [0, 3, 8], "uncertainti": [0, 1, 4, 7, 8, 9, 12, 14], "quantif": 0, "explain": [0, 1, 4, 5, 9], "mind": 0, "thi": [0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13], "librari": [0, 7], "search": [0, 1, 3, 8, 9], "best": [0, 1, 8, 9], "ml": [0, 4, 9], "algorithm": [0, 3, 4, 7, 8, 9, 10, 11, 12, 13], "molecular": [0, 1, 3, 4, 6, 7, 8, 9], "descriptor": [0, 4, 5, 9, 11], "given": [0, 1, 3, 6, 7, 8, 9, 10], "data": [0, 1, 3, 4, 8, 9, 11, 12, 13, 14], "itself": [0, 6], "done": [0, 6], "emploi": [0, 3, 6, 7, 8], "latest": [0, 9], "state": [0, 6, 12], "art": [0, 6], "estim": [0, 1, 3, 4, 7, 8, 9, 11], "packag": [0, 1, 3, 5, 6, 7], "further": [0, 9], "document": [0, 6, 7], "github": [0, 6, 8, 12], "page": 0, "here": [0, 3, 6, 7, 8, 9, 12, 13], "public": [0, 1, 3, 4, 6, 8, 9], "avail": [0, 4, 6, 7, 8], "structur": [0, 1, 3, 6, 7, 8, 9], "around": [0, 6, 7], "train": [0, 1, 3, 4, 7, 8, 9, 11, 12, 13], "mani": [0, 1, 6, 9], "differ": [0, 1, 3, 6, 8, 9, 12], "paramet": [0, 1, 3, 6, 7, 8, 9, 11, 12, 13, 14], "onli": [0, 1, 3, 7, 8, 9, 12, 13], "dataset": [0, 1, 7, 8, 9, 11, 12], "usual": [0, 1, 6, 7, 9], "cross": [0, 1, 6, 9, 12], "valid": [0, 1, 3, 7, 8, 9, 11, 12], "pick": 0, "evalu": [0, 4, 5, 6], "its": [0, 1, 6, 9, 11], "perform": [0, 3, 8, 11, 12, 14], "test": [0, 1, 4, 7, 8, 9, 11, 12, 13], "prod": [0, 6], "re": [0, 6, 8], "merg": [0, 7, 8, 12], "ha": [0, 1, 6, 7, 8, 9, 12], "drawback": [0, 6], "left": [0, 6, 7], "result": [0, 1, 3, 6, 7, 8, 9], "big": [0, 6], "benefit": [0, 6], "final": [0, 1, 6, 9], "all": [0, 1, 3, 6, 7, 8, 9, 11, 12], "let": [0, 6, 7], "s": [0, 6, 7], "look": [0, 1, 6, 7, 9], "trivial": 0, "exampl": [0, 3, 7, 8, 9], "weight": [0, 1, 3, 6, 8, 9, 11], "set": [0, 3, 4, 7, 8, 9, 10, 11, 12, 13], "50": [0, 1, 3, 6, 8, 9], "molecul": [0, 1, 3, 6, 7, 8, 9], "we": [0, 3, 6, 7, 8, 9, 12, 13], "start": [0, 4, 6, 7], "format": [0, 3, 6, 7, 8, 10], "It": [0, 1, 3, 6, 7, 8, 9], "contain": [0, 3, 6, 8], "four": 0, "main": [0, 3, 6, 7, 8], "section": [0, 6, 7], "locat": [0, 6], "column": [0, 3, 7, 8, 11, 12, 13, 14], "detail": [0, 3, 6, 7, 8, 9, 10], "about": [0, 6, 7], "which": [0, 1, 3, 6, 7, 8, 9, 12], "below": [0, 3, 6, 7, 8], "task": [0, 3, 7, 8, 9, 11], "training_dataset_fil": [0, 6, 7, 8], "drd2": [0, 6], "subset": [0, 1, 6, 7, 9], "csv": [0, 3, 4, 6, 8], "input_column": [0, 3, 6, 7, 8, 11], "canon": [0, 6, 8, 12], "response_column": [0, 3, 6, 7, 8, 11], "molwt": [0, 6], "mode": [0, 6, 8, 9, 11], "regress": [0, 1, 7, 9, 11, 12], "cross_valid": [0, 6, 9, 11, 12], "5": [0, 1, 3, 6, 7, 8, 9, 12], "direct": [0, 1, 6, 9, 11], "maxim": [0, 1, 6, 9], "n_trial": [0, 6, 8, 9, 11], "100": [0, 1, 3, 6, 7, 8, 9, 10], "n_startup_tri": [0, 6, 8, 9], "30": [0, 1, 6, 7, 9], "name": [0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14], "ecfp": [0, 4, 6, 8, 9, 11], "radiu": [0, 3, 6, 8, 11], "3": [0, 1, 3, 4, 6, 7, 8, 9], "nbit": [0, 3, 6, 8, 9, 11], "2048": [0, 3, 6, 8], "maccs_kei": [0, 4, 6, 8, 11], "randomforestregressor": [0, 4, 6, 9, 11], "max_depth": [0, 1, 9, 11], "low": [0, 1, 3, 6, 7, 8, 9, 11], "2": [0, 1, 3, 6, 7, 8, 9, 12, 13], "high": [0, 1, 3, 6, 8, 9, 11], "32": [0, 1, 6, 9], "n_estim": [0, 1, 6, 9, 11], "10": [0, 1, 3, 6, 7, 8, 9, 12], "250": [0, 1, 6, 9], "max_featur": [0, 1, 9, 11], "auto": [0, 1, 6, 8, 9], "ridg": [0, 4, 6, 9, 11], "alpha": [0, 1, 6, 7, 8, 9, 11], "0": [0, 1, 3, 4, 6, 7, 8, 9, 12, 13], "lasso": [0, 4, 6, 9, 11], "xgbregressor": [0, 4, 6, 9, 11], "learning_r": [0, 1, 9, 11], "1": [0, 1, 3, 4, 6, 7, 8, 9, 10, 12, 13], "specifi": [0, 1, 6, 7, 8, 9, 11], "In": [0, 1, 3, 6, 7, 8, 9], "rel": [0, 6], "path": [0, 1, 3, 6, 7, 8, 9, 10], "folder": [0, 6, 7], "ar": [0, 1, 3, 6, 7, 8, 9, 11, 12, 13], "want": [0, 6, 7], "fold": [0, 1, 6, 7, 9, 12, 13], "valu": [0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14], "object": [0, 1, 5, 7, 9, 10, 11, 12], "function": [0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 14], "standard": [0, 1, 7, 9, 12, 14], "scikit": [0, 6, 8, 12, 13], "learn": [0, 1, 3, 7, 8, 9, 12, 13], "have": [0, 3, 6, 7, 8, 9, 12], "total": [0, 6, 7], "trial": [0, 1, 9, 10, 11], "first": [0, 1, 3, 6, 7, 8, 9, 12], "startup": [0, 6], "should": [0, 1, 3, 6, 7, 8, 9, 12], "random": [0, 1, 4, 9, 12], "explor": [0, 6], "get": [0, 6, 7, 8], "stuck": 0, "earli": [0, 1, 6, 8, 9], "one": [0, 3, 7, 8, 9, 12, 13], "local": [0, 6], "minimum": [0, 1, 3, 8, 9, 12, 13], "two": [0, 1, 6, 7, 9, 12, 13], "free": [0, 3, 8], "pair": [0, 6], "ani": [0, 3, 6, 7, 8, 9, 12], "when": [0, 1, 6, 7, 8, 9, 12, 13], "our": [0, 6, 7], "time": [0, 1, 3, 7, 8, 9], "can": [0, 1, 3, 6, 7, 8, 9, 12, 13], "deploi": 0, "singular": [0, 6], "To": [0, 6, 7], "insid": [0, 8], "follow": [0, 3, 6, 7, 8, 9], "syntax": 0, "exec": 0, "sif": 0, "project": [0, 1, 9], "cc": [0, 6, 7], "mai": [0, 1, 3, 6, 7, 8, 9], "qsartuna_latest": 0, "opt": 0, "venv": [0, 6], "bin": [0, 6, 7, 12, 13], "config": [0, 1, 5, 6, 8], "regression_drd2_50": 0, "buildconfig": [0, 5, 6, 8, 10], "outpath": 0, "target": [0, 1, 6, 7, 9, 12, 14], "pkl": [0, 1, 6, 9], "sinc": [0, 3, 6, 7, 8, 12], "long": [0, 7], "avoid": [0, 6, 12], "login": 0, "node": 0, "queue": 0, "instead": [0, 1, 3, 6, 7, 8, 9, 12], "script": 0, "give": [0, 6], "sbatch": 0, "sh": 0, "ntask": 0, "cpu": 0, "per": [0, 1, 7, 9], "mem": 0, "4g": 0, "partit": 0, "core": [0, 7, 9], "illustr": [0, 6, 7], "how": [0, 1, 3, 6, 7, 8, 9], "chose": 0, "chang": [0, 6], "directori": [0, 6, 10], "cd": 0, "project_fold": 0, "optunaaz": 0, "version": [0, 7, 9], "optunaaz_latest": 0, "complet": [0, 3, 6, 8], "creat": [0, 7, 10], "pickl": [0, 6], "your": [0, 6, 7], "home": 0, "under": [0, 6], "built": [0, 3, 7, 8, 9], "infer": [0, 6, 7, 8], "input": [0, 1, 3, 4, 6, 8, 9, 12, 13, 14], "smile": [0, 3, 6, 7, 8, 10, 11, 12, 13], "output": [0, 1, 6, 7, 8, 9, 12, 14], "note": [0, 1, 3, 7, 8, 9, 11, 12, 13], "_": [0, 6], "point": [0, 1, 7, 9, 12, 13], "most": [0, 6, 7], "recent": [0, 6], "legaci": 0, "requir": [0, 3, 6, 7, 8], "same": [0, 1, 6, 7, 9], "modifi": [0, 8], "abov": [0, 6, 7], "suppli": [0, 1, 3, 6, 7, 8, 9], "qsartuna_": 0, "replac": [0, 6, 10], "e": [0, 1, 3, 7, 8, 9, 12, 14], "g": [0, 3, 7, 8, 12, 14], "qsartuna_2": 0, "1_model": 0, "would": [0, 3, 6, 7, 8], "gener": [0, 1, 3, 6, 7, 8, 9, 12, 13], "tri": 0, "dure": [0, 1, 3, 6, 7, 8, 9], "mlflow": [0, 5, 8, 11], "track": [0, 3, 5, 8, 9], "ui": 0, "modul": [0, 5, 6], "load": [0, 1, 6, 7, 9], "Then": 0, "open": [0, 1, 6, 9], "link": 0, "browser": 0, "If": [0, 1, 3, 6, 8, 9, 12, 13], "you": [0, 1, 6, 7, 9], "scp": 0, "forward": [0, 1, 9], "port": 0, "separ": [0, 3, 7, 8], "ssh": 0, "session": 0, "non": [0, 1, 3, 6, 7, 8, 9], "machin": [0, 1, 3, 6, 7, 8, 9], "n": [0, 1, 6, 7, 9, 10], "l": 0, "localhost": 0, "5000": 0, "user": [0, 1, 3, 4, 6, 8, 9, 11, 12, 13, 14], "intranet": 0, "net": 0, "just": [0, 6], "execut": 0, "select": [0, 1, 3, 6, 7, 8, 9], "experi": [0, 7, 10], "after": [0, 1, 3, 6, 7, 8, 9, 10], "choos": [0, 4], "compar": [0, 6], "comparison": [0, 6, 7], "show": [0, 6, 7], "call": [0, 1, 3, 6, 8, 9, 12], "well": [0, 6, 7], "metric": [0, 1, 6, 8, 9, 11], "At": 0, "bottom": 0, "plot": [0, 6, 7, 9, 11], "For": [0, 1, 3, 6, 7, 8, 9, 12], "x": [0, 1, 3, 6, 7, 8, 9, 12, 13], "axi": [0, 6, 7], "number": [0, 1, 3, 6, 7, 8, 9, 10], "y": [0, 1, 7, 8, 9, 12, 13], "cvmean": 0, "r2": [0, 6, 7, 9], "more": [0, 1, 3, 7, 8, 9, 10], "click": 0, "individu": [0, 1, 6, 7, 9], "There": [0, 1, 6, 7, 9], "access": [0, 3, 8], "conda": 0, "environ": [0, 3, 6, 8], "instal": [0, 6], "purg": 0, "miniconda3": 0, "my_env_with_qsartuna": 0, "pip": [0, 6], "activ": [0, 1, 6, 7, 9, 11, 12, 14], "case": [0, 1, 6, 7, 8, 9], "check": [0, 6, 8, 11, 12], "m": [0, 6, 8], "http": [0, 3, 6, 7, 8, 9, 12], "com": [0, 6, 7, 8, 12], "molecularai": [0, 6], "releas": [0, 4, 6, 7], "download": [0, 6], "tar": [0, 6], "gz": [0, 6], "three_step_opt_build_merg": [0, 5, 6], "import": [0, 6], "buildconfig_best": [0, 6, 8], "build_best": [0, 6, 8], "build_merg": [0, 6, 8], "modelmod": [0, 6, 8, 9], "optimizationdirect": [0, 6, 9], "optconfig": [0, 1, 5, 6, 8, 10, 11], "optimizationconfig": [0, 6, 8, 9], "svr": [0, 4, 6, 9, 11], "randomforest": 0, "pl": [0, 1, 9], "dataread": [0, 5, 6], "ecfp_count": [0, 4, 6, 8, 11], "prepar": [0, 4, 7], "new": [0, 1, 6, 7, 9], "studi": [0, 3, 6, 8, 9, 10, 11], "study_nam": [0, 6, 8], "my_studi": [0, 6], "make": [0, 1, 6, 7, 9, 12, 13, 14], "write": [0, 6], "out": [0, 1, 6, 7, 9], "print": [0, 6, 7], "dump": [0, 6], "indent": [0, 6], "save": [0, 6], "class": [1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14], "optunaz": [1, 3, 6, 7, 13, 14], "sourc": [1, 3, 8, 9, 10, 11, 12, 13, 14], "adaboost": [1, 9], "classifi": [1, 6, 8, 9, 11], "an": [1, 3, 6, 7, 8, 9, 10, 12, 13], "meta": [1, 6, 9], "begin": [1, 6, 7, 9, 12, 13], "fit": [1, 3, 6, 7, 8, 9], "origin": [1, 3, 6, 7, 8, 9, 12], "addit": [1, 6, 9], "copi": [1, 7, 9, 10], "where": [1, 6, 7, 9], "incorrectli": [1, 9], "instanc": [1, 6, 7, 9], "adjust": [1, 9], "subsequ": [1, 9], "focu": [1, 9], "difficult": [1, 6, 9], "adaboostclassifierparametersnestim": [1, 9], "adaboostclassifierparameterslearningr": [1, 9], "The": [1, 3, 7, 8, 9, 10, 12, 14], "maximum": [1, 3, 6, 7, 8, 9, 12, 13], "boost": [1, 3, 8, 9], "termin": [1, 9], "perfect": [1, 9], "procedur": [1, 3, 7, 8, 9], "stop": [1, 6, 9], "titl": [1, 3, 6, 7, 8, 9, 10, 12, 13, 14], "appli": [1, 3, 6, 7, 8, 9, 12, 13, 14], "each": [1, 3, 6, 7, 8, 9, 12], "classifierat": [1, 9], "iter": [1, 6, 9, 12, 13], "A": [1, 3, 7, 8, 9], "higher": [1, 6, 9], "rateincreas": [1, 9], "contribut": [1, 3, 6, 8, 9], "trade": [1, 9], "off": [1, 6, 7, 9, 12, 13], "between": [1, 6, 7, 9], "learning_rateand": [1, 9], "int": [1, 3, 8, 9, 12, 13], "float": [1, 6, 7, 9, 10, 12, 13, 14], "linear": [1, 7, 9], "model": [1, 3, 4, 7, 8, 9, 10, 12, 13, 14], "l1": [1, 9], "prior": [1, 7, 9], "regular": [1, 6, 9], "spars": [1, 9], "coeffici": [1, 9], "tend": [1, 9], "prefer": [1, 9], "solut": [1, 6, 9], "fewer": [1, 9], "zero": [1, 3, 8, 9], "effect": [1, 6, 7, 9, 12], "reduc": [1, 6, 9], "featur": [1, 3, 6, 8, 9], "upon": [1, 6, 9], "depend": [1, 6, 7, 9], "lassoparametersalpha": [1, 9], "constant": [1, 9], "multipli": [1, 9], "term": [1, 6, 9], "control": [1, 6, 7, 9, 12], "strength": [1, 3, 8, 9], "must": [1, 6, 9], "neg": [1, 6, 7, 9], "i": [1, 3, 6, 7, 8, 9], "inf": [1, 6, 8, 9], "equival": [1, 9], "ordinari": [1, 9], "least": [1, 6, 9], "squar": [1, 6, 9], "solv": [1, 6, 9], "linearregress": [1, 9], "numer": [1, 7, 9], "reason": [1, 7, 9], "us": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14], "advis": [1, 6, 7, 9], "implement": [1, 3, 6, 8, 9, 12], "k": [1, 6, 7, 9, 12, 13], "nearest": [1, 6, 9], "neighbor": [1, 6, 9, 12, 13], "vote": [1, 9], "principl": [1, 9], "behind": [1, 9], "method": [1, 3, 7, 8, 9, 11, 12], "find": [1, 6, 9], "predefin": [1, 4, 9, 12, 14], "sampl": [1, 6, 9, 12, 13], "closest": [1, 9], "distanc": [1, 6, 9], "label": [1, 6, 7, 8, 9, 12, 13], "from": [1, 3, 4, 8, 9, 10, 12, 13, 14], "defin": [1, 3, 6, 7, 8, 9, 10, 12], "despit": [1, 6, 9], "simplic": [1, 9], "success": [1, 6, 9], "larg": [1, 7, 9], "classif": [1, 4, 7, 8, 9, 11, 12], "problem": [1, 6, 7, 8, 9], "n_neighbor": [1, 9, 11], "kneighborsclassifierparametersn_neighbor": [1, 9], "default": [1, 7, 8, 9, 12, 13], "kneighbor": [1, 9], "queri": [1, 6, 7, 9], "list": [1, 3, 4, 6, 7, 8, 9, 12, 14], "comput": [1, 3, 7, 8, 9, 12], "minkowski": [1, 6, 9], "euclidean": [1, 9], "regressor": [1, 6, 8, 9, 11], "kneighborsregressorparametersn_neighbor": [1, 9], "logist": [1, 9], "rather": [1, 3, 6, 7, 8, 9], "than": [1, 3, 6, 7, 8, 9], "also": [1, 3, 6, 7, 8, 9, 12], "known": [1, 3, 6, 7, 8, 9], "literatur": [1, 9], "logit": [1, 9], "entropi": [1, 7, 9], "maxent": [1, 9], "log": [1, 4, 9, 10, 11, 12, 14], "probabl": [1, 4, 7, 9], "describ": [1, 3, 6, 8, 9, 12], "possibl": [1, 6, 7, 9, 12, 13], "outcom": [1, 9], "singl": [1, 6, 9], "solver": [1, 9, 11], "c": [1, 3, 6, 7, 8, 9, 11], "logisticregressionparametersparameterc": [1, 9], "try": [1, 6, 7, 9], "sag": [1, 9], "saga": [1, 9], "fast": [1, 6, 9], "converg": [1, 6, 9], "guarante": [1, 9], "approxim": [1, 6, 9], "scale": [1, 3, 7, 8, 9, 12, 14], "preprocess": [1, 4, 8, 9, 10, 13, 14], "scaler": [1, 3, 8, 9], "invers": [1, 9], "posit": [1, 3, 6, 8, 9], "like": [1, 3, 6, 7, 8, 9], "support": [1, 6, 8, 9], "vector": [1, 3, 6, 8, 9, 12, 14], "smaller": [1, 6, 9], "stronger": [1, 9], "decomposit": [1, 9], "partial": [1, 6, 9], "form": [1, 3, 6, 7, 8, 9, 12], "compon": [1, 3, 6, 8, 9], "fundament": [1, 9], "relat": [1, 3, 6, 7, 8, 9], "matric": [1, 9], "thei": [1, 3, 6, 7, 8, 9], "latent": [1, 9], "variabl": [1, 6, 7, 9], "approach": [1, 3, 6, 7, 8, 9], "covari": [1, 4, 8, 9], "space": [1, 7, 9, 12, 13], "multidimension": [1, 9], "varianc": [1, 6, 7, 9], "other": [1, 6, 7, 9, 12], "word": [1, 6, 9], "both": [1, 6, 7, 9], "lower": [1, 6, 9], "dimension": [1, 9], "subspac": [1, 6, 8, 9], "transform": [1, 4, 8, 9, 10], "n_compon": [1, 9, 11], "ncompon": [1, 9], "keep": [1, 6, 7, 9, 12], "min": [1, 6, 7, 9, 12], "n_sampl": [1, 9], "n_featur": [1, 9], "n_target": [1, 9], "forest": [1, 4, 7, 9], "decis": [1, 6, 7, 9, 12, 14], "tree": [1, 6, 9], "variou": [1, 6, 8, 9], "sub": [1, 6, 9], "averag": [1, 3, 6, 7, 8, 9, 12], "improv": [1, 3, 6, 8, 9], "accuraci": [1, 6, 9], "over": [1, 6, 9], "randomforestclassifierparametersmaxdepth": [1, 9], "randomforestclassifierparametersnestim": [1, 6, 9], "depth": [1, 6, 9, 11], "considerwhen": [1, 9], "split": [1, 4, 8, 9, 12, 13, 14], "thenconsid": [1, 9], "sqrt": [1, 6, 7, 9], "log2": [1, 7, 9, 12, 14], "randomforestregressorparametersmaxdepth": [1, 9], "randomforestregressorparametersnestim": [1, 9], "l2": [1, 9], "loss": [1, 3, 6, 8, 9], "norm": [1, 7, 9], "tikhonov": [1, 9], "base": [1, 3, 4, 6, 8, 9, 10, 11, 12, 13, 14], "libsvm": [1, 9], "quadrat": [1, 9], "impract": [1, 9], "beyond": [1, 9], "ten": [1, 9], "thousand": [1, 9], "svcparametersparameterc": [1, 9], "1e": [1, 9], "gamma": [1, 9, 11], "0001": [1, 9], "proport": [1, 6, 9], "strictli": [1, 9], "penalti": [1, 9], "kernel": [1, 9], "epsilon": [1, 9], "complex": [1, 6, 9], "hard": [1, 3, 8, 9], "coupl": [1, 9], "10000": [1, 9], "svrparametersparameterc": [1, 9], "svrparametersgamma": [1, 9], "maxdepth": [1, 9], "nestim": [1, 9], "learningr": [1, 9], "xgboost": [1, 9, 11], "gradient": [1, 9], "stand": [1, 9], "extrem": [1, 6, 9], "paper": [1, 3, 6, 8, 9], "greedi": [1, 9], "friedman": [1, 9], "learner": [1, 9], "round": [1, 6, 7, 9], "prf": [1, 4, 7, 9], "probabilist": [1, 4, 9], "seen": [1, 6, 7, 9], "hybrid": [1, 6, 9], "similar": [1, 3, 6, 7, 8, 9, 12, 13], "take": [1, 3, 6, 7, 8, 9, 12], "real": [1, 6, 7, 9, 12, 13], "threshold": [1, 3, 4, 6, 8, 9, 12, 13, 14], "represent": [1, 3, 4, 8, 9], "ptr": [1, 4, 6, 9, 12], "howev": [1, 3, 6, 7, 8, 9], "belong": [1, 3, 6, 7, 8, 9], "inact": [1, 6, 7, 9, 12, 14], "use_py_gini": [1, 9, 11], "use_py_leaf": [1, 9, 11], "prfclassifierparametersmaxdepth": [1, 9], "prfclassifierparametersnestim": [1, 9], "min_py_sum_leaf": [1, 9, 11], "prfclassifierparametersminpysumleaf": [1, 9], "gini": [1, 9], "true": [1, 3, 6, 7, 8, 9, 12, 13], "py": [1, 6, 7, 9], "leav": [1, 9], "leaf": [1, 9], "allow": [1, 3, 6, 7, 8, 9], "prune": [1, 6, 9], "propag": [1, 9], "small": [1, 7, 9], "thu": [1, 6, 9], "pth": [1, 9], "scheme": [1, 9], "noisi": [1, 9], "chemprop": [1, 3, 4, 8, 9], "deep": [1, 6, 9], "properti": [1, 3, 6, 7, 8, 9, 10], "network": [1, 3, 6, 8, 9], "messag": [1, 6, 9], "pass": [1, 3, 6, 7, 8, 9, 12], "neural": [1, 6, 8, 9], "d": [1, 3, 6, 8, 9], "mpnn": [1, 9], "encod": [1, 9], "graph": [1, 3, 6, 8, 9], "feed": [1, 9], "ffnn": [1, 9], "multi": [1, 3, 8, 9], "layer": [1, 3, 6, 8, 9], "perceptron": [1, 9], "wa": [1, 3, 6, 7, 8, 9], "present": [1, 6, 7, 9], "analyz": [1, 6, 9], "optuna": [1, 4, 6, 8, 9, 10, 11], "optims": [1, 9], "hyperopt": [1, 9], "ensemble_s": [1, 6, 9, 11], "epoch": [1, 6, 9, 11], "aggreg": [1, 6, 7, 9, 11, 12, 13], "aggregation_norm": [1, 6, 9, 11], "chempropparametersaggregation_norm": [1, 9], "200": [1, 6, 9], "q": [1, 3, 6, 8, 9, 11], "batch_siz": [1, 6, 9, 11], "chempropparametersbatch_s": [1, 9], "chempropparametersdepth": [1, 9], "6": [1, 6, 7, 9], "dropout": [1, 9, 11], "chempropparametersdropout": [1, 9], "4": [1, 3, 6, 7, 8, 9, 12, 13], "04": [1, 6, 9], "features_gener": [1, 6, 9, 11], "ffn_hidden_s": [1, 6, 9, 11], "chempropparametersffn_hidden_s": [1, 9], "300": [1, 6, 9], "2400": [1, 9], "ffn_num_lay": [1, 6, 9, 11], "chempropparametersffn_num_lay": [1, 9], "final_lr_ratio_exp": [1, 6, 9, 11], "chempropparametersfinal_lr_ratio_exp": [1, 9], "hidden_s": [1, 6, 9, 11], "chempropparametershidden_s": [1, 9], "init_lr_ratio_exp": [1, 6, 9, 11], "chempropparametersinit_lr_ratio_exp": [1, 9], "max_lr_exp": [1, 6, 9, 11], "chempropparametersmax_lr_exp": [1, 9], "warmup_epochs_ratio": [1, 6, 9, 11], "chempropparameterswarmup_epochs_ratio": [1, 9], "ensembl": [1, 9, 11], "initialis": [1, 6, 9], "provid": [1, 3, 6, 7, 8, 9, 12], "size": [1, 3, 6, 7, 8, 9], "run": [1, 3, 4, 7, 8, 9, 10], "increas": [1, 6, 7, 9, 12, 13], "400": [1, 9], "sum": [1, 6, 9], "atom": [1, 3, 6, 8, 9, 12, 13], "divid": [1, 6, 9], "up": [1, 3, 6, 8, 9, 10], "batch": [1, 9, 12], "step": [1, 7, 8, 9], "visibl": [1, 9], "randomli": [1, 6, 7, 9], "some": [1, 3, 6, 7, 8, 9], "element": [1, 9, 12, 13], "tensor": [1, 9], "p": [1, 3, 8, 9], "bernoulli": [1, 9], "distribut": [1, 6, 7, 9], "channel": [1, 9], "independ": [1, 7, 9], "everi": [1, 6, 9], "proven": [1, 9], "techniqu": [1, 7, 9], "prevent": [1, 6, 9], "co": [1, 7, 9], "adapt": [1, 3, 8, 9], "neuron": [1, 9], "hidden": [1, 6, 9], "ffn": [1, 6, 9], "exponenti": [1, 7, 9], "rate": [1, 9], "bond": [1, 3, 8, 9], "ratio": [1, 9], "linearli": [1, 9], "init_lr": [1, 9], "max_lr": [1, 9], "afterward": [1, 7, 9], "decreas": [1, 7, 9], "final_lr": [1, 9], "without": [1, 6, 9, 12], "within": [1, 3, 8, 9, 12, 13], "hyperparamet": [1, 4, 6, 8, 9], "side": [1, 3, 8, 9], "inform": [1, 3, 8, 9, 10], "nb": [1, 3, 6, 7, 8, 9], "quick": [1, 4, 9], "simpl": [1, 7, 9], "sensibl": [1, 6, 7, 8, 9], "author": [1, 6, 8, 9], "do": [1, 6, 7, 9, 12], "num_it": [1, 6, 9, 11], "search_parameter_level": [1, 6, 9, 11], "dictat": [1, 9], "larger": [1, 3, 6, 7, 8, 9], "chempropregressorpretrain": [1, 6, 9], "pretrin": [1, 9], "pretrain": [1, 6, 9], "carri": [1, 9], "previous": [1, 9], "qsartuna": [1, 9], "chempropparametersepoch": [1, 6, 9], "frzn": [1, 9, 11], "pretrained_model": [1, 6, 9, 11], "none": [1, 3, 6, 8, 9, 10, 12, 13, 14], "fine": [1, 9], "tune": [1, 3, 4, 6, 8, 9], "decid": [1, 9], "freez": [1, 9], "transfer": [1, 9], "frozen": [1, 9], "str": [1, 3, 6, 8, 9, 10, 11, 12, 13, 14], "calibr": [1, 4, 8, 9], "isoton": [1, 6, 9], "vennab": [1, 9], "cv": [1, 6, 9], "With": [1, 3, 8, 9], "across": [1, 6, 7, 9, 12], "fals": [1, 3, 6, 7, 8, 9, 12], "obtain": [1, 6, 7, 9], "unbias": [1, 9], "offer": [1, 3, 6, 8, 9], "p0": [1, 6, 9], "vs": [1, 6, 7, 9], "p1": [1, 6, 9], "discord": [1, 6, 9], "type": [1, 3, 6, 7, 8, 9, 12], "union": [1, 3, 8, 9], "calibratedclassifiercvensembl": [1, 9], "calibratedclassifiercvmethod": [1, 9], "n_fold": [1, 6, 9, 11], "whether": [1, 3, 7, 8, 9, 12, 14], "agnost": [1, 6, 9], "interv": [1, 6, 9], "encompass": [1, 9], "aleator": [1, 9], "epistem": [1, 9], "back": [1, 6, 9], "strong": [1, 9], "theoret": [1, 6, 9], "thank": [1, 9], "conform": [1, 9], "mapie_alpha": [1, 6, 9, 11], "05": [1, 6, 7, 9], "01": [1, 6, 9], "99": [1, 6, 9], "see": [3, 6, 7, 8, 9, 12, 13], "gedeck": [3, 8], "et": [3, 7, 8], "al": [3, 7, 8], "qsar": [3, 4, 6, 7, 8], "good": [3, 6, 7, 8], "practic": [3, 8], "fingerprint": [3, 8, 9], "wai": [3, 6, 7, 8], "daylight": [3, 8], "enumer": [3, 6, 8, 9], "custom": [3, 6, 8], "ref": [3, 8, 10], "16": [3, 6, 7, 8], "hash": [3, 6, 8, 9, 10], "code": [3, 6, 7, 8], "style": [3, 6, 7, 8], "implicitli": [3, 8], "largest": [3, 6, 8], "refer": [3, 6, 8, 10, 11], "toward": [3, 6, 7, 8], "binari": [3, 6, 8, 9], "extend": [3, 6, 7, 8], "connect": [3, 6, 8], "roger": [3, 8], "circular": [3, 8], "morgan": [3, 8, 9], "invari": [3, 8], "getmorganfingerprintasbitvect": [3, 8], "rdkit": [3, 6, 7, 8, 9], "systemat": [3, 8], "record": [3, 6, 7, 8], "neighborhood": [3, 8, 9], "h": [3, 6, 7, 8], "multipl": [3, 6, 8, 12, 13], "runtim": [3, 8], "substructur": [3, 6, 8], "map": [3, 6, 7, 8], "integ": [3, 7, 8, 12, 13], "length": [3, 6, 8], "identifi": [3, 6, 7, 8], "diamet": [3, 8], "append": [3, 6, 7, 8, 9], "ecfp4": [3, 8], "correspond": [3, 6, 7, 8, 9], "returnrdkit": [3, 6, 8], "consid": [3, 6, 8, 12, 13], "while": [3, 6, 7, 8, 12], "bit": [3, 6, 8], "sometim": [3, 6, 7, 8], "bool": [3, 8, 9, 12, 13], "calculate_from_mol": [3, 8], "mol": [3, 6, 7, 8], "return": [3, 6, 7, 8, 10, 11, 12, 13], "numpi": [3, 6, 7, 8, 12, 13], "arrai": [3, 6, 8, 12, 13], "count": [3, 6, 8, 9], "gethashedmorganfingerprint": [3, 8], "appear": [3, 8, 11], "usefeatur": [3, 6, 8, 11], "fcfp": [3, 8], "normal": [3, 6, 7, 8, 9], "ones": [3, 6, 8], "definit": [3, 8, 12], "gobbi": [3, 8], "popping": [3, 8], "biotechnolog": [3, 8], "bioengin": [3, 8], "61": [3, 6, 8], "47": [3, 6, 8], "54": [3, 6, 8], "1998": [3, 6, 8], "lead": [3, 7, 8], "score": [3, 4, 8, 9, 10, 12, 14], "fp": [3, 6, 8], "maxpath": [3, 6, 8, 11], "fpsize": [3, 6, 8, 11], "macc": [3, 6, 8], "system": [3, 7, 8], "often": [3, 6, 8], "mdl": [3, 8], "kei": [3, 6, 7, 8, 10, 11], "compani": [3, 8], "calcul": [3, 6, 8, 12, 13, 14], "keyset": [3, 8], "construct": [3, 8, 11], "optim": [3, 4, 7, 8, 9, 11], "durant": [3, 8], "reoptim": [3, 8], "drug": [3, 8], "discoveri": [3, 8], "166": [3, 6, 8], "2d": [3, 8, 9], "essenti": [3, 7, 8], "answer": [3, 8], "fragment": [3, 8], "question": [3, 8], "explicitli": [3, 6, 7, 8], "exist": [3, 8], "sens": [3, 8], "matter": [3, 8], "becaus": [3, 6, 7, 8], "address": [3, 8], "specif": [3, 6, 7, 8, 11], "repres": [3, 6, 7, 8], "9": [3, 6, 7, 8], "1049": [3, 8], "distinct": [3, 6, 7, 8, 9], "rdkit_nam": [3, 6, 8, 11], "unscal": [3, 8], "These": [3, 6, 7, 8, 12], "physchem": [3, 6, 8], "caution": [3, 7, 8], "208": [3, 6, 8], "includ": [3, 6, 7, 8], "clogp": [3, 6, 8], "mw": [3, 6, 8], "ring": [3, 7, 8], "rotat": [3, 8], "fraction": [3, 6, 7, 8, 12, 13], "sp3": [3, 8], "kier": [3, 8], "indic": [3, 6, 7, 8, 12, 13], "etc": [3, 6, 8], "tpsa": [3, 6, 8], "slogp": [3, 8], "group": [3, 7, 8, 12, 13], "vsa": [3, 8], "moe": [3, 8], "charg": [3, 8], "www": [3, 8], "org": [3, 6, 8], "doc": [3, 6, 8], "gettingstartedinpython": [3, 8], "html": [3, 6, 7, 8, 9], "whose": [3, 8], "been": [3, 6, 7, 8], "level": [3, 6, 7, 8, 9], "One": [3, 7, 8], "advantag": [3, 8], "interpret": [3, 8], "mean": [3, 6, 7, 8, 9, 12], "physicochem": [3, 8], "intuit": [3, 8], "understood": [3, 8], "option": [3, 4, 7, 8, 9, 11, 12, 13, 14], "jazzy_nam": [3, 6, 8, 11], "jazzy_filt": [3, 6, 8], "jazzi": [3, 8], "hydrat": [3, 8], "energi": [3, 8], "hydrogen": [3, 8], "acceptor": [3, 6, 8], "donor": [3, 6, 8], "found": [3, 6, 8], "doi": [3, 6, 8], "1038": [3, 8], "s41598": [3, 8], "023": [3, 8], "30089": [3, 8], "mmff94": [3, 8], "minimis": [3, 8], "1000da": [3, 8], "compound": [3, 6, 7, 8, 12, 13], "dict": [3, 8, 9, 10, 11], "calculate_from_smi": [3, 6, 8], "smi": [3, 8, 10], "string": [3, 6, 7, 8, 11, 12, 13, 14], "ndarrai": [3, 8], "z": [3, 8, 12, 14], "peptid": [3, 6, 8, 12, 14], "unfittedsklearnscal": [3, 8], "mol_data": [3, 8], "moldata": [3, 8], "file_path": [3, 8], "smiles_column": [3, 8], "fittedsklearnscal": [3, 8], "alia": [3, 8, 9], "precomput": [3, 7, 8], "file": [3, 7, 8, 10, 11, 12, 13], "header": [3, 8], "line": [3, 4, 6, 7, 8, 10], "row": [3, 6, 7, 8], "comma": [3, 6, 7, 8], "respons": [3, 7, 8], "pre": [3, 7, 8], "zscalesdescriptor": [3, 8, 11], "were": [3, 6, 7, 8], "propos": [3, 8], "sandberg": [3, 8], "proteogen": [3, 8], "amino": [3, 6, 8], "acid": [3, 6, 8], "nmr": [3, 8], "thin": [3, 8], "chromatographi": [3, 8], "tlc": [3, 8], "1021": [3, 6, 8], "jm9700575": [3, 8], "captur": [3, 6, 7, 8], "lipophil": [3, 8], "steric": [3, 8], "bulk": [3, 8], "polariz": [3, 8], "electron": [3, 8], "polar": [3, 8], "electroneg": [3, 8], "heat": [3, 8], "electrophil": [3, 8], "anoth": [3, 6, 8], "optimis": [3, 6, 8, 9, 10], "either": [3, 7, 8, 9], "through": [3, 6, 8], "_and_": [3, 8], "auxiliari": [3, 6, 8, 12, 14], "continu": [3, 6, 8], "learnt": [3, 6, 8], "manner": [3, 6, 8], "intent": [3, 6, 8], "much": [3, 8], "remain": [3, 7, 8, 12], "deriv": [3, 6, 7, 8], "cautiou": [3, 8], "upload": [3, 8], "_all_": [3, 8], "ruder": [3, 8], "io": [3, 6, 8, 9], "index": [3, 6, 7, 8], "auxiliarytask": [3, 8], "aux_weight_pc": [3, 6, 8, 9, 11], "20": [3, 6, 7, 8], "info": [3, 6, 8], "percentag": [3, 8], "wrap": [3, 6, 8], "certain": [3, 6, 7, 8], "rang": [3, 6, 7, 8, 12, 13], "scaleddescriptorparamet": [3, 8], "cach": [3, 6, 7, 8, 9], "composit": [3, 6, 8], "concaten": [3, 8], "button": [3, 8], "pleas": [3, 6, 7, 8, 10], "compat": [3, 6, 8], "intro": 4, "background": 4, "json": [4, 6, 9, 11], "command": [4, 6], "interfac": [4, 6, 8, 11, 12], "python": [4, 6, 8, 12], "jupyt": [4, 6], "notebook": [4, 6], "introduct": 4, "translat": [4, 6], "sdf": [4, 6, 8], "need": 4, "deal": [4, 12], "duplic": [4, 8, 9, 12], "dedupl": [4, 6, 8, 10], "experiment": [4, 6, 12, 14], "error": [4, 6], "cli": 4, "tutori": 4, "remov": [4, 7, 8, 9, 12, 13], "advanc": [4, 7, 8], "functoinail": 4, "adaboostclassifi": [4, 6, 9, 11], "kneighborsclassifi": [4, 6, 9, 11], "kneighborsregressor": [4, 6, 9, 11], "logisticregress": [4, 6, 9, 11], "plsregress": [4, 6, 9, 11], "randomforestclassifi": [4, 6, 9, 11], "svc": [4, 6, 9, 11], "prfclassifi": [4, 6, 9, 11], "chempropregressor": [4, 6, 9, 11], "chempropclassifi": [4, 6, 9, 11], "chemprophyperoptclassifi": [4, 6, 9, 11], "chemprophyperoptregressor": [4, 6, 9, 11], "chemprophyperoptregressorpretrain": 4, "calibratedclassifiercvwithva": [4, 6, 9, 11], "mapi": [4, 9, 11], "avalon": [4, 8, 9, 11], "pathfp": [4, 6, 8, 11], "unscaledphyschemdescriptor": [4, 6, 8, 11], "unscaledjazzydescriptor": [4, 6, 8, 11], "unscaledzscalesdescriptor": [4, 8, 11], "physchemdescriptor": [4, 8, 11], "jazzydescriptor": [4, 8, 11], "precomputeddescriptorfromfil": [4, 6, 8, 11], "zscale": [4, 6, 8, 12], "smilesfromfil": [4, 6, 8, 11], "smilesandsideinfofromfil": [4, 6, 8, 11], "scaleddescriptor": [4, 8, 11], "compositedescriptor": [4, 6, 8, 11], "tempor": [4, 6, 12], "stratifi": [4, 6, 12], "scaffoldsplit": [4, 7, 12], "modeldatatransform": [4, 6, 7, 8, 12], "vectorfromcolumn": [4, 6, 8, 12], "keepfirst": [4, 7, 12], "keeplast": [4, 7, 12], "keeprandom": [4, 7, 12], "keepmin": [4, 7, 12], "keepmax": [4, 7, 12], "keepavg": [4, 7, 12], "keepmedian": [4, 6, 7, 12], "keepkeepallnodedupl": 4, "report": [4, 6, 7], "coverag": 4, "subpackag": 5, "submodul": 5, "build_from_opt": [5, 8], "content": 5, "util": [5, 6, 7, 8, 13, 14], "files_path": [5, 8], "load_json": [5, 8], "schema": [5, 8, 11], "builder": 5, "metirc": 5, "model_writ": 5, "optbuild": 5, "schemagen": 5, "visual": [5, 9, 11], "intend": 6, "necessari": 6, "gui": 6, "autom": [6, 7], "reinvent": 6, "varieti": 6, "them": [6, 7, 9], "so": [6, 7, 9], "hyper": [6, 9], "influenc": [6, 7, 9], "automat": [6, 7], "idea": [6, 7], "read": [6, 7, 8], "otherwis": [6, 12], "might": [6, 7, 12], "skip": [6, 7], "toi": 6, "chosen": 6, "whole": [6, 7], "less": [6, 7], "minut": 6, "holdout": [6, 7], "readi": 6, "next": [6, 7], "few": [6, 7], "head": [6, 7], "molwt_gt_330": 6, "cc1cc": 6, "nc": [6, 7], "o": [6, 7], "c2cccc": 6, "coc3ccc": 6, "br": [6, 7], "cc3": [6, 7], "c2": [6, 7], "no1": 6, "387": 6, "233": 6, "nc1ccc": 6, "f": [6, 7, 12], "cc1f": 6, "nc1sccc1": 6, "c1nc2ccccc2s1": 6, "4360000000001": 6, "coc": 6, "c1ccccc1nc": 6, "c1cc": 6, "nn1cc1ccccc1": 6, "380": 6, "36000000000007": 6, "ccoc": 6, "sc1nc": 6, "c2ccccc2": 6, "ccc1c": 6, "312": 6, "39400000000006": 6, "ccc": [6, 7], "c1nn": [6, 7], "cc2ccccc2": 6, "c2ccccc12": 6, "349": 6, "4340000000001": 6, "brc1ccccc1occcoc1cccc2cccnc12": 6, "358": 6, "235": 6, "ccccn1c": 6, "coc2cccc": 6, "oc": 6, "nc2ccccc21": 6, "310": 6, "39700000000005": 6, "ccoc1cccc": 6, "c2sc3nc": 6, "c4ccc": 6, "cc4": 6, "ccc3c2n": 6, "c1": [6, 7], "407": 6, "4700000000001": 6, "coc1ccc": 6, "nc2ccc": 6, "cc2": 6, "c2ccc": 6, "cc1oc": 6, "454": 6, "54800000000023": 6, "sy": [6, 7], "sklearn": [6, 11], "kljk345": [6, 7], "pycharmproject": 6, "public_qptuna": 6, "lib": [6, 7], "python3": [6, 7], "site": [6, 7], "tqdm": 6, "21": [6, 7], "tqdmwarn": 6, "iprogress": 6, "updat": [6, 7], "ipywidget": 6, "readthedoc": [6, 9], "en": [6, 9], "stabl": [6, 8], "user_instal": 6, "autonotebook": 6, "notebook_tqdm": 6, "typic": [6, 7], "test_dataset_fil": [6, 8], "random_se": [6, 9], "42": [6, 7, 12, 13], "seed": [6, 7, 8, 12, 13], "reproduc": [6, 12, 14], "setup": [6, 9], "basic": [6, 8, 9], "importlib": 6, "reload": 6, "basicconfig": 6, "getlogg": 6, "disabl": [6, 7, 11], "np": [6, 7], "seterr": 6, "ignor": 6, "warn": [6, 7], "filterwarn": 6, "categori": 6, "futurewarn": 6, "runtimewarn": 6, "functool": 6, "partialmethod": 6, "__init__": [6, 9], "flood": 6, "decpreci": 6, "simplefilt": 6, "def": [6, 7, 9], "arg": [6, 8, 9], "kwarg": [6, 9], "stderr": 6, "render": [6, 7], "red": 6, "2024": 6, "07": 6, "02": 6, "13": [6, 7], "17": [6, 7], "26": [6, 7], "561": 6, "memori": [6, 8], "714": 6, "study_name_0": 6, "27": [6, 7], "022": 6, "finish": 6, "3594": 6, "2228073972638": 6, "39": [6, 7], "algorithm_nam": [6, 11], "randomforestregressor_algorithm_hash": 6, "f1ac01e1bba332215ccbd0c29c9ac3c3": 6, "max_depth__f1ac01e1bba332215ccbd0c29c9ac3c3": 6, "n_estimators__f1ac01e1bba332215ccbd0c29c9ac3c3": 6, "max_features__f1ac01e1bba332215ccbd0c29c9ac3c3": 6, "lt": [6, 7], "randomforestmaxfeatur": [6, 9], "gt": [6, 7], "34": [6, 7], "171": 6, "5029": 6, "734616310275": 6, "svr_algorithm_hash": 6, "ea7ccc7ef4a9329af0d4e39eb6184933": 6, "gamma__ea7ccc7ef4a9329af0d4e39eb6184933": 6, "039054412752107935": 6, "c__ea7ccc7ef4a9329af0d4e39eb6184933": 6, "1242780840717016e": 6, "429": 6, "4242": 6, "092751193529": 6, "579": 6, "3393": 6, "577488426015": 6, "ridge_algorithm_hash": 6, "cfa1990d5153c8812982f034d788d7e": 6, "alpha__cfa1990d5153c8812982f034d788d7e": 6, "06877704223043679": 6, "644": 6, "427": 6, "45250420148204": 6, "lasso_algorithm_hash": 6, "5457f609662e44f04dcc9423066d2f58": 6, "alpha__5457f609662e44f04dcc9423066d2f58": 6, "7896547008552977": 6, "698": 6, "3387": 6, "245629616474": 6, "plsregression_algorithm_hash": 6, "9f2f76e479633c0bf18cf2912fed9eda": 6, "n_components__9f2f76e479633c0bf18cf2912fed9eda": 6, "853": 6, "734620250011": 6, "3661540064603184": 6, "1799882524170321": 6, "28": [6, 7], "029": 6, "7": [6, 7, 9], "9650": 6, "026568221794": 6, "kneighborsregressor_algorithm_hash": 6, "1709d2c39117ae29f6c9debe7241287b": 6, "metric__1709d2c39117ae29f6c9debe7241287b": 6, "kneighborsmetr": [6, 9], "n_neighbors__1709d2c39117ae29f6c9debe7241287b": 6, "weights__1709d2c39117ae29f6c9debe7241287b": 6, "kneighborsweight": [6, 9], "uniform": [6, 9], "070": 6, "8": [6, 7, 9], "5437": 6, "151635569594": 6, "05083825348819038": 6, "336": 6, "2669": 6, "8534551928174": 6, "373": 6, "4341": 6, "586120152291": 6, "7921825998469865": 6, "532": 6, "11": [6, 7], "5514": 6, "404088878843": 6, "680": 6, "12": [6, 7], "5431": 6, "634989239215": 6, "722": 6, "3530": 6, "5496618991288": 6, "765": 6, "14": [6, 7], "3497": 6, "6833185436312": 6, "793": 6, "15": [6, 7], "4382": 6, "16208862162": 6, "831": 6, "734620031822": 6, "002825619931800395": 6, "309885135051862e": 6, "09": 6, "870": 6, "679": 6, "3109044887755": 6, "16827992999009767": 6, "932": 6, "18": [6, 7], "2550": 6, "114129318373": 6, "974": 6, "19": [6, 7], "4847": 6, "085792360169": 6, "735431606118867": 6, "29": 6, "016": 6, "268760278916": 6, "0014840820994557746": 6, "04671166881768783": 6, "096": 6, "4783": 6, "0470154796785": 6, "135": 6, "22": [6, 7], "3905": 6, "0064899852296": 6, "259": 6, "23": [6, 7], "4030": 6, "45773791647": 6, "340": 6, "24": [6, 7], "4681": 6, "602145939593": 6, "381": 6, "25": [6, 7], "4398": 6, "544034028325": 6, "6452011213193165": 6, "474": 6, "4454": 6, "143979828408": 6, "503": 6, "533": 6, "600": 6, "4397": 6, "330360587512": 6, "617": 6, "682": 6, "31": [6, 7], "2602": 6, "7561184287083": 6, "715": 6, "5267": 6, "388279961089": 6, "2015560027548533": 6, "794": 6, "33": 6, "4863": 6, "581760751052": 6, "836": 6, "388": 6, "96473594016675": 6, "5528259214839937": 6, "906": 6, "35": 6, "5539": 6, "698232987626": 6, "6400992020612235": 6, "962": 6, "36": 6, "5180": 6, "5533034102455": 6, "8968910439566395": 6, "005": 6, "37": 6, "4989": 6, "929984864281": 6, "04458440839692226": 6, "492108041427977": 6, "034": 6, "38": [6, 7], "103": 6, "6528": 6, "215066535042": 6, "16700143339733753": 6, "240": 6, "40": [6, 7], "4168": 6, "7955967552625": 6, "311": 6, "41": 6, "6177": 6, "060727800014": 6, "401": 6, "3963": 6, "906954658343": 6, "435": 6, "43": 6, "6805334166565": 6, "013186009009851564": 6, "001008958590140135": 6, "501": 6, "44": 6, "9300": 6, "86840721566": 6, "547": 6, "45": [6, 7], "83": 6, "87968210939489": 6, "382674443425525e": 6, "565": 6, "46": 6, "594": 6, "626": 6, "48": 6, "717": 6, "49": 6, "3660": 6, "9359502556": 6, "767": 6, "688": 6, "5244070398325": 6, "5267860995545326": 6, "813": 6, "51": 6, "690": 6, "6494438072099": 6, "8458809314722497": 6, "848": 6, "52": 6, "691": 6, "1197058420935": 6, "9167866889210807": 6, "898": 6, "53": 6, "3111710449325": 6, "945685900574672": 6, "934": 6, "9665592812149": 6, "8936837761725833": 6, "970": 6, "55": 6, "4682747008223": 6, "5183865279530455": 6, "030": 6, "56": 6, "687": 6, "5230947231512": 6, "3771771681361766": 6, "078": 6, "57": 6, "4503442069594": 6, "3663259819415374": 6, "127": 6, "58": 6, "686": 6, "9553733616618": 6, "2925652230875628": 6, "174": 6, "59": 6, "370": 6, "2038330506566": 6, "3962903248948568": 6, "222": 6, "60": 6, "377": 6, "25988028857313": 6, "45237513161879": 6, "270": 6, "379": 6, "8933285317637": 6, "4741161933311207": 6, "319": 6, "62": 6, "374": 6, "50897467366013": 6, "4290962207409417": 6, "356": 6, "63": [6, 7], "376": 6, "5588572940058": 6, "4464295711264585": 6, "416": 6, "64": 6, "237448916406": 6, "4687500034684213": 6, "65": 6, "375": 6, "7474776359051": 6, "4395650011783436": 6, "504": 6, "66": 6, "362": 6, "2834906299732": 6, "3326755354190032": 6, "542": 6, "67": 6, "357": 6, "3474880122588": 6, "2887212943233457": 6, "591": 6, "68": 6, "354": 6, "279045046449": 6, "2577677164664005": 6, "642": 6, "69": 6, "347": 6, "36894395697703": 6, "1672928587680225": 6, "706": 6, "70": 6, "345": 6, "17697390093394": 6, "1242367255308854": 6, "757": 6, "71": 6, "74610809299037": 6, "1728352983905301": 6, "807": 6, "72": 6, "23464281634324": 6, "1265380781508565": 6, "856": 6, "73": 6, "344": 6, "6848312222365": 6, "0829896313820404": 6, "902": 6, "74": [6, 7], "9111966504334": 6, "1070414661080543": 6, "966": 6, "75": 6, "70116419828565": 6, "0875643695329498": 6, "026": 6, "76": 6, "62647974688133": 6, "0716281620790837": 6, "089": 6, "77": 6, "6759429204596": 6, "0456289319914898": 6, "141": 6, "78": 6, "343": 6, "58131497761616": 6, "0010195360522613": 6, "193": 6, "79": 6, "342": 6, "7290581014813": 6, "9073210715005748": 6, "254": 6, "80": [6, 7], "67866114080107": 6, "9166305667100072": 6, "317": 6, "81": 6, "6440308445311": 6, "9248722692093634": 6, "367": 6, "82": 6, "02085648448934": 6, "8776928646870886": 6, "1662266300702": 6, "867592364677856": 6, "457": 6, "84": 6, "30158716569775": 6, "8599491178327108": 6, "497": 6, "85": 6, "2803074848341": 6, "8396948389352923": 6, "86": 6, "28301101884045": 6, "8396651775801683": 6, "587": 6, "87": 6, "6781906268143": 6, "8356021935129933": 6, "639": 6, "88": 6, "0405418264898": 6, "7430046191126949": 6, "677": 6, "89": 6, "77203208258476": 6, "9015965341429055": 6, "90": 6, "363": 6, "1622720320929": 6, "6746575663752555": 6, "91": 6, "7403796626193": 6, "9057564666836629": 6, "797": 6, "92": 6, "63579667712696": 6, "9332275205203372": 6, "93": [6, 7], "6886425884964": 6, "9433063264508291": 6, "94": 6, "9341048659705": 6, "884739221967487": 6, "935": 6, "95": [6, 7], "63507445779743": 6, "9381000493689634": 6, "986": 6, "96": 6, "06021011302374": 6, "963138023068903": 6, "97": 6, "9990546212019": 6, "9601651093867907": 6, "066": 6, "98": 6, "3821": 6, "2267845437514": 6, "117": 6, "6786067133016": 6, "721603508336166": 6, "seaborn": [6, 7], "sn": [6, 7], "set_them": 6, "darkgrid": 6, "default_reg_scor": 6, "ax": [6, 7], "scatterplot": 6, "trials_datafram": 6, "xlabel": [6, 7], "ylabel": [6, 7], "ojbect": 6, "interest": [6, 7], "neg_mean_squared_error": [6, 9], "highlight": 6, "color": [6, 7], "cv_test": 6, "user_attrs_test_scor": 6, "lambda": [6, 12], "item": [6, 10], "idx": [6, 7], "v": 6, "hue": 6, "palett": 6, "set1": 6, "inspect": 6, "apischema": [6, 8], "buildconfig_as_dict": 6, "serial": 6, "response_typ": [6, 7, 8], "deduplication_strategi": [6, 7, 8], "split_strategi": [6, 7, 8], "nosplit": [6, 12], "save_intermediate_fil": [6, 8], "log_transform": [6, 7, 8], "log_transform_bas": [6, 7, 8], "null": 6, "log_transform_neg": [6, 7, 8], "log_transform_unit_convers": [6, 7, 8], "probabilistic_threshold_represent": [6, 7, 8], "probabilistic_threshold_representation_threshold": [6, 7, 8], "probabilistic_threshold_representation_std": [6, 7, 8], "metadata": [6, 8, 9, 10, 11], "shuffl": [6, 9, 11, 12, 13], "best_trial": [6, 9, 11], "best_valu": [6, 9, 11], "tracking_rest_endpoint": [6, 9], "best_build": 6, "rb": 6, "predict_from_smil": [6, 8], "cc1": [6, 7], "43103985": 6, "177": 6, "99850936": 6, "now": [6, 7, 9], "panda": [6, 7], "pd": [6, 7], "df": [6, 12, 13], "read_csv": 6, "expect": [6, 7, 10], "matplotlib": [6, 7], "pyplot": [6, 7], "plt": [6, 7], "scatter": 6, "lim": 6, "max": [6, 7, 12], "diagon": 6, "r2_score": 6, "mean_squared_error": 6, "mean_absolute_error": 6, "y_true": [6, 8, 11], "y_pred": [6, 8, 11], "rmse": 6, "ad": [6, 7, 12, 13], "mae": 6, "absolut": 6, "8566354978126369": 6, "204909888075044": 6, "298453946973815": 6, "accept": [6, 7], "again": 6, "hopefulli": [6, 7], "littl": 6, "better": [6, 7, 8, 12], "send": 6, "strategi": [6, 8], "current": 6, "observ": [6, 7], "last": [6, 7, 12], "alreadi": [6, 7], "sort": [6, 7, 12, 13], "oldest": [6, 7, 12, 13], "newest": [6, 7, 12, 13], "end": [6, 7, 12, 13], "extern": 6, "tool": 6, "excel": 6, "ensur": [6, 7, 8, 9], "unballanc": 6, "work": [6, 7], "come": [6, 7], "measur": [6, 7], "fact": 6, "disregard": 6, "stereochemistri": [6, 7], "even": [6, 7], "sever": 6, "median": [6, 7, 12], "factor": [6, 7], "replic": [6, 7], "robust": [6, 7], "outlier": [6, 7], "acorss": 6, "trust": 6, "kept": 6, "splitter": [6, 7, 8, 10], "track_to_mlflow": [6, 9], "my_study_stratified_split": 6, "922": 6, "963": 6, "046": 6, "1856": 6, "4459752935309": 6, "123": 6, "1692": 6, "0451328577294": 6, "2918844591266672": 6, "592": 6, "1378": 6, "9731014410709": 6, "471164936778079": 6, "2658": 6, "13214897931": 6, "804": 6, "2059": 6, "3079659969176": 6, "330": [6, 7], "280": 6, "17777558722315": 6, "7001901522391756": 6, "422": 6, "3551": 6, "475476217507": 6, "466": 6, "2124": 6, "9660426577593": 6, "509": 6, "1686": 6, "5737716985532": 6, "9841058851292832": 6, "552": 6, "1702": 6, "174704715547": 6, "861494545249233": 6, "578": 6, "621": 6, "1204": 6, "636967895143": 6, "5238298142840006": 6, "676": 6, "228": 6, "44505332657158": 6, "9836853549192415": 6, "729": 6, "3949": 6, "499774068696": 6, "04535826280986047": 6, "012999584021838e": 6, "829": 6, "2856": 6, "917927507731": 6, "linear_model": 6, "_coordinate_desc": 6, "678": 6, "convergencewarn": 6, "did": 6, "regularis": 6, "dualiti": 6, "gap": 6, "306e": 6, "toler": 6, "824e": 6, "cd_fast": 6, "enet_coordinate_desc": 6, "882": 6, "2554": 6, "2079198900733": 6, "10588223712643852": 6, "1261": 6, "484274761188": 6, "0950442632698256": 6, "965": 6, "282": 6, "6478019258886": 6, "2920636100136971": 6, "004": 6, "1814": 6, "6019641143478": 6, "048": 6, "1284": 6, "7430070920798": 6, "1729012287538991": 6, "237": 6, "98783693000647": 6, "1721667984096773": 6, "192": 6, "2129": 6, "55317061882": 6, "4997740833423": 6, "779895470793612": 6, "260941957410989e": 6, "279": 6, "1740": 6, "8894369939983": 6, "02841448247455669": 6, "698e": 6, "280e": 6, "820e": 6, "352e": 6, "770e": 6, "3317": 6, "417858905051": 6, "003050380617617421": 6, "404": 6, "448": 6, "1256": 6, "7270466276807": 6, "1594144041655936": 6, "491": 6, "1245": 6, "1399766270456": 6, "336730512398918": 6, "583": 6, "2908": 6, "3563960057677": 6, "628": 6, "1775": 6, "55204856041": 6, "721": 6, "1257": 6, "9288888831513": 6, "1441514794000534": 6, "808": 6, "98174313112844": 6, "1939105579414777": 6, "900": 6, "3054": 6, "7066202193805": 6, "944": 6, "1227": 6, "082986184029": 6, "909508127148669": 6, "988": 6, "1676": 6, "7481962719485": 6, "4307837873914335": 6, "079": 6, "307965996918": 6, "168": 6, "3441": 6, "9109103644514": 6, "211": 6, "1670": 6, "5213862925175": 6, "07945856808433427": 6, "264": 6, "2756": 6, "046839500092": 6, "320": 6, "4997735530674": 6, "022099719935614482": 6, "4657380646234507e": 6, "08": 6, "0862402902634642": 6, "12519632281925502": 6, "467": 6, "3438": 6, "566583971217": 6, "524": 6, "4422556954731": 6, "19967589906728334": 6, "016e": 6, "618": 6, "359": [6, 7], "7639743940817": 6, "059252880514551576": 6, "662": 6, "1246": 6, "7813032646238": 6, "3074782262329858": 6, "755": 6, "2224": 6, "3845873049813": 6, "810": 6, "1673": 6, "9639799911165": 6, "2737740844660712": 6, "896": 6, "3163": 6, "129883232068": 6, "987": 6, "2753": 6, "414173913392": 6, "057": 6, "263": 6, "1352845182604": 6, "627030918721665": 6, "105": 6, "271": 6, "2979718788249": 6, "8548903728617034": 6, "165": 6, "277": 6, "86441431259567": 6, "9605867591283856": 6, "227": 6, "4329099850367": 6, "9537398361705693": 6, "274": 6, "3838070241422": 6, "9045589309769144": 6, "334": 6, "260": 6, "4460398258507": 6, "5589021326002044": 6, "383": 6, "257": 6, "95032410206767": 6, "5053759377103249": 6, "444": 6, "256": 6, "5958038666581": 6, "4789082433356577": 6, "495": 6, "253": 6, "4269973575198": 6, "4281024602273042": 6, "560": 6, "249": 6, "40822811603962": 6, "3546313579812586": 6, "620": 6, "245": 6, "71101688809983": 6, "2913960369109012": 6, "675": 6, "247": 6, "88538215472033": 6, "3274897484709072": 6, "737": 6, "244": 6, "23847775159297": 6, "2647865635312279": 6, "803": 6, "59033004585282": 6, "3228443521984092": 6, "863": 6, "243": 6, "40694430653753": 6, "2489205103047292": 6, "928": 6, "223": 6, "85145692792733": 6, "8934822741396387": 6, "990": [6, 7], "221": 6, "94026043724057": 6, "8552798675517863": 6, "219": 6, "60947928367543": 6, "8149866573467666": 6, "108": 6, "84441955310717": 6, "8531301788095305": 6, "170": 6, "24134912135943": 6, "8418420411160932": 6, "232": 6, "34805357903284": 6, "883998932301903": 6, "293": 6, "99342925522842": 6, "8564564664338091": 6, "353": 6, "50886633416462": 6, "8672069097403997": 6, "415": 6, "61235541906441": 6, "8482856353268698": 6, "479": 6, "217": 6, "7749814513912": 6, "7823980442129331": 6, "538": 6, "216": 6, "00225784039503": 6, "7113129125761161": 6, "601": 6, "8736767409489": 6, "6250904023479531": 6, "666": 6, "94414119442342": 6, "6227757503715069": 6, "731": 6, "45936690929625": 6, "6343056785694773": 6, "63861804615567": 6, "6302707941523814": 6, "860": 6, "1969": 6, "3749442111905": 6, "00019861806798724335": 6, "586529041453": 6, "923": 6, "215": 6, "82051598778696": 6, "6518244359516081": 6, "06387687700067": 6, "6440087841656821": 6, "041": 6, "24994687849525": 6, "6393212787552464": 6, "106": 6, "92984604804667": 6, "6232144947646524": 6, "25506613319246": 6, "603388647930941": 6, "2733": 6, "5772576431627": 6, "287": 6, "29854648789728": 6, "5873312673596333": 6, "16592450348784": 6, "4337907998582289": 6, "410": 6, "68514116107337": 6, "6695836226711808": 6, "475": 6, "220": 6, "8939514172608": 6, "4420925048614356": 6, "535": 6, "72299797702155": 6, "6960582933068138": 6, "69285146262294": 6, "69078828949453": 6, "665": 6, "0538787714827": 6, "7144357045239296": 6, "728": 6, "4213281391621": 6, "7353090312302926": 6, "74724725664498": 6, "92653950485437e": 6, "858": 6, "12287184152592": 6, "7183304951103088": 6, "22186485689846": 6, "7234233661662641": 6, "977": 6, "2720": 6, "793752592223": 6, "042": 6, "3855763846717": 6, "4726201914486088": 6, "By": 6, "roc_auc": [6, 9], "model_evalu": 6, "amongst": 6, "regression_scor": 6, "classification_scor": 6, "explained_vari": [6, 9], "max_error": [6, 9], "neg_mean_absolute_error": [6, 9], "neg_median_absolute_error": [6, 9], "average_precis": [6, 9], "balanced_accuraci": [6, 9], "f1": [6, 9], "f1_macro": [6, 9], "f1_micro": [6, 9], "f1_weight": [6, 9], "jaccard": [6, 9], "jaccard_macro": [6, 9], "jaccard_micro": [6, 9], "jaccard_weight": [6, 9], "neg_brier_scor": [6, 9], "precis": [6, 7, 9], "precision_macro": [6, 9], "precision_micro": [6, 9], "precision_weight": [6, 9], "recal": [6, 9], "recall_macro": [6, 9], "recall_micro": [6, 9], "recall_weight": [6, 9], "auc_pr_cal": [6, 8, 9], "bedroc": [6, 8, 9], "concordance_index": [6, 8, 9], "my_study_r2": 6, "945": 6, "947": 6, "072": 6, "011171868665159623": 6, "197": 6, "08689402230378174": 6, "283": 6, "12553701248394863": 6, "141096648805748": 6, "4893466963980463e": 6, "3039309544203818": 6, "20182749628697164": 6, "485": 6, "8187194367176578": 6, "558": 6, "4647239019719945": 6, "6574750183038587": 6, "611": 6, "8614818478547979": 6, "3974313630683448": 6, "705": 6, "12769795082909816": 6, "773": 6, "8639946428338224": 6, "2391884918766034": 6, "838": 6, "12553701248377633": 6, "00044396482429275296": 6, "3831436879125245e": 6, "892": 6, "12553700871203702": 6, "00028965395242758657": 6, "99928292425642e": 6, "2935582042429075": 6, "976": 6, "18476333152695587": 6, "8190707459213998": 6, "4060379177903557": 6, "118": 6, "12206148974315871": 6, "3105263811279067": 6, "344271094811757": 6, "3562469062424869": 6, "670604991178476": 6, "316": [6, 7], "045959695906983344": 6, "8583939656024446": 6, "5158832554303112": 6, "433": 6, "3062574078515544": 6, "487": 6, "11657354998283716": 6, "0009327650919528738": 6, "062479210472502": 6, "586": 6, "629": 6, "8498478905829554": 6, "1366172066709432": 6, "733": 6, "1276979508290982": 6, "786": 6, "13519830637607919": 6, "92901911959232": 6, "999026012594694": 6, "839": 6, "8198078293055633": 6, "5888977841391714": 6, "878": 6, "8201573964824842": 6, "19435298754153707": 6, "958": 6, "013": 6, "6285506249643193": 6, "35441495011256785": 6, "11934070343348298": 6, "145": 6, "4374125584543907": 6, "2457809516380005": 6, "213": 6, "3625576518621392": 6, "6459129458824919": 6, "36175556871883746": 6, "8179058888285398": 6, "285": 6, "8202473217121523": 6, "0920052840435055": 6, "372": 6, "3672927879319306": 6, "8677032984759461": 6, "402": 6, "445": 6, "40076792599874356": 6, "2865764368847064": 6, "26560316846701765": 6, "632": 6, "41215254857081174": 6, "671": 6, "763": 6, "00461414372160085": 6, "27282533524183633": 6, "919": 6, "10220127407364991": 6, "975": 6, "30323404130582854": 6, "3044553805553568": 6, "6437201185807124": 6, "076": 6, "41502276709562": 6, "10978379088847677": 6, "120": 6, "36160209098547913": 6, "022707289534838138": 6, "175": 6, "2916101445983833": 6, "936e": 6, "782e": 6, "434e": 6, "977e": 6, "276": 6, "8609413020928532": 6, "04987590926279814": 6, "794e": 6, "830e": 6, "906e": 6, "578e": 6, "8610289662757457": 6, "019211413400468974": 6, "754e": 6, "843e": 6, "507e": 6, "493": 6, "8610070549049179": 6, "018492644772509947": 6, "840e": 6, "513e": 6, "924e": 6, "8569771623635769": 6, "008783442408928633": 6, "243e": 6, "014e": 6, "700": 6, "8624781673814641": 6, "05782221001517797": 6, "113e": 6, "935e": 6, "122e": 6, "798": 6, "8618589507037001": 6, "02487072255316275": 6, "886": 6, "864754359721037": 6, "2079910754941946": 6, "946": 6, "8622236413326235": 6, "333215560931422": 6, "009": 6, "861832165638517": 6, "3628098560209365": 6, "068": 6, "8620108533993581": 6, "34240779695521706": 6, "142": 6, "8638540565650902": 6, "26493714991266293": 6, "8629799500771645": 6, "30596394512914815": 6, "8621408609583922": 6, "33648829357762355": 6, "351": 6, "8638132124078156": 6, "2679814646317183": 6, "424": 6, "863983758876634": 6, "24062119162159595": 6, "500": 6, "8627356047945115": 6, "3141728910335158": 6, "8639203054085788": 6, "23391390640786494": 6, "8570103863991635": 6, "6124885145996103": 6, "742": 6, "8647961976727571": 6, "2059976546070975": 6, "830": 6, "8648312544921793": 6, "20266060662750784": 6, "926": 6, "8648431452862716": 6, "20027647978240445": 6, "010": 6, "8648491459660418": 6, "1968919999787333": 6, "8650873115156988": 6, "174598921162764": 6, "204": 6, "8650350577921149": 6, "16468002989641095": 6, "8649412283687147": 6, "1606717091615047": 6, "986e": 6, "396": [6, 7], "8649537211609554": 6, "14694925097689848": 6, "506": 6, "8649734575435447": 6, "147612713300643": 6, "446e": 6, "8648761002838515": 6, "14440434705706803": 6, "398e": 6, "775": 6, "8639826593122782": 6, "1265357179513065": 6, "690e": 6, "875": 6, "864435565531768": 6, "1374245525868926": 6, "938": 6, "8590221951825531": 6, "49890830155012533": 6, "8649098880804443": 6, "1573428812070292": 6, "405e": 6, "864536410656637": 6, "13886104722511608": 6, "8597401050431873": 6, "47746341180045787": 6, "8537465461603838": 6, "050e": 6, "8642643827090003": 6, "13446778921611002": 6, "175e": 6, "8641621818665252": 6, "1286796719653316": 6, "625": 6, "864182755916388": 6, "13303218726548235": 6, "693": 6, "1255357440899417": 6, "021711452917433944": 6, "559714273835951e": 6, "758": 6, "8604596648091501": 6, "43644874418279245": 6, "463e": 6, "861": 6, "8635689909135862": 6, "10940922083495383": 6, "951": 6, "8648544336551733": 6, "1912756875742137": 6, "8648496595672595": 6, "19628449928540487": 6, "8452625121122099": 6, "4324661283995224": 6, "149": 6, "8378670635846416": 6, "839206620815206": 6, "002e": 6, "082e": 6, "8649365368153895": 6, "07270781179126021": 6, "8875676754699953": 6, "0006995169897945908": 6, "586e": 6, "618e": 6, "234e": 6, "484": 6, "8730555131061773": 6, "0018186269840273495": 6, "12553508835019533": 6, "04867556317570456": 6, "0011658455138452": 6, "284e": 6, "177e": 6, "664": 6, "8586292788613132": 6, "005078762921098462": 6, "anyalgorithm": 6, "__args__": 6, "consider": [6, 7], "modif": [6, 12], "establish": 6, "rf": 6, "account": [6, 7, 8], "though": 6, "treat": [6, 7], "pdf": [6, 9], "denot": [6, 12, 13], "determinist": [6, 7], "quantiti": 6, "tradit": [6, 7], "discret": 6, "discretis": [6, 12, 14], "bioactiv": [6, 7], "integr": 6, "afford": [6, 7], "particularli": 6, "liklihood": 6, "membership": [6, 7], "iopscienc": 6, "iop": 6, "articl": [6, 7], "3847": 6, "1538": 6, "3881": 6, "aaf101": 6, "pxc50": [6, 7], "p24863": 6, "enabl": [6, 7], "alwai": [6, 7], "734": 6, "joblib": [6, 8], "577": 6, "joblibcollisionwarn": 6, "collis": 6, "180": 6, "self": [6, 9], "_cached_cal": 6, "shelv": 6, "00": 6, "764": 6, "08099580623289632": 6, "prfclassifier_algorithm_hash": 6, "efe0ba9870529a6cde0dd3ad22447cbb": 6, "max_depth__efe0ba9870529a6cde0dd3ad22447cbb": 6, "n_estimators__efe0ba9870529a6cde0dd3ad22447cbb": 6, "max_features__efe0ba9870529a6cde0dd3ad22447cbb": 6, "prfclassifiermaxfeatur": [6, 9], "min_py_sum_leaf__efe0ba9870529a6cde0dd3ad22447cbb": 6, "use_py_gini__efe0ba9870529a6cde0dd3ad22447cbb": 6, "use_py_leafs__efe0ba9870529a6cde0dd3ad22447cbb": 6, "408": [6, 7], "07261454017489567": 6, "780": 6, "08791063872794351": 6, "911": 6, "07114663955819509": 6, "879": 6, "06537440628140882": 6, "446": 6, "05680450487193368": 6, "968": 6, "543": 6, "0656836821774901": 6, "333": 6, "07863564862376404": 6, "329": 6, "0648840199215795": 6, "014": 6, "07861037073288182": 6, "608": 6, "06669924317660021": 6, "997": 6, "06734611679947522": 6, "526": 6, "06810559387741143": 6, "0528189695245453": 6, "best_built": 6, "demonstr": [6, 7], "purpos": [6, 7], "transduct": 6, "example_smil": 6, "get_set": [6, 7, 8], "b": [6, 7], "outsid": [6, 7, 8], "likelihood": 6, "problemat": 6, "except": [6, 8], "valueerror": 6, "As": [6, 7], "raw": [6, 7, 8, 12], "760": 6, "800": 6, "w": 6, "801": 6, "fail": 6, "traceback": 6, "_optim": 6, "196": 6, "_run_trial": 6, "value_or_valu": 6, "func": 6, "128": 6, "__call__": 6, "_validate_algo": 6, "rais": [6, 8], "summaris": 6, "handl": 6, "via": [6, 7, 12], "convent": [6, 7], "classic": 6, "relev": 6, "cutoff": [6, 7, 12], "ouput": 6, "reflect": [6, 7], "arguabl": 6, "mpo": 6, "pub": 6, "ac": 6, "full": [6, 9], "jcim": 6, "9b00237": 6, "slide": 6, "googl": 6, "14pbd9ltxzfpsjhyxykflxnk8q80lhvnjimg8a3wqcrm": 6, "edit": 6, "calcault": 6, "directli": [6, 7], "later": [6, 7], "smilesbaseddescriptor": 6, "architectur": [6, 7], "quickli": 6, "867": 6, "868": 6, "root": [6, 9, 10], "enqueu": [6, 8], "manual": 6, "activation__668a7428ff5cdb271b01c0925e8fea45": 6, "relu": [6, 9], "aggregation__668a7428ff5cdb271b01c0925e8fea45": 6, "aggregation_norm__668a7428ff5cdb271b01c0925e8fea45": 6, "batch_size__668a7428ff5cdb271b01c0925e8fea45": 6, "depth__668a7428ff5cdb271b01c0925e8fea45": 6, "dropout__668a7428ff5cdb271b01c0925e8fea45": 6, "features_generator__668a7428ff5cdb271b01c0925e8fea45": 6, "ffn_hidden_size__668a7428ff5cdb271b01c0925e8fea45": 6, "ffn_num_layers__668a7428ff5cdb271b01c0925e8fea45": 6, "final_lr_ratio_exp__668a7428ff5cdb271b01c0925e8fea45": 6, "hidden_size__668a7428ff5cdb271b01c0925e8fea45": 6, "init_lr_ratio_exp__668a7428ff5cdb271b01c0925e8fea45": 6, "max_lr_exp__668a7428ff5cdb271b01c0925e8fea45": 6, "warmup_epochs_ratio__668a7428ff5cdb271b01c0925e8fea45": 6, "chempropregressor_algorithm_hash": 6, "668a7428ff5cdb271b01c0925e8fea45": 6, "301": 6, "6833": 6, "034983241957": 6, "chempropactiv": [6, 9], "chempropaggreg": [6, 9], "ensemble_size__668a7428ff5cdb271b01c0925e8fea45": 6, "epochs__668a7428ff5cdb271b01c0925e8fea45": 6, "chempropfeatures_gener": [6, 9], "6445": 6, "608102397302": 6, "1700": 6, "2300": 6, "safe": 6, "nan": [6, 8, 12, 13], "prompt": 6, "due": [6, 7, 8], "deactiv": 6, "own": 6, "still": 6, "commun": 6, "facilit": [6, 7, 9], "preset": 6, "enqu": 6, "bayesian": 6, "suggest": 6, "split_chemprop": [6, 9], "flag": [6, 7, 12, 13], "n_chemprop_tri": [6, 9], "desir": 6, "undirect": 6, "shown": [6, 7], "aspect": [6, 8], "princip": [6, 7], "expand": 6, "differnt": 6, "rememb": 6, "unless": 6, "alter": [6, 9], "characterist": [6, 7], "too": [6, 9], "limit": [6, 7, 9], "vice": [6, 9], "versa": [6, 9], "extens": [6, 9], "trail": [6, 9], "applic": [6, 7, 9], "chanc": 6, "help": 6, "caruana": 6, "particular": 6, "achiev": [6, 7], "st": 6, "figur": [6, 7], "signal": 6, "aka": 6, "could": [6, 7], "share": [6, 12, 13], "until": [6, 9], "longer": [6, 7], "mt": 6, "onc": [6, 7, 12], "knowledg": 6, "order": [6, 7, 9, 12], "earlier": [6, 7], "accompi": 6, "train_side_info": 6, "clog": 6, "surfac": 6, "area": [6, 7], "psa": 6, "265": 6, "22475": 6, "8088": 6, "883": 6, "32297": 6, "6237": 6, "835": 6, "33334": 6, "2804": 6, "314": 6, "26075": 6, "2533": 6, "498": 6, "278": 6, "18917": 6, "5102": 6, "694": 6, "246": 6, "12575": 6, "7244": 6, "255": 6, "14831": 6, "4338": 6, "895": 6, "302": 6, "26838": 6, "2041": 6, "22298": 6, "match": 6, "train_side_info_cl": 6, "clogp_gt2": 6, "clogs_gt": 6, "acceptors_gt5": 6, "donors_gt0": 6, "area_gt250": 6, "psa_lt0": 6, "aux": [6, 8, 10], "03": 6, "350": 6, "443": 6, "5817": 6, "944008002311": 6, "chemprophyperoptregressor_algorithm_hash": 6, "db9e60f9b8f0a43eff4b41917b6293d9": 6, "ensemble_size__db9e60f9b8f0a43eff4b41917b6293d9": 6, "epochs__db9e60f9b8f0a43eff4b41917b6293d9": 6, "features_generator__db9e60f9b8f0a43eff4b41917b6293d9": 6, "num_iters__db9e60f9b8f0a43eff4b41917b6293d9": 6, "search_parameter_level__db9e60f9b8f0a43eff4b41917b6293d9": 6, "chempropsearch_parameter_level": [6, 9], "aux_weight_pc__db9e60f9b8f0a43eff4b41917b6293d9": 6, "5796": 6, "34392897437": 6, "439": 6, "5795": 6, "086720713623": 6, "470": 6, "241": 6, "5820": 6, "227555999914": 6, "322": 6, "5852": 6, "160071204277": 6, "inlfuenc": 6, "henc": [6, 7], "percent": 6, "product": 6, "user_attrs_trial_ran": 6, "drop": [6, 7, 8], "erron": 6, "__": 6, "params_aux_weight_pc": 6, "conclud": [6, 7], "produc": 6, "overrid": [6, 9], "situat": [6, 7], "along": 6, "potenti": [6, 7], "compris": 6, "incompat": 6, "whilst": [6, 7], "desciptor": 6, "grei": [6, 7], "tial": 6, "what": 6, "design": 6, "unpromis": 6, "why": [6, 7], "poor": 6, "sampler": 6, "incompta": 6, "repeatedli": 6, "hyerparamet": 6, "ident": 6, "9525489095524835": 6, "aux_weight_pc__cfa1990d5153c8812982f034d788d7e": 6, "777": 6, "4824": 6, "686269039228": 6, "7731425652872588": 6, "819": 6, "849": 6, "4409": 6, "946844928445": 6, "791002332112292": 6, "021": [6, 7], "167": 6, "329624779366306": 6, "00015024763718638216": 6, "269": 6, "523": 6, "4396": 6, "722635068717": 6, "559": 6, "753": 6, "4577379164707": 6, "790": 6, "960": 6, "consult": 6, "incompitbl": 6, "algo": [6, 9], "occur": 6, "assign": [6, 7], "doe": [6, 7, 8, 9, 12], "params_algorithm_nam": 6, "move_legend": 6, "upper": [6, 7], "bbox_to_anchor": [6, 7], "overview": 6, "never": 6, "successfulli": 6, "absenc": 6, "8th": 6, "miss": [6, 8, 12, 13], "associ": [6, 7], "asid": 6, "mitig": 6, "overal": [6, 7], "serv": [6, 11], "argument": [6, 8], "tl": 6, "wider": 6, "activation__e0d3a442222d4b38f3aa1434851320db": 6, "aggregation__e0d3a442222d4b38f3aa1434851320db": 6, "aggregation_norm__e0d3a442222d4b38f3aa1434851320db": 6, "batch_size__e0d3a442222d4b38f3aa1434851320db": 6, "depth__e0d3a442222d4b38f3aa1434851320db": 6, "dropout__e0d3a442222d4b38f3aa1434851320db": 6, "features_generator__e0d3a442222d4b38f3aa1434851320db": 6, "ffn_hidden_size__e0d3a442222d4b38f3aa1434851320db": 6, "ffn_num_layers__e0d3a442222d4b38f3aa1434851320db": 6, "final_lr_ratio_exp__e0d3a442222d4b38f3aa1434851320db": 6, "hidden_size__e0d3a442222d4b38f3aa1434851320db": 6, "init_lr_ratio_exp__e0d3a442222d4b38f3aa1434851320db": 6, "max_lr_exp__e0d3a442222d4b38f3aa1434851320db": 6, "warmup_epochs_ratio__e0d3a442222d4b38f3aa1434851320db": 6, "e0d3a442222d4b38f3aa1434851320db": 6, "4937": 6, "540075659691": 6, "ensemble_size__e0d3a442222d4b38f3aa1434851320db": 6, "epochs__e0d3a442222d4b38f3aa1434851320db": 6, "retrain": 6, "954": 6, "043": 6, "5114": 6, "7131239123555": 6, "chempropregressorpretrained_algorithm_hash": 6, "dfc518a76317f23d95e5aa5a3eac77f0": 6, "frzn__dfc518a76317f23d95e5aa5a3eac77f0": 6, "chempropfrzn": [6, 9], "epochs__dfc518a76317f23d95e5aa5a3eac77f0": 6, "cover": 6, "global": 6, "job": [6, 7], "fair": 6, "1545": 6, "tl_studi": 6, "loc": [6, 7], "params_epoch": 6, "fillna": 6, "astyp": [6, 7], "agg": 6, "join": [6, 7], "params_chempropregressor_algorithm_hash": 6, "isna": 6, "annot": 6, "172": 6, "5891": 6, "7552821093905": 6, "140": 6, "5890": 6, "94653501547": 6, "77dfc8230317e08504ed5e643243fbc2": 6, "frzn__77dfc8230317e08504ed5e643243fbc2": 6, "epochs__77dfc8230317e08504ed5e643243fbc2": 6, "181": 6, "right": [6, 7], "ncol": 6, "world": [6, 7, 12, 13], "penultim": [6, 9], "chemprop_model": 6, "heatmap": 6, "predictor": [6, 8], "chemprop_fingerprint": 6, "fingerprint_typ": 6, "mpn": 6, "cbar_kw": 6, "semi": 6, "supervis": 6, "altern": [6, 7], "last_ffn": 6, "howeev": 6, "respect": [6, 7], "kind": [6, 7, 12], "confid": 6, "calibratedclassifiercv": 6, "understand": 6, "predict_proba": [6, 8], "among": 6, "gave": 6, "close": [6, 7], "actual": [6, 7], "topic": 6, "sigmoid": [6, 9], "review": 6, "those": [6, 7, 8], "calibration_curv": 6, "collect": 6, "defaultdict": 6, "precision_scor": 6, "recall_scor": 6, "f1_score": 6, "brier_score_loss": 6, "log_loss": 6, "roc_auc_scor": 6, "n_job": [6, 9, 11], "calibrated_rf": 6, "calibrated_model": 6, "173": 6, "110": 6, "8353535353535354": 6, "calibratedclassifiercvwithva_algorithm_hash": 6, "e788dfbfc5075967acb5ddf9d971ea20": 6, "n_folds__e788dfbfc5075967acb5ddf9d971ea20": 6, "max_depth__e788dfbfc5075967acb5ddf9d971ea20": 6, "n_estimators__e788dfbfc5075967acb5ddf9d971ea20": 6, "max_features__e788dfbfc5075967acb5ddf9d971ea20": 6, "uncalibr": 6, "uncalibrated_rf": 6, "uncalibrated_model": 6, "566": 6, "915": 6, "8185858585858585": 6, "randomforestclassifier_algorithm_hash": 6, "167e1e88dd2a80133e317c78f009bdc9": 6, "max_depth__167e1e88dd2a80133e317c78f009bdc9": 6, "n_estimators__167e1e88dd2a80133e317c78f009bdc9": 6, "max_features__167e1e88dd2a80133e317c78f009bdc9": 6, "conserv": 6, "1000": [6, 7], "random_st": [6, 12, 13], "calibrated_predict": 6, "uncalibrated_predict": 6, "cal_df": 6, "datafram": [6, 7, 8, 11, 12], "boxplot": 6, "melt": 6, "set_ylabel": [6, 7], "behaviour": [6, 7], "curv": [6, 7], "reliabl": 6, "diagram": 6, "against": 6, "figsiz": [6, 7], "ax1": 6, "subplot2grid": 6, "rowspan": 6, "ax2": 6, "perfectli": [6, 7], "pred": 6, "fraction_of_posit": 6, "mean_predicted_valu": 6, "n_bin": 6, "brier": 6, "2f": 6, "hist": 6, "histtyp": 6, "lw": 6, "set_ylim": 6, "legend": [6, 7], "set_titl": 6, "set_xlabel": [6, 7], "center": [6, 7], "tight_layout": [6, 7], "compos": 6, "refin": 6, "notic": 6, "significantli": 6, "cell": 6, "accur": 6, "alloc": 6, "y_prob": 6, "ye": 6, "score_nam": 6, "__name__": 6, "capit": 6, "score_df": 6, "set_index": 6, "decim": 6, "roc": 6, "auc": [6, 8], "184705": 6, "547129": 6, "830565": 6, "744048": 6, "784929": 6, "716536": 6, "175297": 6, "529474": 6, "811209": 6, "818452": 6, "814815": 6, "714104": 6, "va": 6, "multipoint": 6, "0c00476": 6, "margin": [6, 7], "bounari": 6, "548": 6, "537": 6, "8213131313131313": 6, "79765fbec1586f3c917ff30de274fdb4": 6, "n_folds__79765fbec1586f3c917ff30de274fdb4": 6, "max_depth__79765fbec1586f3c917ff30de274fdb4": 6, "n_estimators__79765fbec1586f3c917ff30de274fdb4": 6, "max_features__79765fbec1586f3c917ff30de274fdb4": 6, "uncert": [6, 8], "chem": [6, 7, 8], "allchem": 6, "pandastool": [6, 7], "rdconfig": 6, "datastruct": 6, "train_df": 6, "addmoleculecolumntofram": 6, "includefingerprint": 6, "getmorganfingerprint": 6, "nn": 6, "bulktanimotosimilar": 6, "add": [6, 7, 8, 10], "va_pr": 6, "va_uncert": 6, "dtm": 6, "trelli": 6, "fig": [6, 7], "subplot": [6, 7], "sharei": 6, "regplot": 6, "referenc": 6, "boundari": [6, 7, 12, 14], "neither": 6, "nor": 6, "dissimilar": 6, "cp_pred_ensembl": 6, "cp_uncert_ensembl": 6, "916": 6, "959": 6, "activation__fd833c2dde0b7147e6516ea5eebb2657": 6, "aggregation__fd833c2dde0b7147e6516ea5eebb2657": 6, "aggregation_norm__fd833c2dde0b7147e6516ea5eebb2657": 6, "batch_size__fd833c2dde0b7147e6516ea5eebb2657": 6, "depth__fd833c2dde0b7147e6516ea5eebb2657": 6, "dropout__fd833c2dde0b7147e6516ea5eebb2657": 6, "features_generator__fd833c2dde0b7147e6516ea5eebb2657": 6, "ffn_hidden_size__fd833c2dde0b7147e6516ea5eebb2657": 6, "ffn_num_layers__fd833c2dde0b7147e6516ea5eebb2657": 6, "final_lr_ratio_exp__fd833c2dde0b7147e6516ea5eebb2657": 6, "hidden_size__fd833c2dde0b7147e6516ea5eebb2657": 6, "init_lr_ratio_exp__fd833c2dde0b7147e6516ea5eebb2657": 6, "max_lr_exp__fd833c2dde0b7147e6516ea5eebb2657": 6, "warmup_epochs_ratio__fd833c2dde0b7147e6516ea5eebb2657": 6, "chempropclassifier_algorithm_hash": 6, "fd833c2dde0b7147e6516ea5eebb2657": 6, "65625": 6, "ensemble_size__fd833c2dde0b7147e6516ea5eebb2657": 6, "epochs__fd833c2dde0b7147e6516ea5eebb2657": 6, "midpoint": 6, "mont": 6, "carlo": 6, "virtual": [6, 8], "468": 6, "activation__c73885c5d5a4182168b8b002d321965a": 6, "aggregation__c73885c5d5a4182168b8b002d321965a": 6, "aggregation_norm__c73885c5d5a4182168b8b002d321965a": 6, "batch_size__c73885c5d5a4182168b8b002d321965a": 6, "depth__c73885c5d5a4182168b8b002d321965a": 6, "dropout__c73885c5d5a4182168b8b002d321965a": 6, "features_generator__c73885c5d5a4182168b8b002d321965a": 6, "ffn_hidden_size__c73885c5d5a4182168b8b002d321965a": 6, "ffn_num_layers__c73885c5d5a4182168b8b002d321965a": 6, "final_lr_ratio_exp__c73885c5d5a4182168b8b002d321965a": 6, "hidden_size__c73885c5d5a4182168b8b002d321965a": 6, "init_lr_ratio_exp__c73885c5d5a4182168b8b002d321965a": 6, "max_lr_exp__c73885c5d5a4182168b8b002d321965a": 6, "warmup_epochs_ratio__c73885c5d5a4182168b8b002d321965a": 6, "c73885c5d5a4182168b8b002d321965a": 6, "46875": 6, "ensemble_size__c73885c5d5a4182168b8b002d321965a": 6, "epochs__c73885c5d5a4182168b8b002d321965a": 6, "cp_pred_dropout": 6, "cp_uncert_dropout": 6, "previou": 6, "proabil": 6, "va_predict": 6, "correl": [6, 7], "drouput": 6, "uncertatinti": 6, "cp_uncert_delta": 6, "categor": [6, 12], "unit": [6, 7], "parsabl": 6, "date": 6, "cast": 6, "appropri": 6, "befor": [6, 7, 12], "choic": [6, 12], "822": 6, "862": 6, "4430": 6, "271946796234": 6, "mapie_algorithm_hash": 6, "976d211e4ac64e5568d369bcddd3aeb1": 6, "mapie_alpha__976d211e4ac64e5568d369bcddd3aeb1": 6, "max_depth__976d211e4ac64e5568d369bcddd3aeb1": 6, "n_estimators__976d211e4ac64e5568d369bcddd3aeb1": 6, "max_features__976d211e4ac64e5568d369bcddd3aeb1": 6, "analysi": [6, 7, 8], "perfom": 6, "post": 6, "mapie_pr": 6, "mapie_unc": 6, "bar": 6, "visualis": 6, "errorbar": 6, "yerr": 6, "ab": 6, "fmt": 6, "black": [6, 7], "ecolor": 6, "grai": 6, "elinewidth": 6, "capsiz": 6, "move": [6, 10], "analys": [6, 7], "width": 6, "alpha_impact": 6, "ma": 6, "unc_df": 6, "unc": 6, "reset_index": [6, 7], "concat": 6, "lineplot": 6, "err_styl": 6, "se": 6, "incorpor": 6, "tradition": 6, "unsupport": 6, "kernelexplain": [6, 8], "shaplei": 6, "explan": 6, "slundberg": 6, "game": 6, "credit": 6, "theori": 6, "publish": 6, "comopsit": 6, "540": 6, "_ridg": 6, "userwarn": [6, 7], "matrix": 6, "dual": 6, "34035600917066766": 6, "676421027478709": 6, "dga": 6, "dgp": 6, "dgtot": 6, "sa": 6, "sdc": 6, "sdx": 6, "numhacceptor": 6, "numhdonor": 6, "maxabsestateindex": 6, "maxestateindex": 6, "minabsestateindex": 6, "minestateindex": 6, "qed": 6, "sp": 6, "heavyatommolwt": 6, "exactmolwt": 6, "numvalenceelectron": 6, "numradicalelectron": 6, "maxpartialcharg": 6, "minpartialcharg": 6, "maxabspartialcharg": 6, "minabspartialcharg": 6, "fpdensitymorgan1": 6, "fpdensitymorgan2": 6, "fpdensitymorgan3": 6, "bcut2d_mwhi": 6, "bcut2d_mwlow": 6, "bcut2d_chghi": 6, "bcut2d_chglo": 6, "bcut2d_logphi": 6, "bcut2d_logplow": 6, "bcut2d_mrhi": 6, "bcut2d_mrlow": 6, "avgipc": 6, "balabanj": 6, "bertzct": 6, "chi0": 6, "chi0n": 6, "chi0v": 6, "chi1": 6, "chi1n": 6, "chi1v": 6, "chi2n": 6, "chi2v": 6, "chi3n": 6, "chi3v": 6, "chi4n": 6, "chi4v": 6, "hallkieralpha": 6, "ipc": 6, "kappa1": 6, "kappa2": 6, "kappa3": 6, "labuteasa": 6, "peoe_vsa1": 6, "peoe_vsa10": 6, "peoe_vsa11": 6, "peoe_vsa12": 6, "peoe_vsa13": 6, "peoe_vsa14": 6, "peoe_vsa2": 6, "peoe_vsa3": 6, "peoe_vsa4": 6, "peoe_vsa5": 6, "peoe_vsa6": 6, "peoe_vsa7": 6, "peoe_vsa8": 6, "peoe_vsa9": 6, "smr_vsa1": 6, "smr_vsa10": 6, "smr_vsa2": 6, "smr_vsa3": 6, "smr_vsa4": 6, "smr_vsa5": 6, "smr_vsa6": 6, "smr_vsa7": 6, "smr_vsa8": 6, "smr_vsa9": 6, "slogp_vsa1": 6, "slogp_vsa10": 6, "slogp_vsa11": 6, "slogp_vsa12": 6, "slogp_vsa2": 6, "slogp_vsa3": 6, "slogp_vsa4": 6, "slogp_vsa5": 6, "slogp_vsa6": 6, "slogp_vsa7": 6, "slogp_vsa8": 6, "slogp_vsa9": 6, "estate_vsa1": 6, "estate_vsa10": 6, "estate_vsa11": 6, "estate_vsa2": 6, "estate_vsa3": 6, "estate_vsa4": 6, "estate_vsa5": 6, "estate_vsa6": 6, "estate_vsa7": 6, "estate_vsa8": 6, "estate_vsa9": 6, "vsa_estate1": 6, "vsa_estate10": 6, "vsa_estate2": 6, "vsa_estate3": 6, "vsa_estate4": 6, "vsa_estate5": 6, "vsa_estate6": 6, "vsa_estate7": 6, "vsa_estate8": 6, "vsa_estate9": 6, "fractioncsp3": 6, "heavyatomcount": 6, "nhohcount": 6, "nocount": 6, "numaliphaticcarbocycl": 6, "numaliphaticheterocycl": 6, "numaliphaticr": 6, "numaromaticcarbocycl": 6, "numaromaticheterocycl": 6, "numaromaticr": 6, "numheteroatom": 6, "numrotatablebond": 6, "numsaturatedcarbocycl": 6, "numsaturatedheterocycl": 6, "numsaturatedr": 6, "ringcount": 6, "mollogp": 6, "molmr": 6, "fr_al_coo": 6, "fr_al_oh": 6, "fr_al_oh_notert": 6, "fr_arn": 6, "fr_ar_coo": 6, "fr_ar_n": 6, "fr_ar_nh": 6, "fr_ar_oh": 6, "fr_coo": 6, "fr_coo2": 6, "fr_c_o": 6, "fr_c_o_nocoo": 6, "fr_c_": 6, "fr_hoccn": 6, "fr_imin": 6, "fr_nh0": 6, "fr_nh1": 6, "fr_nh2": 6, "fr_n_o": 6, "fr_ndealkylation1": 6, "fr_ndealkylation2": 6, "fr_nhpyrrol": 6, "fr_sh": 6, "fr_aldehyd": 6, "fr_alkyl_carbam": 6, "fr_alkyl_halid": 6, "fr_allylic_oxid": 6, "fr_amid": 6, "fr_amidin": 6, "fr_anilin": 6, "fr_aryl_methyl": 6, "fr_azid": 6, "fr_azo": 6, "fr_barbitur": 6, "fr_benzen": 6, "fr_benzodiazepin": 6, "fr_bicycl": 6, "fr_diazo": 6, "fr_dihydropyridin": 6, "fr_epoxid": 6, "fr_ester": 6, "fr_ether": 6, "fr_furan": 6, "fr_guanido": 6, "fr_halogen": 6, "fr_hdrzine": 6, "fr_hdrzone": 6, "fr_imidazol": 6, "fr_imid": 6, "fr_isocyan": 6, "fr_isothiocyan": 6, "fr_keton": 6, "fr_ketone_topliss": 6, "fr_lactam": 6, "fr_lacton": 6, "fr_methoxi": 6, "fr_morpholin": 6, "fr_nitril": 6, "fr_nitro": 6, "fr_nitro_arom": 6, "fr_nitro_arom_nonortho": 6, "fr_nitroso": 6, "fr_oxazol": 6, "fr_oxim": 6, "fr_para_hydroxyl": 6, "fr_phenol": 6, "fr_phenol_noorthohbond": 6, "fr_phos_acid": 6, "fr_phos_est": 6, "fr_piperdin": 6, "fr_piperzin": 6, "fr_priamid": 6, "fr_prisulfonamd": 6, "fr_pyridin": 6, "fr_quatn": 6, "fr_sulfid": 6, "fr_sulfonamd": 6, "fr_sulfon": 6, "fr_term_acetylen": 6, "fr_tetrazol": 6, "fr_thiazol": 6, "fr_thiocyan": 6, "fr_thiophen": 6, "fr_unbrch_alkan": 6, "fr_urea": 6, "shap_valu": 6, "2227": 6, "042023e": 6, "2229": 6, "025199e": 6, "2228": 6, "802158e": 6, "2267": 6, "387276e": 6, "2230": 6, "106653e": 6, "1784": 6, "598471e": 6, "1785": 6, "584": 6, "ns": 6, "995": 6, "996": 6, "845": 6, "846": 6, "1375": 6, "1376": 6, "s1": 6, "n1c": 6, "1570": 6, "contrinubt": 6, "datset": 6, "unscaledphyschemjazzi": 6, "rank": [6, 8], "usag": 6, "978": 6, "032": 6, "818": 6, "t": [6, 7, 9], "kekul": 6, "unkekul": 6, "rational": 6, "rationale_scor": 6, "386": 6, "097": 6, "ch3": 6, "ch": 6, "389": [6, 7], "151": 6, "c1c": 6, "c1n": 6, "ch2": 6, "nh2": 6, "nn1cc1c": 6, "384": 6, "720": 6, "c1cccc": 6, "871": 6, "854": 6, "contian": 6, "second": 6, "dummi": 6, "third": 6, "smallest": 6, "made": [6, 7], "fourth": 6, "irregularli": 6, "xc50": [6, 7], "log10": [6, 7, 12, 14], "6th": 6, "convers": [6, 7, 12, 14], "logbas": [6, 7, 12, 14], "logneg": [6, 7, 12, 14], "negat": [6, 7, 12, 14], "transformed_studi": 6, "transform_exampl": 6, "028": 6, "5959493772536109": 6, "6571993250300608": 6, "169": 6, "1511102853256885": 6, "2487063317112765": 6, "288": 6, "6714912461080983": 6, "2725944467796781": 6, "369": 6, "194926264155893": 6, "395": 6, "7520919188596032": 6, "469": 6, "7803723847416691": 6, "499": 6, "6397753979196248": 6, "528": 6, "151110299986041": 6, "151110111437006": 6, "5410418750776741": 6, "612": 6, "7183231137124538": 6, "640": 6, "2721824844856162": 6, "716": 6, "1900929470222508": 6, "745": 6, "774": 6, "5585323973564646": 6, "3169218304262786": 6, "980": 6, "7974925066137679": 6, "008": 6, "218395226466336": 6, "039": 6, "1474226942497083": 6, "054": 6, "083": 6, "0239005731675412": 6, "160": 6, "191": 6, "178901060853144": 6, "27137790098830755": 6, "2710284516876423": 6, "361": 6, "6273152492418945": 6, "438": 6, "496": 6, "1907041717628215": 6, "3209075619139279": 6, "545": 6, "2709423025014604": 6, "609": 6, "3133943310851415": 6, "657": 6, "257769959239938": 6, "735": 6, "40359637945134746": 6, "817": 6, "4127882135896648": 6, "905": 6, "9246005133276612": 6, "003": 6, "8908739215746116": 6, "035": 6, "107536316777608": 6, "067": 6, "098": 6, "054360360588395": 6, "129": 6, "5428179904345867": 6, "5696273642213351": 6, "194": 6, "27099769667470536": 6, "1580741708125475": 6, "2709564785634315": 6, "10900413894771653": 6, "268": 6, "2709799905898163": 6, "13705914456987853": 6, "27097230608092054": 6, "12790870116376127": 6, "337": 6, "2709499903064464": 6, "10123180962907431": 6, "2710895886052581": 6, "26565663774320425": 6, "411": 6, "2708711012023424": 6, "005637048678674678": 6, "27092322402109364": 6, "06902647427781451": 6, "482": 6, "2712140349882": 6, "4076704953178294": 6, "515": 6, "27090080367174": 6, "04187106800188596": 6, "550": 6, "27086925247190047": 6, "003371853599610078": 6, "2708933298483799": 6, "032781796328385376": 6, "623": 6, "27087205624489635": 6, "006806773659187283": 6, "658": 6, "2708869511176179": 6, "025009489814943348": 6, "695": 6, "2711465077924297": 6, "3311125627707556": 6, "2708756855936628": 6, "011249102380159387": 6, "766": 6, "27087301924224993": 6, "007985924302396141": 6, "802": 6, "2708685399954944": 6, "00249856291483601": 6, "27121879554836553": 6, "4130244908975993": 6, "880": 6, "2708693196600531": 6, "0034541978803366022": 6, "918": 6, "27110195265802334": 6, "27994943662091765": 6, "956": 6, "2708682582859318": 6, "0021532199144365088": 6, "27087024523986086": 6, "0045884092728113585": 6, "27087351807632193": 6, "008596600952859433": 6, "2710818633795896": 6, "2567049271070902": 6, "109": 6, "27103241786565463": 6, "1990111983307052": 6, "146": 6, "2710350879598171": 6, "20214459724424078": 6, "183": 6, "2708688328221868": 6, "00285750520671645": 6, "27100832234449684": 6, "17064008990759916": 6, "258": 6, "27268613236193845": 6, "8725420109733135": 6, "296": 6, "27119617446689237": 6, "387533542012365": 6, "2708691110831552": 6, "0031985656730512953": 6, "27086852174155146": 6, "002476186542950981": 6, "27135383618835024": 6, "5626643670396761": 6, "449": 6, "2709819654433871": 6, "1394077979875128": 6, "488": [6, 8], "2718548944510965": 6, "0858347526799794": 6, "1508084699212935": 6, "03329943145150872": 6, "00025672309762227527": 6, "27249853374634975": 6, "702026434077893": 6, "604": 6, "27095660957755363": 6, "10916094511173127": 6, "643": 6, "27102160995407715": 6, "18630665884100353": 6, "681": 6, "27095708822582026": 6, "10973377642487026": 6, "27088222008661084": 6, "019235980282946118": 6, "762": 6, "2708703086029017": 6, "004666043957133775": 6, "799": 6, "27095279044622245": 6, "1045877457096882": 6, "840": 6, "2709408288690431": 6, "09023455456986404": 6, "9289218260898663": 6, "8200088368788958": 6, "917": 6, "27086675101898655": 6, "00030502148265565063": 6, "957": 6, "2710491243757999": 6, "21858260742423916": 6, "001": 6, "1491615840508995": 6, "024725853754515203": 6, "040": 6, "2709462479577586": 6, "0967427718847167": 6, "default_studi": 6, "252": 6, "332": 6, "3501": 6, "942111261296": 6, "5451": 6, "207265576796": 6, "459": 6, "1049201007814": 6, "9964": 6, "541364058234": 6, "3543": 6, "953608539901": 6, "570": 6, "6837": 6, "057544630979": 6, "613": 6, "2507": 6, "1794330606067": 6, "650": 6, "21534": 6, "719219668405": 6, "726": 6, "2899": 6, "736555614694": 6, "294e": 6, "760e": 6, "21674": 6, "445000284228": 6, "1049203123567": 6, "1049192609138": 6, "877": 6, "3630": 6, "72768093756": 6, "907": 6, "3431": 6, "942816967268": 6, "6908": 6, "462045154488": 6, "5964": 6, "65935954044": 6, "036": 6, "21070": 6, "107195348774": 6, "065": 6, "4977": 6, "068508997133": 6, "133": 6, "8873": 6, "669262669626": 6, "21387": 6, "63697424318": 6, "202": 6, "9958": 6, "573006910125": 6, "5182695600183": 6, "428": 6, "20684": 6, "56412138056": 6, "544": 6, "150": 6, "3435882510586": 6, "571": 6, "7068": 6, "705383113378": 6, "599": 6, "7150": 6, "482090052133": 6, "077": 6, "203": 6, "93637462922368": 6, "2570": 6, "5111262532305": 6, "21987": 6, "659957192194": 6, "9889": 6, "493204596083": 6, "413": 6, "7172": 6, "208490771303": 6, "9804": 6, "512701665093": 6, "555": 6, "585": 6, "9165": 6, "74081120673": 6, "0280270800017": 6, "161": 6, "1602933782954": 6, "888460860864": 6, "864": 6, "8414": 6, "932694243476": 6, "2270": 6, "540799189147": 6, "10383": 6, "79559309305": 6, "20815": 6, "025469865475": 6, "206": 6, "7560385808573": 6, "5264": 6, "4700789389035": 6, "3668": 6, "255064135424": 6, "156": 6, "12174877890536": 6, "793408178086295": 6, "99902820845678": 6, "157": 6, "371632749506": 6, "88307313087517": 6, "140915461519354": 6, "218": 6, "153": 6, "66773675231477": 6, "177324126813716": 6, "77906017834145": 6, "186": 6, "52056745848623": 6, "4565714180547": 6, "6710444346508": 6, "294": 6, "30976119334312": 6, "62916671166313": 6, "023639423189294": 6, "053696900694": 6, "914617418880486": 6, "31140591484044": 6, "201": 6, "33573874994386": 6, "569769302718845": 6, "5781354926491789": 6, "412": 6, "190": 6, "1384885119049": 6, "87666716965626": 6, "2537791489618": 6, "451": 6, "076949848299": 6, "9559574710535281": 6, "0032830967319653665": 6, "764974036324": 6, "03910427457823": 6, "406811480459925": 6, "164": 6, "4477304958181": 6, "701690847791482": 6, "819274780536123": 6, "567": 6, "87939164358104": 6, "32187661108304": 6, "660320437878754": 6, "607": 6, "01705178481896": 6, "61397716361812": 6, "603665957830847": 6, "645": 6, "155": 6, "73257312230092": 6, "759645965959294": 6, "503212714246787": 6, "684": 6, "154": 6, "46848394144124": 6, "8546740801317": 6, "35327336610912": 6, "724": 6, "20421802817864": 6, "57596974747163": 6, "84756262407801": 6, "51233215278089": 6, "3564642040401464": 6, "5034542273159819": 6, "207": 6, "68667089892196": 6, "034895878929095": 6, "03653571911285094": 6, "842": 6, "102": 6, "52277054278186": 6, "01961499216484045": 6, "670937191883546": 6, "881": 6, "28722475694815": 6, "012434370509176538": 6, "34222704431493": 6, "921": 6, "87402050281146": 6, "008452015347522093": 6, "914863578437455": 6, "38847505937936": 6, "01573542234868893": 6, "99307522974174": 6, "999": 6, "96336195786391": 6, "009845516063879428": 6, "59422914099683": 6, "19345618324213": 6, "009382525091504246": 6, "35573659237662": 6, "080": 6, "30772721342525": 6, "010579672066291478": 6, "35550323165882": 6, "23970902543148": 6, "013369359066405863": 6, "4744102498801": 6, "34331248758777": 6, "011398351701814368": 6, "54146340620301": 6, "195": 6, "104535853341": 6, "011708779850509646": 6, "682286191624579e": 6, "0653774146952": 6, "009806826677473646": 6, "90274406278985": 6, "64646042813787": 6, "0038598153381434685": 6, "20918134828555": 6, "68420472011734": 6, "0032474576673554513": 6, "35551178979624": 6, "85985201823172": 6, "003187930738019005": 6, "29431603544847": 6, "399": 6, "21583898009355": 6, "003122319313153475": 6, "83526418992966": 6, "437": 6, "34787242859676": 6, "002781955938462633": 6, "76228981520067": 6, "478": 6, "70914272129673": 6, "0023173546614751305": 6, "3000082904498813": 6, "519": 6, "10492031097328": 6, "002606064524407": 6, "7861330234653922e": 6, "1049154281806": 6, "0029210589377408366": 6, "200933937391094e": 6, "10492028002287": 6, "06431564840324226": 6, "2981641934644904e": 6, "56066541774658": 6, "0010848843623839548": 6, "151493073951163": 6, "76337597039308": 6, "004134805589645341": 6, "88115336652716": 6, "58009587759925": 6, "004763418454688096": 6, "02920758025023": 6, "113": 6, "35230417583477": 6, "0009098023238189749": 6, "57100980886017": 6, "809": 6, "30807467406214": 6, "03739791555156691": 6, "12818940557025": 6, "850": 6, "44100655116532": 6, "006380481141720477": 6, "4882351186755": 6, "891": 6, "35181001564942": 6, "0036244007454981787": 6, "608797806921866": 6, "124": 6, "3719027482892": 6, "0014198536004321608": 6, "05588994284273": 6, "28568052794907": 6, "005434972462746285": 6, "215759789700954": 6, "06": 6, "018": 6, "20325": 6, "66479442037": 6, "9696417046589247": 6, "132": 6, "21507621375022": 6, "0004528978867024753": 6, "80386923876023": 6, "85570350846885": 6, "0016948043699497222": 6, "455627755557016": 6, "contrast": [6, 7], "relplot": 6, "col": [6, 7], "facet_kw": 6, "axisgrid": [6, 7], "facetgrid": 6, "0x7fb3797f6b30": 6, "noramlis": 6, "unlog": 6, "yield": [6, 7, 12, 13], "mse": 6, "1126": 6, "56968721": 6, "20237903": 6, "revers": [6, 7, 12, 14], "onto": 6, "action": 6, "importantli": 6, "easili": [6, 7], "94824194": 6, "92008694": 6, "instruct": 6, "untransform": 6, "wish": 6, "cut": [6, 7], "10um": 6, "ptr_config_log_transform": 6, "ptr_transformed_studi": 6, "ptr_and_transform_exampl": 6, "518": 6, "002341918451736245": 6, "805": 6, "0024908979029632677": 6, "847": 6, "007901407671048116": 6, "888": 6, "00496231674623194": 6, "0026848278110363512": 6, "0010872728889471893": 6, "000": 6, "008706109201510277": 6, "027": 6, "093": 6, "002999462459688867": 6, "00825680029907454": 6, "148": 6, "007901407993550248": 6, "007901405163828307": 6, "0021653695362066753": 6, "002869169486971014": 6, "0010855652626111146": 6, "00550533804299308": 6, "002236800860454562": 6, "006105985607235417": 6, "004846526544994462": 6, "006964668794465202": 6, "670": 6, "699": 6, "008384326901042542": 6, "730": 6, "001082194093844804": 6, "761": 6, "0010807084256204563": 6, "948": 6, "005505338042993082": 6, "979": 6, "005247934991526694": 6, "0010803393728928605": 6, "005218354425190125": 6, "138": 6, "004999207507691546": 6, "0015694919308122948": 6, "326": 6, "0019757694194001384": 6, "421": 6, "002341918451736244": 6, "453": 6, "00368328296527152": 6, "521": 6, "003412828259848677": 6, "551": 6, "004412110711416997": 6, "616": 6, "647": 6, "0021743798524909573": 6, "0022761245849848527": 6, "0010805768178458735": 6, "750": 6, "001080400188305814": 6, "784": 6, "0010805009783570441": 6, "0010804680472500541": 6, "0010803723579987025": 6, "890": 6, "001080969596032512": 6, "925": 6, "0010800333715082816": 6, "0010802574700236845": 6, "0010814994986419817": 6, "037": 6, "001080161136846237": 6, "071": 6, "0010800254136811547": 6, "107": 6, "0010801290036870739": 6, "001080037482216557": 6, "179": 6, "0010801015705851358": 6, "0010812122378841013": 6, "0010800531021304936": 6, "291": 6, "00108004162698813": 6, "328": 6, "0010800223466649803": 6, "364": 6, "0010815197263834202": 6, "0010800257029027847": 6, "0010810223438672223": 6, "0010800211339555509": 6, "513": 6, "0010800296871141684": 6, "0010800437739166451": 6, "0010809366267195716": 6, "627": 6, "001080725386603206": 6, "0010807368035830652": 6, "704": 6, "0010800236072155854": 6, "741": 6, "0010806223050773966": 6, "779": 6, "0010876516369772728": 6, "00108142358144501": 6, "857": 6, "0010800248050489667": 6, "894": 6, "001080022268085466": 6, "0010820922958715991": 6, "969": 6, "0010805094397523254": 6, "007": 6, "0010841993753324146": 6, "007899735988203994": 6, "086": 6, "0010868762004637347": 6, "001080400750193767": 6, "163": 6, "0010806791616300314": 6, "0010804028029753213": 6, "0010800812188506515": 6, "0010800299598580359": 6, "0010803843696362083": 6, "001080333048974234": 6, "394": [6, 7], "432": 6, "001080014645182176": 6, "473": 6, "0010807968027851892": 6, "516": 6, "007907028395366658": 6, "553": 6, "0010803563024666294": 6, "inted": 6, "opter": 6, "probabilst": 6, "lossi": 6, "anywai": 6, "intention": 6, "clip": [6, 7], "cannot": 6, "timepoint": 6, "aux_column": [6, 8], "accord": [6, 7, 8], "aux_col_config": 6, "aux_descriptors_dataset": 6, "train_with_conc": 6, "aux1": 6, "aux_col_studi": 6, "covariate_exampl": 6, "aux1_model": 6, "323": 6, "5186": 6, "767663956718": 6, "522": 6, "4679": 6, "740824270968": 6, "575": 6, "4890": 6, "6705099499995": 6, "3803": 6, "9324375833753": 6, "667": 6, "3135": 6, "6497388676926": 6, "2518812859375": 6, "778": 6, "4309": 6, "124112370974": 6, "30159424580074": 6, "897": 6, "4357": 6, "02827013125": 6, "1437929337522": 6, "45281013": 6, "shape": [6, 7], "thrown": [6, 8], "prediciton": 6, "regardless": 6, "utilis": [6, 7], "seper": 6, "vector_covariate_config": 6, "precomputed_descriptor": 6, "train_with_fp": 6, "aux_transform": [6, 8], "vector_covariate_studi": 6, "vector_aux_exampl": 6, "vector_covariate_model": 6, "2200": 6, "6817959410578": 6, "011994365911634164": 6, "95660880078": 6, "029071783512897825": 6, "5798": 6, "564494725643": 6, "022631709120790048": 6, "2198637677605415": 6, "972": 6, "2899178898048": 6, "8916194399474267": 6, "556": 6, "3336440433073": 6, "5914093983615214": 6, "614": 6, "653": 6, "3036472748931": 6, "6201811079699818": 6, "3807": 6, "8035919667395": 6, "901e": 6, "892e": 6, "914e": 6, "752": 6, "5019": 6, "459500770764": 6, "1376436589359351": 6, "4017711284796": 6, "893": 6, "771": 6, "797115414836": 6, "74340620175102": 6, "train_smil": [6, 8], "train_i": [6, 8], "train_aux": [6, 8], "test_smil": [6, 8], "test_i": [6, 8], "test_aux": [6, 8], "512": 6, "legth": 6, "39754917": 6, "465": 6, "06352766": 6, "52031134": 6, "341": 6, "89875316": 6, "371": 6, "5516046": 6, "85042171": 6, "436": 6, "33406203": 6, "91439129": 6, "80585907": 6, "346": 6, "48565041": 6, "protein": [6, 12, 14], "alongsid": 6, "chemic": [6, 7, 12, 13], "sequenc": [6, 12, 14], "former": 6, "wherea": 6, "latter": [6, 7], "interact": 6, "basi": [6, 7], "toxinpred3": 6, "No": [6, 9, 12], "demponstr": 6, "zscale_covariate_config": 6, "zscale_covariate_studi": 6, "zscale_aux_exampl": 6, "zscale_covariate_model": 6, "458": 6, "8886986575836505": 6, "kneighborsclassifier_algorithm_hash": 6, "e51ca55089f389fc37a736adb2aa0e42": 6, "metric__e51ca55089f389fc37a736adb2aa0e42": 6, "n_neighbors__e51ca55089f389fc37a736adb2aa0e42": 6, "weights__e51ca55089f389fc37a736adb2aa0e42": 6, "unlik": 6, "21269231": 6, "91153846": 6, "29038462": 6, "69846154": 6, "22230769": 6, "99521739": 6, "59826087": 6, "34695652": 6, "03086957": 6, "13391304": 6, "08083333": 6, "6125": 6, "82916667": 6, "05083333": 6, "56083333": 6, "02178571": 6, "91785714": 6, "45392857": 6, "37642857": 6, "03107143": 6, "93357143": 6, "78964286": 6, "62928571": 6, "50857143": 6, "50107143": 6, "1232": 6, "3364": 6, "2328": 6, "1368": 6, "2304": 6, "7062": 6, "x_": 6, "vmin": 6, "vmax": 6, "cmap": 6, "spectral": 6, "248bit": 6, "128bit": 6, "minimz": 6, "consist": 6, "generaliz": 6, "minimize_std_dev": 6, "minimise_std_dev": [6, 9], "std": [6, 7, 12, 14], "dev": [6, 7], "example_multi": 6, "parameter_analysi": 6, "set_metric_nam": 6, "740": 6, "4008740644240856": 6, "9876203329634794": 6, "331": 6, "3561484909673425": 6, "9875061220991906": 6, "472": 6, "7856521165563053": 6, "21863029956806662": 6, "525": 6, "9125905675311808": 6, "7861693342190089": 6, "603": 6, "5238765412750027": 6, "2789424384877304": 6, "5348363849100434": 6, "5741725628917808": 6, "746": 6, "0072511048320134": 6, "2786318125997387": 6, "9625764609276656": 6, "27575381401822424": 6, "1114006274062536": 6, "7647766019001522": 6, "7801680863916906": 6, "2725738454485389": 6, "121": 6, "785652116470164": 6, "21863029955530786": 6, "152": 6, "785651973436432": 6, "21863032832257323": 6, "6101359993004856": 6, "3011280543457062": 6, "209": 6, "5361950698070447": 6, "23560786523195643": 6, "5356113574175657": 6, "5769721187181905": 6, "543430366921729": 6, "514747412346662": 6, "508": [6, 8], "5194661889628072": 6, "40146744515282495": 6, "659": 6, "659749443628722": 6, "6659085938841998": 6, "876": 6, "1068495306229729": 6, "24457822094737378": 6, "8604898820838102": 6, "7086875504668667": 6, "949": 6, "5919869916997383": 6, "2367498627927979": 6, "2497762395862362": 6, "10124660026536195": 6, "205": 6, "study_name_1": 6, "669": 6, "0621601907738047": 6, "2749020946925899": 6, "xxx": 6, "values_neg_mean_squared_error": 6, "values_standard": 6, "twinx": 6, "r": 6, "floor": 6, "ceil": 6, "align": 6, "set_ytick": 6, "linspac": 6, "set_xtick": 6, "text": [6, 7, 8, 12], "pareto": 6, "front": 6, "plot_pareto_front": 6, "plot_param_import": 6, "dictionari": [6, 10], "ordereddict": 6, "descend": 6, "algortihm": 6, "impact": 6, "durat": 6, "total_second": 6, "target_nam": 6, "relationship": 6, "plot_parallel_coordin": [6, 8, 9, 11], "param": [6, 7, 9, 10], "taken": [6, 7], "101": 6, "precomputed_config": 6, "precomputed_studi": 6, "precomputed_exampl": 6, "precomputed_model": 6, "785": 6, "788": 6, "3014": 6, "274803630188": 6, "471088599086": 6, "03592375122963953": 6, "511": 6, "3029": 6, "113810544919": 6, "8153295905650357": 6, "4358": 6, "575772003129": 6, "unseen": 6, "caus": 6, "111": 6, "new_molecul": 6, "112": 6, "tempfil": 6, "temp": [6, 7], "store": [6, 7, 11], "temporari": [6, 10], "extract": 6, "1st": 6, "example_fp": 6, "namedtemporaryfil": 6, "temp_fil": 6, "len": [6, 7], "to_csv": 6, "292": 6, "65709987": 6, "64327077": 6, "common": 7, "proper": 7, "optuna_az": 7, "process": [7, 8], "draw": 7, "ipythonconsol": 7, "ipython": 7, "displai": 7, "os": 7, "listdir": 7, "isfil": 7, "walk": 7, "handi": 7, "var": 7, "1v": 7, "9y_z128d7gvcp8mf8q0pz3ch0000gq": 7, "ipykernel_82497": 7, "796203442": 7, "deprecationwarn": 7, "deprec": 7, "med": 7, "titles": 7, "fontsiz": 7, "labels": 7, "xtick": 7, "ytick": 7, "rcparam": 7, "whitegrid": 7, "set_styl": 7, "white": 7, "inlin": 7, "3336016810": 7, "matplotlibdeprecationwarn": 7, "ship": 7, "v0_8": 7, "api": [7, 8], "boolean": 7, "nomin": 7, "convert": [7, 12], "conduct": 7, "primarydf": 7, "loadsdf": 7, "inchi": 7, "skeletonspher": 7, "nm": 7, "id": 7, "romol": 7, "ic50": 7, "\u00b5m": 7, "c1ccc2c": 7, "co2": 7, "004320939": 7, "1s": 7, "c8h7no2": 7, "c10": 7, "qrcgftxrxymjo": 7, "uhfffaoysa": 7, "86075": 7, "kinas": 7, "p38": 7, "rdchem": 7, "0x7fd1c0d34040": 7, "c1ccc": 7, "ccc2ccccc2occ3ccc": 7, "882397308": 7, "c22h20o3": 7, "c23": 7, "ytdaoqyeyfcini": 7, "89637": 7, "kd": 7, "retinoid": 7, "receptor": 7, "0x7fd1f8f965e0": 7, "130299026": 7, "0x7fd1f8f96650": 7, "nh": 7, "48148606": 7, "c9h7no": 7, "c11": 7, "lisfmebwquvkpj": 7, "n93": 7, "n82": 7, "n65": 7, "n36": 7, "n33": 7, "ki": 7, "nki": 7, "carbon": 7, "anhydras": 7, "xii": 7, "ncarbon": 7, "0x7fd1f8f966c0": 7, "nc1ccccn1": 7, "c7h8n2o": 7, "h2": 7, "5h": 7, "qrokotbwfzitjz": 7, "86233": 7, "nicotin": 7, "phosphoribosyltransferas": 7, "0x7fd1f8f96730": 7, "renam": 7, "conveni": [7, 8, 9, 12], "rest": 7, "moltosmil": 7, "isomericsmil": 7, "c1coc2ccccc2n1": 7, "004321": 7, "coc2ccccc2ccc2ccccc2": 7, "882397": 7, "130299": 7, "c1ccc2ccccc2": 7, "481486": 7, "stick": 7, "engin": 7, "assum": [7, 12, 13], "stage": 7, "slightli": 7, "pose": 7, "wise": 7, "uniqu": 7, "outlin": 7, "occurr": 7, "preserv": 7, "vari": 7, "recommend": 7, "abil": 7, "being": 7, "df_po": 7, "dedup": [7, 12], "df_rnd": 7, "df_max": 7, "df_avg": 7, "df_med": 7, "deduplidc": 7, "397": 7, "indici": 7, "coc1cc2ncnc": 7, "nc3ccc": 7, "scc4ccccc4": 7, "cl": 7, "c3": 7, "c2cc1oc": 7, "282579": 7, "912929": 7, "cc1cccc": 7, "nc2ncnc3ccc": 7, "c4ccccc4": 7, "cc23": 7, "n2cc": 7, "cc2c": 7, "nc2cccc": 7, "n2": 7, "065502": 7, "390": 7, "958607": 7, "392": 7, "oc2cccc": 7, "cn1nc": 7, "c2cnc": 7, "c3ccc": 7, "nc1c1": 7, "oc1nc": 7, "oc2cc": 7, "c3ccccc3": 7, "c3cccc": 7, "cn": 7, "936291": 7, "uniquify_by_posit": 7, "uniquify_randomli": 7, "essenc": 7, "uniquify_by_valu": 7, "highest": 7, "minim": [7, 9], "densiti": 7, "dpi": 7, "kdeplot": 7, "shade": 7, "orang": 7, "ndigit": 7, "blue": 7, "keepaverag": 7, "deeppink": 7, "hold": [7, 8], "assess": 7, "aim": 7, "simpli": 7, "sai": 7, "veri": 7, "intern": [7, 10], "resembl": 7, "easiest": 7, "especi": 7, "reli": 7, "stochast": 7, "initi": [7, 8, 9], "train_ran": 7, "test_ran": 7, "time_column": 7, "old": 7, "datapoint": [7, 10, 12, 13], "accru": 7, "entri": [7, 12, 13], "timestamp": 7, "top": 7, "df_med_tempor": 7, "fake": 7, "insert": 7, "nccccccoc1ccc2c": 7, "n1cc": 7, "cc1c": 7, "684240": 7, "1037": 7, "481464": 7, "1036": 7, "c1cn": 7, "n2c": 7, "nc3cccc": 7, "n3": 7, "cc3cc3": 7, "732625": 7, "1035": 7, "568332": 7, "1034": 7, "790259": 7, "1033": 7, "train_tempor": 7, "test_tempor": 7, "highli": 7, "skew": 7, "respcol": 7, "fd": [7, 12, 13], "histogram": [7, 12, 13], "determin": [7, 12, 13], "balanc": 7, "train_str": 7, "test_str": 7, "realist": 7, "deplopi": 7, "emul": [7, 12, 13], "hop": 7, "opportun": 7, "seri": 7, "push": 7, "domain": 7, "realibl": 7, "challeng": 7, "scaf_split": 7, "train_sca": 7, "test_sca": 7, "ground": 7, "df_val": 7, "roughli": [7, 9], "evid": 7, "pronounc": 7, "dodgerblu": 7, "middl": 7, "saffold": 7, "discuss": 7, "propreti": 7, "endpoint": 7, "routin": 7, "linearis": 7, "variat": 7, "gaussian": 7, "realiti": 7, "nearli": 7, "exhibit": 7, "superior": 7, "wide": 7, "xc50_data": 7, "keepallnodedupl": [7, 12], "pxc50_data": 7, "zip": 7, "jointplot": 7, "suptitl": 7, "plot_margin": 7, "rugplot": 7, "crimson": 7, "height": 7, "clip_on": 7, "jointgrid": 7, "0x7fd1f984f670": 7, "heteroscedast": 7, "homoscedast": 7, "transorm": 7, "0x7fd1eb924700": 7, "logartihm": 7, "power": [7, 12, 14], "um": 7, "dataset_transform": 7, "THe": 7, "0x7fd1db908550": 7, "had": 7, "reverse_transform": [7, 12], "0x7fd1bc05b4c0": 7, "mervin": 7, "framework": 7, "somewher": 7, "unavoid": 7, "ideal": 7, "deviat": [7, 12, 14], "\u03c3": 7, "heterogen": 7, "versu": 7, "assimil": 7, "hypothesi": 7, "degre": 7, "p_": 7, "activityt": 7, "cumul": 7, "cdf": 7, "eq": 7, "equal": [7, 9], "delta": 7, "vec": 7, "frac": 7, "erf": 7, "overrightarrow": 7, "sigma": 7, "concret": 7, "arbitrari": 7, "unknown": 7, "therefor": 7, "schemat": 7, "lookup": 7, "tabl": 7, "sd": 7, "scenario": [7, 12, 13], "philosoph": 7, "delimit": [7, 12, 14], "operand": 7, "censor": 7, "far": 7, "granular": 7, "therebi": 7, "combin": 7, "becom": 7, "jcheminf": 7, "biomedcentr": 7, "1186": 7, "s13321": 7, "00539": 7, "sec12": 7, "pxc50_threshold": 7, "pxc50_std": 7, "exmapl": 7, "ptr_data": 7, "gather": 7, "certainti": 7, "lower_reproduc": 7, "upper_reproduc": 7, "dataload": 7, "somewhat": 7, "invert": 7, "bell": 7, "kde": 7, "behav": 7, "patch": 7, "mpatch": 7, "line2d": 7, "ax_joint": 7, "axhlin": 7, "linestyl": 7, "ax_marg_x": 7, "axvlin": 7, "ax_marg_i": 7, "region": 7, "uncert_color": 7, "purpl": 7, "uncert_region": 7, "rectangl": 7, "fill": 7, "add_patch": 7, "box": 7, "nthreshold": 7, "nptr": 7, "nregion": 7, "fancybox": 7, "borderaxespad": 7, "leg": 7, "get_legend": 7, "legendhandl": 7, "set_color": 7, "set_alpha": 7, "tight": 7, "layout": 7, "subplots_adjust": 7, "set_size_inch": 7, "1725493911": 7, "attribut": 7, "minor": 7, "legend_handl": 7, "dash": 7, "histrogram": 7, "aforement": 7, "ptrtransform": [7, 12, 14], "ptr_transform": 7, "histplot": 7, "stat": 7, "scipi": 7, "resp_col": [7, 8], "pearsonr": 7, "std_df": 7, "groupbi": 7, "mdn_df": 7, "std_vs_median": 7, "suffix": 7, "_std": 7, "_median": 7, "dropna": 7, "activity_std": 7, "activity_median": 7, "088539": 7, "674782": 7, "265123": 7, "138620": 7, "157605": 7, "stdev": 7, "stat_func": 7, "plot_joint": 7, "zorder": 7, "0x7fd1def2f8b0": 7, "signific": 7, "assumpt": 7, "fulfil": 7, "ptr_train_ran": 7, "ptr_test_ran": 7, "ptr_train_str": 7, "ptr_test_str": 7, "ptr_train_tempor": 7, "ptr_test_tempor": 7, "ptr_train_sca": 7, "ptr_test_sca": 7, "xlim": 7, "pypoetri": 7, "virtualenv": 7, "_qsktrft": 7, "py3": 7, "warn_singular": 7, "msg": 7, "peak": 7, "extem": 7, "dsitribut": 7, "awai": 7, "bias": 7, "enum": [8, 9, 10, 12], "building_configuration_enum": [8, 10], "configuration_enum": [8, 10], "interface_enum": [8, 10], "model_runner_enum": [8, 10], "objective_enum": [8, 10], "optimization_configuration_enum": [8, 10], "prediction_configuration_enum": [8, 10], "return_values_enum": [8, 10], "visualization_enum": [8, 10], "merge_train_and_test_data": 8, "isvalid": 8, "read_data": 8, "filenam": [8, 10], "smiles_col": [8, 10, 12, 13], "aux_col": 8, "invalid": 8, "pars": [8, 9, 11], "tupl": [8, 12, 13], "ambigu": 8, "smiles_": 8, "y_": [8, 10, 12], "aux_": 8, "factori": [8, 9], "intermediate_training_dataset_fil": 8, "intermediate_test_dataset_fil": 8, "get_merged_set": 8, "check_set": 8, "scalingfittingerror": 8, "descriptor_str": 8, "insuffici": 8, "unfittedsklearnscla": 8, "novalidsmil": 8, "mol_from_smi": 8, "numpy_from_rdkit": 8, "dtype": [8, 12], "moldescriptor": 8, "nameparameterdataclass": [8, 9, 12], "abc": [8, 9, 12], "abstract": [8, 9, 12], "parallel_compute_descriptor": 8, "n_core": 8, "parallel": 8, "rdkitdescriptor": 8, "liter": [8, 9, 12, 13], "pathlib": 8, "get_fitted_scaler_for_fp": 8, "saved_param": 8, "get_fitted_scal": 8, "set_unfitted_scaler_data": 8, "fp_info": 8, "canonicalsmil": 8, "scaffold": [8, 12, 13], "genericscaffold": 8, "validdescriptor": 8, "descriptor_from_config": 8, "return_failed_idx": 8, "configur": [8, 9, 10, 11], "score_al": 8, "get_scor": 8, "score_all_smil": 8, "get_train_test_scor": 8, "get_merged_train_scor": 8, "get_ecfp_fpinfo": 8, "get_ecfpcount_fpinfo": 8, "explain_ecfp": 8, "len_feat": 8, "get_fp_info": 8, "exp_df": 8, "descript": [8, 9], "fp_idx": 8, "strt_idx": 8, "runshap": 8, "x_pred": 8, "shap": 8, "shapexplain": 8, "popul": 8, "explainpr": 8, "shallow": 8, "validate_cls_input": 8, "pi_zero": 8, "pr": 8, "melloddi": 8, "sparsechem": 8, "imbal": 8, "bedroc_scor": [8, 9], "truchon": 8, "j": 8, "bayli": 8, "screen": 8, "bad": 8, "recognit": 8, "2007": 8, "concord": 8, "statist": 8, "qualiti": 8, "harald": 8, "On": 8, "surviv": 8, "bound": 8, "2008": 8, "1209": 8, "1216": 8, "posterior": 8, "mark": 8, "abstractmethod": [8, 9], "predict_uncert": 8, "quantifi": 8, "qsartunamodel": 8, "nonetyp": [8, 9], "sent": 8, "get_metadata": 8, "train_scor": [8, 11], "test_scor": [8, 10, 11], "get_transform": 8, "perform_ptr": 8, "wrap_model": 8, "save_model": 8, "novaliddescriptor": 8, "null_scor": 8, "predict_pl": 8, "model_path": 8, "inference_path": 8, "argserror": 8, "issu": [8, 12], "uncertaintyerror": 8, "correctli": 8, "auxcovariatemiss": 8, "precomputederror": 8, "validate_arg": 8, "validate_uncertainti": 8, "check_precomp_arg": 8, "validate_set_precomput": 8, "validate_aux": 8, "doctitl": 8, "docstr": 8, "type_base_schema": 8, "tp": 8, "wyfo": 8, "json_schema": 8, "patch_schema_gener": 8, "patch_schema_optunaz": 8, "split_optim": 8, "base_chemprop_param": 8, "alg": [8, 9], "pop": 8, "fix": [8, 9], "run_studi": 8, "storag": [8, 11], "trial_number_offset": [8, 10], "log_scor": 8, "main_scor": 8, "outfnam": 8, "plot_by_configur": 8, "conf": 8, "plot_slic": [8, 9, 11], "folder_path": 8, "file_format": [8, 9, 11], "png": [8, 9], "plot_contour": [8, 9, 11], "static": 8, "plot_histori": [8, 9, 11], "set_build_cach": 9, "preexist": 9, "remove_algo_hash": 9, "buildconfig_from_tri": 9, "encode_nam": 9, "cenam": 9, "suggest_alg_param": 9, "suggest_aux_param": 9, "desc": 9, "check_invalid_descriptor_param": 9, "adaboostclassifierparamet": 9, "lassoparamet": 9, "kneighborsclassifierparamet": 9, "kneighborsregressorparamet": 9, "logisticregressionparamet": 9, "plsparamet": 9, "randomforestparamet": 9, "ridgeparamet": 9, "svcparamet": 9, "svrparamet": 9, "xgbregressorparamet": 9, "prfclassifierparamet": 9, "bootstrap": 9, "new_syn_data_frac": 9, "chempropregressorparamet": 9, "chempropclassifierparamet": 9, "chempropregressorpretrainedparamet": 9, "chemprophyperoptclassifierparamet": 9, "chemprophyperoptregressorparamet": 9, "calibratedclassifiercvparamet": 9, "mapieparamet": 9, "regressionscor": 9, "classificationscor": 9, "closer": 9, "greater": 9, "manhattan": 9, "trainarg": 9, "tanh": 9, "leakyrelu": 9, "prelu": 9, "selu": 9, "elu": 9, "turn": [9, 12, 13], "morgan_count": 9, "rdkit_2d": 9, "rdkit_2d_norm": 9, "mpnn_first_ffn": 9, "mpnn_last_ffn": 9, "linked_hidden_s": 9, "constrain": 9, "l3": 9, "init_lr_exp": 9, "final_lr_exp": 9, "warmup_epoch": 9, "l4": 9, "l5": 9, "l6": 9, "l7": 9, "l8": 9, "isanyof": 9, "obj": [9, 10], "detect_mode_from_alg": 9, "copy_path_for_scaled_descriptor": 9, "cv_split_strategi": 9, "use_cach": 9, "optuna_storag": 9, "set_cach": 9, "set_algo_hash": 9, "declar": 9, "pydant": 9, "don": 9, "classmethod": 9, "1024": 9, "shorter": 9, "output_fold": [9, 11], "use_xvfb": [9, 11], "imagefileformat": 9, "jpeg": 9, "jpg": 9, "svg": 9, "move_up_directori": 10, "attach_root_path": 10, "attach": 10, "loadjson": 10, "add_ellipsi": 10, "max_length": 10, "shorten_nam": 10, "mlflowcallback": 10, "tracking_uri": 10, "callback": 10, "uri": 10, "server": 10, "set_tracking_uri": 10, "prepare_tag": 10, "tag": 10, "tmp_buildconfig": 10, "create_depend": 10, "remove_schema_properti": 10, "add_boolean_guards_for_schema_properti": 10, "replacekei": 10, "input_": 10, "replacevalu": 10, "addsibl": 10, "delsibl": 10, "sibl": 10, "getref": 10, "context": 10, "recurs": 10, "nest": 10, "copytitl": 10, "oneof": 10, "replaceenum": 10, "singleton": 10, "const": 10, "addtitl": 10, "get_authorization_head": 10, "trackingdata": 10, "trial_numb": [10, 11], "trial_valu": 10, "trial_stat": 10, "all_cv_test_scor": 10, "dataclass": 10, "removeprefix": 10, "prefix": 10, "round_scor": 10, "internaltrackingcallback": 10, "progress": 10, "buildtrackingdata": 10, "response_column_nam": 10, "test_point": 10, "track_build": 10, "mkdict": 10, "load_df_from_fil": 10, "remove_failed_idx": 10, "failed_idx": 10, "md5_hash": 10, "md5": 10, "buildingconfigurationenum": 11, "configurationenum": 11, "general_hyperparamet": 11, "hyper_paramet": 11, "general_regressor": 11, "general_classifi": 11, "metadata_besttri": 11, "metadata_bestvalu": 11, "general_dis": 11, "general_paramet": 11, "task_optim": 11, "task_build": 11, "data_inputcolumn": 11, "data_responsecolumn": 11, "data_train": 11, "data_test": 11, "descriptors_avalon": 11, "descriptors_avalon_nbit": 11, "descriptors_ecfp": 11, "descriptors_ecfp_radiu": 11, "descriptors_ecfp_nbit": 11, "descriptors_ecfpcount": 11, "descriptors_ecfpcounts_radiu": 11, "descriptors_ecfpcounts_usefeatur": 11, "descriptors_pathfp": 11, "descriptors_pathfp_maxpath": 11, "descriptors_pathfp_fps": 11, "descriptors_maccskei": 11, "descriptors_unsc_physchem": 11, "descriptors_physchem": 11, "descriptors_physchem_rdkitnam": 11, "descriptors_unsc_jazzi": 11, "descriptors_jazzi": 11, "descriptors_jazzy_jazzynam": 11, "descriptors_precomput": 11, "descriptors_precomputed_fil": 11, "descriptors_precomputed_input_columnn": 11, "descriptors_precomputed_response_column": 11, "descriptors_unsc_zscal": 11, "descriptors_zscal": 11, "descriptors_smil": 11, "descriptors_smiles_and_si": 11, "descriptors_smiles_and_si_fil": 11, "descriptors_smiles_and_si_input_column": 11, "descriptors_smiles_and_si_aux_weight_pc": 11, "descriptors_sc": 11, "descriptors_scaled_descriptor": 11, "descriptors_scaled_descriptor_paramet": 11, "descriptors_composit": 11, "settings_mod": 11, "settings_mode_regress": 11, "settings_mode_classif": 11, "settings_cross_valid": 11, "settings_direct": 11, "settings_n_tri": 11, "settings_n_job": 11, "settings_shuffl": 11, "algorithms_low": 11, "algorithms_high": 11, "algorithms_q": 11, "algorithms_interface_sklearn": 11, "algorithms_interface_xgboost": 11, "algorithms_rfregressor": 11, "algorithms_rfclassifi": 11, "algorithms_rf_max_featur": 11, "algorithms_rf_max_depth": 11, "algorithms_rf_n_estim": 11, "algorithms_svr": 11, "algorithms_svr_c": 11, "algorithms_svr_gamma": 11, "algorithms_svc": 11, "algorithms_svc_c": 11, "algorithms_svc_gamma": 11, "algorithms_lasso": 11, "algorithms_lasso_alpha": 11, "algorithms_kneighborsclassifi": 11, "algorithms_kneighborsregressor": 11, "algorithms_kneighbors_n_neighbor": 11, "algorithms_kneighbors_metr": 11, "algorithms_kneighbors_weight": 11, "algorithms_ridg": 11, "algorithms_ridge_alpha": 11, "algorithms_plsregress": 11, "algorithms_plsregression_n_compon": 11, "algorithms_logisticregress": 11, "algorithms_logisticregression_solv": 11, "algorithms_logisticregression_c": 11, "algorithms_adaboostclassifi": 11, "algorithms_adaboostclassifier_n_estim": 11, "algorithms_adaboostclassifier_learning_r": 11, "algorithms_xgbregressor": 11, "algorithms_xgbregressor_max_depth": 11, "algorithms_xgbregressor_n_estim": 11, "algorithms_xgbregressor_learning_r": 11, "algorithms_prf": 11, "algorithms_prf_max_featur": 11, "algorithms_prf_max_depth": 11, "algorithms_prf_n_estim": 11, "algorithms_prf_minpysumleaf": 11, "algorithms_prf_use_py_gini": 11, "algorithms_prf_use_py_leaf": 11, "algorithms_chemprop": 11, "basechemprop": 11, "algorithms_chemprop_regressor": 11, "algorithms_chemprop_hyperopt_regressor": 11, "algorithms_chemprop_classifi": 11, "algorithms_chemprop_hyperopt_classifi": 11, "algorithms_chemprop_activ": 11, "algorithms_chemprop_aggreg": 11, "algorithms_chemprop_aggregation_norm": 11, "algorithms_chemprop_batch_s": 11, "algorithms_chemprop_depth": 11, "algorithms_chemprop_dropout": 11, "algorithms_chemprop_epoch": 11, "algorithms_chemprop_ensemble_s": 11, "algorithms_chemprop_features_gener": 11, "algorithms_chemprop_ffn_hidden_s": 11, "algorithms_chemprop_ffn_num_lay": 11, "algorithms_chemprop_frzn": 11, "algorithms_chemprop_final_lr_ratio_exp": 11, "algorithms_chemprop_hidden_s": 11, "algorithms_chemprop_num_it": 11, "algorithms_chemprop_init_lr_ratio_exp": 11, "algorithms_chemprop_max_lr_exp": 11, "algorithms_chemprop_pretrained_model": 11, "algorithms_chemprop_search_parameter_level": 11, "algorithms_chemprop_startup_random_it": 11, "startup_random_it": 11, "algorithms_chemprop_warmup_epochs_ratio": 11, "algorithms_calibratedclassifiercv": 11, "algorithms_calibratedclassifiercv_ensembl": 11, "algorithms_calibratedclassifiercv_estim": 11, "algorithms_calibratedclassifiercv_method": 11, "algorithms_calibratedclassifiercv_n_fold": 11, "algorithms_calibratedclassifiercv_param": 11, "calibrated_param": 11, "algorithms_mapi": 11, "algorithms_mapie_alpha": 11, "interfaceenum": 11, "sklearn_set": 11, "xgboost_set": 11, "chemprop_set": 11, "prf_set": 11, "calibrated_set": 11, "modelrunnerdataframeenum": 11, "modelrunn": 11, "objectiveenum": 11, "attribute_trial_train_scor": 11, "extra_column_besthit": 11, "besthit": 11, "optimizationconfigurationenum": 11, "predictionconfigurationenum": 11, "data_dataset": 11, "sklearnreturnvalueenum": 11, "cross_validate_fit_tim": 11, "fit_tim": 11, "cross_validate_score_tim": 11, "score_tim": 11, "cross_validate_test_scor": 11, "cross_validate_train_scor": 11, "xgboostreturnvalueenum": 11, "visualizationenum": 11, "visualization_regressor": 11, "visualization_classifi": 11, "visualization_use_xvfb": 11, "visualization_output_fold": 11, "visualization_file_format": 11, "visualization_plot": 11, "visualization_plots_histori": 11, "visualization_plots_contour": 11, "visualization_plots_parallel_coordin": 11, "visualization_plots_slic": 11, "optuna_system_attrs_numb": 11, "_number": 11, "optuna_system_attrs_intermediate_valu": 11, "intermediate_valu": 11, "optuna_system_attrs_trial_id": 11, "trial_id": 11, "studyuserattr": 11, "trialuserattr": 11, "trialparam": 11, "algorithm_hash": 11, "mlflowlogparam": 11, "sklearnsplitt": 12, "get_n_split": 12, "cvsplitter": 12, "although": 12, "underli": 12, "get_sklearn_splitt": 12, "n_split": 12, "repeat": [12, 13], "edg": [12, 13], "stratifiedshufflesplit": [12, 13], "revert": [12, 13], "empti": 12, "kfold": 12, "affect": 12, "consecut": 12, "fd_bin": 12, "11879": 12, "10297": 12, "adjac": 12, "downstream": 12, "nativ": 12, "histogramstratifiedshufflesplit": 12, "test_fract": 12, "groupingsplitt": 12, "column_nam": [12, 13], "butina_clust": [12, 13], "cluster": [12, 13], "butina": [12, 13], "make_scaffold_gener": [12, 13], "murcko": [12, 13], "hetero": [12, 13], "difficulti": [12, 13], "novel": [12, 13], "datatransform": 12, "logarithm": [12, 14], "base_dict": 12, "ufunc": 12, "base_neg": 12, "reverse_dict": 12, "exp": 12, "transform_df": 12, "transform_on": 12, "reverse_transform_df": 12, "reverse_transform_on": 12, "auxtransform": 12, "transfor": 12, "auxiliary_data": 12, "usabl": [12, 14]}, "objects": {"": [[8, 0, 0, "-", "optunaz"]], "optunaz": [[8, 0, 0, "-", "builder"], [9, 0, 0, "-", "config"], [8, 0, 0, "-", "datareader"], [8, 0, 0, "-", "descriptors"], [8, 0, 0, "-", "evaluate"], [8, 0, 0, "-", "explainability"], [8, 0, 0, "-", "metircs"], [8, 0, 0, "-", "model_writer"], [8, 0, 0, "-", "objective"], [8, 0, 0, "-", "optbuild"], [8, 0, 0, "-", "predict"], [8, 0, 0, "-", "schemagen"], [8, 0, 0, "-", "three_step_opt_build_merge"], [10, 0, 0, "-", "utils"], [8, 0, 0, "-", "visualizer"]], "optunaz.builder": [[8, 1, 1, "", "build"]], "optunaz.config": [[9, 2, 1, "", "Algorithm"], [9, 2, 1, "", "ModelMode"], [9, 2, 1, "", "NameParameterDataclass"], [9, 2, 1, "", "OptimizationDirection"], [9, 2, 1, "", "Task"], [9, 2, 1, "", "Visualization"], [9, 0, 0, "-", "build_from_opt"], [9, 0, 0, "-", "buildconfig"], [9, 0, 0, "-", "optconfig"]], "optunaz.config.ModelMode": [[9, 3, 1, "", "CLASSIFICATION"], [9, 3, 1, "", "REGRESSION"]], "optunaz.config.NameParameterDataclass": [[9, 4, 1, "", "new"]], "optunaz.config.OptimizationDirection": [[9, 3, 1, "", "MAXIMIZATION"], [9, 3, 1, "", "MINIMIZATION"]], "optunaz.config.Task": [[9, 3, 1, "", "BUILDING"], [9, 3, 1, "", "OPTIMIZATION"], [9, 3, 1, "", "PREDICTION"]], "optunaz.config.Visualization": [[9, 2, 1, "", "ImageFileFormat"], [9, 2, 1, "", "Plots"], [9, 3, 1, "", "file_format"], [9, 3, 1, "", "output_folder"], [9, 3, 1, "", "plots"], [9, 3, 1, "", "use_xvfb"]], "optunaz.config.Visualization.ImageFileFormat": [[9, 3, 1, "", "JPEG"], [9, 3, 1, "", "JPG"], [9, 3, 1, "", "PDF"], [9, 3, 1, "", "PNG"], [9, 3, 1, "", "SVG"]], "optunaz.config.Visualization.Plots": [[9, 3, 1, "", "plot_contour"], [9, 3, 1, "", "plot_history"], [9, 3, 1, "", "plot_parallel_coordinate"], [9, 3, 1, "", "plot_slice"]], "optunaz.config.build_from_opt": [[9, 1, 1, "", "buildconfig_from_trial"], [9, 1, 1, "", "check_invalid_descriptor_param"], [9, 1, 1, "", "encode_name"], [9, 1, 1, "", "remove_algo_hash"], [9, 1, 1, "", "set_build_cache"], [9, 1, 1, "", "suggest_alg_params"], [9, 1, 1, "", "suggest_aux_params"]], "optunaz.config.buildconfig": [[9, 2, 1, "", "AdaBoostClassifier"], [9, 2, 1, "", "Algorithm"], [9, 2, 1, "", "BuildConfig"], [9, 2, 1, "", "CalibratedClassifierCVWithVA"], [9, 2, 1, "", "ChemPropClassifier"], [9, 2, 1, "", "ChemPropHyperoptClassifier"], [9, 2, 1, "", "ChemPropHyperoptRegressor"], [9, 2, 1, "", "ChemPropRegressor"], [9, 2, 1, "", "ChemPropRegressorPretrained"], [9, 2, 1, "", "KNeighborsClassifier"], [9, 2, 1, "", "KNeighborsRegressor"], [9, 2, 1, "", "Lasso"], [9, 2, 1, "", "LogisticRegression"], [9, 2, 1, "", "Mapie"], [9, 2, 1, "", "PLSRegression"], [9, 2, 1, "", "PRFClassifier"], [9, 2, 1, "", "RandomForestClassifier"], [9, 2, 1, "", "RandomForestRegressor"], [9, 2, 1, "", "Ridge"], [9, 2, 1, "", "SVC"], [9, 2, 1, "", "SVR"], [9, 2, 1, "", "XGBRegressor"]], "optunaz.config.buildconfig.AdaBoostClassifier": [[9, 2, 1, "", "AdaBoostClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.AdaBoostClassifier.AdaBoostClassifierParameters": [[9, 3, 1, "", "learning_rate"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.buildconfig.Algorithm": [[9, 4, 1, "", "estimator"]], "optunaz.config.buildconfig.BuildConfig": [[9, 2, 1, "", "Metadata"], [9, 2, 1, "", "Settings"], [9, 3, 1, "", "algorithm"], [9, 3, 1, "", "data"], [9, 3, 1, "", "descriptor"], [9, 3, 1, "", "metadata"], [9, 3, 1, "", "settings"], [9, 3, 1, "", "task"]], "optunaz.config.buildconfig.BuildConfig.Metadata": [[9, 3, 1, "", "best_trial"], [9, 3, 1, "", "best_value"], [9, 3, 1, "", "cross_validation"], [9, 3, 1, "", "n_trials"], [9, 3, 1, "", "name"], [9, 3, 1, "", "shuffle"], [9, 3, 1, "", "visualization"]], "optunaz.config.buildconfig.BuildConfig.Settings": [[9, 3, 1, "", "direction"], [9, 3, 1, "", "mode"], [9, 3, 1, "", "n_trials"], [9, 3, 1, "", "scoring"], [9, 3, 1, "", "tracking_rest_endpoint"]], "optunaz.config.buildconfig.CalibratedClassifierCVWithVA": [[9, 2, 1, "", "CalibratedClassifierCVParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.CalibratedClassifierCVWithVA.CalibratedClassifierCVParameters": [[9, 3, 1, "", "ensemble"], [9, 3, 1, "", "estimator"], [9, 3, 1, "", "method"], [9, 3, 1, "", "n_folds"]], "optunaz.config.buildconfig.ChemPropClassifier": [[9, 2, 1, "", "ChemPropClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters": [[9, 3, 1, "", "activation"], [9, 3, 1, "", "aggregation"], [9, 3, 1, "", "aggregation_norm"], [9, 3, 1, "", "aux_weight_pc"], [9, 3, 1, "", "batch_size"], [9, 3, 1, "", "depth"], [9, 3, 1, "", "dropout"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "ffn_hidden_size"], [9, 3, 1, "", "ffn_num_layers"], [9, 3, 1, "", "final_lr_ratio_exp"], [9, 3, 1, "", "hidden_size"], [9, 3, 1, "", "init_lr_ratio_exp"], [9, 3, 1, "", "max_lr_exp"], [9, 3, 1, "", "warmup_epochs_ratio"]], "optunaz.config.buildconfig.ChemPropHyperoptClassifier": [[9, 2, 1, "", "ChemPropHyperoptClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropHyperoptClassifier.ChemPropHyperoptClassifierParameters": [[9, 3, 1, "", "aux_weight_pc"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "num_iters"], [9, 3, 1, "", "search_parameter_level"]], "optunaz.config.buildconfig.ChemPropHyperoptRegressor": [[9, 2, 1, "", "ChemPropHyperoptRegressorParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropHyperoptRegressor.ChemPropHyperoptRegressorParameters": [[9, 3, 1, "", "aux_weight_pc"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "num_iters"], [9, 3, 1, "", "search_parameter_level"]], "optunaz.config.buildconfig.ChemPropRegressor": [[9, 2, 1, "", "ChemPropRegressorParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters": [[9, 3, 1, "", "activation"], [9, 3, 1, "", "aggregation"], [9, 3, 1, "", "aggregation_norm"], [9, 3, 1, "", "aux_weight_pc"], [9, 3, 1, "", "batch_size"], [9, 3, 1, "", "depth"], [9, 3, 1, "", "dropout"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "ffn_hidden_size"], [9, 3, 1, "", "ffn_num_layers"], [9, 3, 1, "", "final_lr_ratio_exp"], [9, 3, 1, "", "hidden_size"], [9, 3, 1, "", "init_lr_ratio_exp"], [9, 3, 1, "", "max_lr_exp"], [9, 3, 1, "", "warmup_epochs_ratio"]], "optunaz.config.buildconfig.ChemPropRegressorPretrained": [[9, 2, 1, "", "ChemPropRegressorPretrainedParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropRegressorPretrained.ChemPropRegressorPretrainedParameters": [[9, 3, 1, "", "epochs"], [9, 3, 1, "", "frzn"], [9, 3, 1, "", "pretrained_model"]], "optunaz.config.buildconfig.KNeighborsClassifier": [[9, 2, 1, "", "KNeighborsClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.KNeighborsClassifier.KNeighborsClassifierParameters": [[9, 3, 1, "", "metric"], [9, 3, 1, "", "n_neighbors"], [9, 3, 1, "", "weights"]], "optunaz.config.buildconfig.KNeighborsRegressor": [[9, 2, 1, "", "KNeighborsRegressorParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.KNeighborsRegressor.KNeighborsRegressorParameters": [[9, 3, 1, "", "metric"], [9, 3, 1, "", "n_neighbors"], [9, 3, 1, "", "weights"]], "optunaz.config.buildconfig.Lasso": [[9, 2, 1, "", "LassoParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.Lasso.LassoParameters": [[9, 3, 1, "", "alpha"]], "optunaz.config.buildconfig.LogisticRegression": [[9, 2, 1, "", "LogisticRegressionParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.LogisticRegression.LogisticRegressionParameters": [[9, 3, 1, "", "C"], [9, 3, 1, "", "solver"]], "optunaz.config.buildconfig.Mapie": [[9, 2, 1, "", "MapieParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.Mapie.MapieParameters": [[9, 3, 1, "", "estimator"], [9, 3, 1, "", "mapie_alpha"]], "optunaz.config.buildconfig.PLSRegression": [[9, 2, 1, "", "PLSParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.PLSRegression.PLSParameters": [[9, 3, 1, "", "n_components"]], "optunaz.config.buildconfig.PRFClassifier": [[9, 2, 1, "", "PRFClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters": [[9, 3, 1, "", "bootstrap"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "min_py_sum_leaf"], [9, 3, 1, "", "n_estimators"], [9, 3, 1, "", "new_syn_data_frac"], [9, 3, 1, "", "use_py_gini"], [9, 3, 1, "", "use_py_leafs"]], "optunaz.config.buildconfig.RandomForestClassifier": [[9, 2, 1, "", "RandomForestParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.RandomForestClassifier.RandomForestParameters": [[9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.buildconfig.RandomForestRegressor": [[9, 2, 1, "", "RandomForestParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.RandomForestRegressor.RandomForestParameters": [[9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.buildconfig.Ridge": [[9, 2, 1, "", "RidgeParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.Ridge.RidgeParameters": [[9, 3, 1, "", "alpha"]], "optunaz.config.buildconfig.SVC": [[9, 2, 1, "", "SVCParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.SVC.SVCParameters": [[9, 3, 1, "", "C"], [9, 3, 1, "", "gamma"]], "optunaz.config.buildconfig.SVR": [[9, 2, 1, "", "SVRParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.SVR.SVRParameters": [[9, 3, 1, "", "C"], [9, 3, 1, "", "gamma"]], "optunaz.config.buildconfig.XGBRegressor": [[9, 2, 1, "", "XGBRegressorParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.XGBRegressor.XGBRegressorParameters": [[9, 3, 1, "", "learning_rate"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig": [[9, 2, 1, "", "AdaBoostClassifier"], [9, 2, 1, "", "Algorithm"], [9, 2, 1, "", "CalibratedClassifierCVEnsemble"], [9, 2, 1, "", "CalibratedClassifierCVMethod"], [9, 2, 1, "", "CalibratedClassifierCVWithVA"], [9, 2, 1, "", "ChemPropActivation"], [9, 2, 1, "", "ChemPropAggregation"], [9, 2, 1, "", "ChemPropClassifier"], [9, 2, 1, "", "ChemPropFeatures_Generator"], [9, 2, 1, "", "ChemPropFrzn"], [9, 2, 1, "", "ChemPropHyperoptClassifier"], [9, 2, 1, "", "ChemPropHyperoptRegressor"], [9, 2, 1, "", "ChemPropRegressor"], [9, 2, 1, "", "ChemPropRegressorPretrained"], [9, 2, 1, "", "ChemPropSearch_Parameter_Level"], [9, 2, 1, "", "ClassificationScore"], [9, 2, 1, "", "KNeighborsClassifier"], [9, 2, 1, "", "KNeighborsMetric"], [9, 2, 1, "", "KNeighborsRegressor"], [9, 2, 1, "", "KNeighborsWeights"], [9, 2, 1, "", "Lasso"], [9, 2, 1, "", "LogisticRegression"], [9, 2, 1, "", "Mapie"], [9, 2, 1, "", "OptimizationConfig"], [9, 2, 1, "", "PLSRegression"], [9, 2, 1, "", "PRFClassifier"], [9, 2, 1, "", "PRFClassifierMaxFeatures"], [9, 2, 1, "", "RandomForestClassifier"], [9, 2, 1, "", "RandomForestMaxFeatures"], [9, 2, 1, "", "RandomForestRegressor"], [9, 2, 1, "", "RegressionScore"], [9, 2, 1, "", "Ridge"], [9, 2, 1, "", "SVC"], [9, 2, 1, "", "SVR"], [9, 2, 1, "", "XGBRegressor"], [9, 1, 1, "", "copy_path_for_scaled_descriptor"], [9, 1, 1, "", "detect_mode_from_algs"], [9, 1, 1, "", "isanyof"]], "optunaz.config.optconfig.AdaBoostClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.AdaBoostClassifier.Parameters": [[9, 2, 1, "", "AdaBoostClassifierParametersLearningRate"], [9, 2, 1, "", "AdaBoostClassifierParametersNEstimators"], [9, 3, 1, "", "learning_rate"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig.AdaBoostClassifier.Parameters.AdaBoostClassifierParametersLearningRate": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.AdaBoostClassifier.Parameters.AdaBoostClassifierParametersNEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.CalibratedClassifierCVEnsemble": [[9, 3, 1, "", "FALSE"], [9, 3, 1, "", "TRUE"]], "optunaz.config.optconfig.CalibratedClassifierCVMethod": [[9, 3, 1, "", "ISOTONIC"], [9, 3, 1, "", "SIGMOID"], [9, 3, 1, "", "VENNABERS"]], "optunaz.config.optconfig.CalibratedClassifierCVWithVA": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.CalibratedClassifierCVWithVA.Parameters": [[9, 3, 1, "", "ensemble"], [9, 3, 1, "", "estimator"], [9, 3, 1, "", "method"], [9, 3, 1, "", "n_folds"]], "optunaz.config.optconfig.ChemPropActivation": [[9, 3, 1, "", "ELU"], [9, 3, 1, "", "LEAKYRELU"], [9, 3, 1, "", "PRELU"], [9, 3, 1, "", "RELU"], [9, 3, 1, "", "SELU"], [9, 3, 1, "", "TANH"]], "optunaz.config.optconfig.ChemPropAggregation": [[9, 3, 1, "", "MEAN"], [9, 3, 1, "", "NORM"], [9, 3, 1, "", "SUM"]], "optunaz.config.optconfig.ChemPropClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters": [[9, 2, 1, "", "ChemPropParametersAggregation_Norm"], [9, 2, 1, "", "ChemPropParametersBatch_Size"], [9, 2, 1, "", "ChemPropParametersDepth"], [9, 2, 1, "", "ChemPropParametersDropout"], [9, 2, 1, "", "ChemPropParametersFFN_Hidden_Size"], [9, 2, 1, "", "ChemPropParametersFFN_Num_Layers"], [9, 2, 1, "", "ChemPropParametersFinal_Lr_Ratio_Exp"], [9, 2, 1, "", "ChemPropParametersHidden_Size"], [9, 2, 1, "", "ChemPropParametersInit_Lr_Ratio_Exp"], [9, 2, 1, "", "ChemPropParametersMax_Lr_Exp"], [9, 2, 1, "", "ChemPropParametersWarmup_Epochs_Ratio"], [9, 3, 1, "", "activation"], [9, 3, 1, "", "aggregation"], [9, 3, 1, "", "aggregation_norm"], [9, 3, 1, "", "batch_size"], [9, 3, 1, "", "depth"], [9, 3, 1, "", "dropout"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "ffn_hidden_size"], [9, 3, 1, "", "ffn_num_layers"], [9, 3, 1, "", "final_lr_ratio_exp"], [9, 3, 1, "", "hidden_size"], [9, 3, 1, "", "init_lr_ratio_exp"], [9, 3, 1, "", "max_lr_exp"], [9, 3, 1, "", "warmup_epochs_ratio"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersAggregation_Norm": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersBatch_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDropout": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Hidden_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Num_Layers": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersHidden_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersInit_Lr_Ratio_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersMax_Lr_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersWarmup_Epochs_Ratio": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropFeatures_Generator": [[9, 3, 1, "", "MORGAN"], [9, 3, 1, "", "MORGAN_COUNT"], [9, 3, 1, "", "NONE"], [9, 3, 1, "", "RDKIT_2D"], [9, 3, 1, "", "RDKIT_2D_NORMALIZED"]], "optunaz.config.optconfig.ChemPropFrzn": [[9, 3, 1, "", "MPNN"], [9, 3, 1, "", "MPNN_FIRST_FFN"], [9, 3, 1, "", "MPNN_LAST_FFN"], [9, 3, 1, "", "NONE"]], "optunaz.config.optconfig.ChemPropHyperoptClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropHyperoptClassifier.Parameters": [[9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "num_iters"], [9, 3, 1, "", "search_parameter_level"]], "optunaz.config.optconfig.ChemPropHyperoptRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropHyperoptRegressor.Parameters": [[9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "num_iters"], [9, 3, 1, "", "search_parameter_level"]], "optunaz.config.optconfig.ChemPropRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters": [[9, 2, 1, "", "ChemPropParametersAggregation_Norm"], [9, 2, 1, "", "ChemPropParametersBatch_Size"], [9, 2, 1, "", "ChemPropParametersDepth"], [9, 2, 1, "", "ChemPropParametersDropout"], [9, 2, 1, "", "ChemPropParametersFFN_Hidden_Size"], [9, 2, 1, "", "ChemPropParametersFFN_Num_Layers"], [9, 2, 1, "", "ChemPropParametersFinal_Lr_Ratio_Exp"], [9, 2, 1, "", "ChemPropParametersHidden_Size"], [9, 2, 1, "", "ChemPropParametersInit_Lr_Ratio_Exp"], [9, 2, 1, "", "ChemPropParametersMax_Lr_Exp"], [9, 2, 1, "", "ChemPropParametersWarmup_Epochs_Ratio"], [9, 3, 1, "", "activation"], [9, 3, 1, "", "aggregation"], [9, 3, 1, "", "aggregation_norm"], [9, 3, 1, "", "batch_size"], [9, 3, 1, "", "depth"], [9, 3, 1, "", "dropout"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "ffn_hidden_size"], [9, 3, 1, "", "ffn_num_layers"], [9, 3, 1, "", "final_lr_ratio_exp"], [9, 3, 1, "", "hidden_size"], [9, 3, 1, "", "init_lr_ratio_exp"], [9, 3, 1, "", "max_lr_exp"], [9, 3, 1, "", "warmup_epochs_ratio"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersAggregation_Norm": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersBatch_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDropout": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Hidden_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Num_Layers": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersHidden_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersInit_Lr_Ratio_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersMax_Lr_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersWarmup_Epochs_Ratio": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressorPretrained": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters": [[9, 2, 1, "", "ChemPropParametersEpochs"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "frzn"], [9, 3, 1, "", "pretrained_model"]], "optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters.ChemPropParametersEpochs": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropSearch_Parameter_Level": [[9, 3, 1, "", "AUTO"], [9, 3, 1, "", "L1"], [9, 3, 1, "", "L2"], [9, 3, 1, "", "L3"], [9, 3, 1, "", "L4"], [9, 3, 1, "", "L5"], [9, 3, 1, "", "L6"], [9, 3, 1, "", "L7"], [9, 3, 1, "", "L8"]], "optunaz.config.optconfig.ClassificationScore": [[9, 3, 1, "", "ACCURACY"], [9, 3, 1, "", "AUC_PR_CAL"], [9, 3, 1, "", "AVERAGE_PRECISION"], [9, 3, 1, "", "BALANCED_ACCURACY"], [9, 3, 1, "", "BEDROC"], [9, 3, 1, "", "CONCORDANCE_INDEX"], [9, 3, 1, "", "F1"], [9, 3, 1, "", "F1_MACRO"], [9, 3, 1, "", "F1_MICRO"], [9, 3, 1, "", "F1_WEIGHTED"], [9, 3, 1, "", "JACCARD"], [9, 3, 1, "", "JACCARD_MACRO"], [9, 3, 1, "", "JACCARD_MICRO"], [9, 3, 1, "", "JACCARD_WEIGHTED"], [9, 3, 1, "", "NEG_BRIER_SCORE"], [9, 3, 1, "", "PRECISION"], [9, 3, 1, "", "PRECISION_MACRO"], [9, 3, 1, "", "PRECISION_MICRO"], [9, 3, 1, "", "PRECISION_WEIGHTED"], [9, 3, 1, "", "RECALL"], [9, 3, 1, "", "RECALL_MACRO"], [9, 3, 1, "", "RECALL_MICRO"], [9, 3, 1, "", "RECALL_WEIGHTED"], [9, 3, 1, "", "ROC_AUC"]], "optunaz.config.optconfig.KNeighborsClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.KNeighborsClassifier.Parameters": [[9, 2, 1, "", "KNeighborsClassifierParametersN_Neighbors"], [9, 3, 1, "", "metric"], [9, 3, 1, "", "n_neighbors"], [9, 3, 1, "", "weights"]], "optunaz.config.optconfig.KNeighborsClassifier.Parameters.KNeighborsClassifierParametersN_Neighbors": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.KNeighborsMetric": [[9, 3, 1, "", "EUCLIDEAN"], [9, 3, 1, "", "MANHATTAN"], [9, 3, 1, "", "MINKOWSKI"]], "optunaz.config.optconfig.KNeighborsRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.KNeighborsRegressor.Parameters": [[9, 2, 1, "", "KNeighborsRegressorParametersN_Neighbors"], [9, 3, 1, "", "metric"], [9, 3, 1, "", "n_neighbors"], [9, 3, 1, "", "weights"]], "optunaz.config.optconfig.KNeighborsRegressor.Parameters.KNeighborsRegressorParametersN_Neighbors": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.KNeighborsWeights": [[9, 3, 1, "", "DISTANCE"], [9, 3, 1, "", "UNIFORM"]], "optunaz.config.optconfig.Lasso": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.Lasso.Parameters": [[9, 2, 1, "", "LassoParametersAlpha"], [9, 3, 1, "", "alpha"]], "optunaz.config.optconfig.Lasso.Parameters.LassoParametersAlpha": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.LogisticRegression": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.LogisticRegression.Parameters": [[9, 3, 1, "", "C"], [9, 2, 1, "", "LogisticRegressionParametersParameterC"], [9, 3, 1, "", "solver"]], "optunaz.config.optconfig.LogisticRegression.Parameters.LogisticRegressionParametersParameterC": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.Mapie": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.Mapie.Parameters": [[9, 3, 1, "", "estimator"], [9, 3, 1, "", "mapie_alpha"]], "optunaz.config.optconfig.OptimizationConfig": [[9, 2, 1, "", "Settings"], [9, 3, 1, "", "algorithms"], [9, 3, 1, "", "data"], [9, 3, 1, "", "description"], [9, 3, 1, "", "descriptors"], [9, 3, 1, "", "mode"], [9, 3, 1, "", "name"], [9, 4, 1, "", "set_algo_hashes"], [9, 4, 1, "", "set_cache"], [9, 3, 1, "", "settings"], [9, 3, 1, "", "task"], [9, 3, 1, "", "visualization"]], "optunaz.config.optconfig.OptimizationConfig.Settings": [[9, 3, 1, "", "cross_validation"], [9, 3, 1, "", "cv_split_strategy"], [9, 3, 1, "", "direction"], [9, 3, 1, "", "minimise_std_dev"], [9, 3, 1, "", "mode"], [9, 3, 1, "", "n_chemprop_trials"], [9, 3, 1, "", "n_jobs"], [9, 3, 1, "", "n_startup_trials"], [9, 3, 1, "", "n_trials"], [9, 3, 1, "", "optuna_storage"], [9, 3, 1, "", "random_seed"], [9, 3, 1, "", "scoring"], [9, 3, 1, "", "shuffle"], [9, 3, 1, "", "split_chemprop"], [9, 3, 1, "", "track_to_mlflow"], [9, 3, 1, "", "tracking_rest_endpoint"], [9, 3, 1, "", "use_cache"]], "optunaz.config.optconfig.PLSRegression": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.PLSRegression.Parameters": [[9, 2, 1, "", "NComponents"], [9, 3, 1, "", "n_components"]], "optunaz.config.optconfig.PLSRegression.Parameters.NComponents": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.PRFClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.PRFClassifier.Parameters": [[9, 2, 1, "", "PRFClassifierParametersMaxDepth"], [9, 2, 1, "", "PRFClassifierParametersMinPySumLeaf"], [9, 2, 1, "", "PRFClassifierParametersNEstimators"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "min_py_sum_leaf"], [9, 3, 1, "", "n_estimators"], [9, 3, 1, "", "use_py_gini"], [9, 3, 1, "", "use_py_leafs"]], "optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersMaxDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersMinPySumLeaf": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersNEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.PRFClassifierMaxFeatures": [[9, 3, 1, "", "AUTO"], [9, 3, 1, "", "LOG2"], [9, 3, 1, "", "SQRT"]], "optunaz.config.optconfig.RandomForestClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.RandomForestClassifier.Parameters": [[9, 2, 1, "", "RandomForestClassifierParametersMaxDepth"], [9, 2, 1, "", "RandomForestClassifierParametersNEstimators"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig.RandomForestClassifier.Parameters.RandomForestClassifierParametersMaxDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.RandomForestClassifier.Parameters.RandomForestClassifierParametersNEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.RandomForestMaxFeatures": [[9, 3, 1, "", "AUTO"], [9, 3, 1, "", "LOG2"], [9, 3, 1, "", "SQRT"]], "optunaz.config.optconfig.RandomForestRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.RandomForestRegressor.Parameters": [[9, 2, 1, "", "RandomForestRegressorParametersMaxDepth"], [9, 2, 1, "", "RandomForestRegressorParametersNEstimators"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig.RandomForestRegressor.Parameters.RandomForestRegressorParametersMaxDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.RandomForestRegressor.Parameters.RandomForestRegressorParametersNEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.RegressionScore": [[9, 3, 1, "", "EXPLAINED_VARIANCE"], [9, 3, 1, "", "MAX_ERROR"], [9, 3, 1, "", "NEG_MEAN_ABSOLUTE_ERROR"], [9, 3, 1, "", "NEG_MEAN_SQUARED_ERROR"], [9, 3, 1, "", "NEG_MEDIAN_ABSOLUTE_ERROR"], [9, 3, 1, "", "R2"]], "optunaz.config.optconfig.Ridge": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.Ridge.Parameters": [[9, 2, 1, "", "Alpha"], [9, 3, 1, "", "alpha"]], "optunaz.config.optconfig.Ridge.Parameters.Alpha": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.SVC": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.SVC.Parameters": [[9, 3, 1, "", "C"], [9, 2, 1, "", "Gamma"], [9, 2, 1, "", "SVCParametersParameterC"], [9, 3, 1, "", "gamma"]], "optunaz.config.optconfig.SVC.Parameters.Gamma": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.SVC.Parameters.SVCParametersParameterC": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.SVR": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.SVR.Parameters": [[9, 3, 1, "", "C"], [9, 2, 1, "", "SVRParametersGamma"], [9, 2, 1, "", "SVRParametersParameterC"], [9, 3, 1, "", "gamma"]], "optunaz.config.optconfig.SVR.Parameters.SVRParametersGamma": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.SVR.Parameters.SVRParametersParameterC": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.XGBRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.XGBRegressor.Parameters": [[9, 2, 1, "", "LearningRate"], [9, 2, 1, "", "MaxDepth"], [9, 2, 1, "", "NEstimators"], [9, 3, 1, "", "learning_rate"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig.XGBRegressor.Parameters.LearningRate": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.XGBRegressor.Parameters.MaxDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.XGBRegressor.Parameters.NEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.datareader": [[8, 2, 1, "", "Dataset"], [8, 1, 1, "", "deduplicate"], [8, 1, 1, "", "isvalid"], [8, 1, 1, "", "merge"], [8, 1, 1, "", "read_data"], [8, 1, 1, "", "split"], [8, 1, 1, "", "transform"]], "optunaz.datareader.Dataset": [[8, 3, 1, "", "aux_column"], [8, 3, 1, "", "aux_transform"], [8, 4, 1, "", "check_sets"], [8, 3, 1, "", "deduplication_strategy"], [8, 4, 1, "", "get_merged_sets"], [8, 4, 1, "", "get_sets"], [8, 3, 1, "", "input_column"], [8, 3, 1, "", "intermediate_test_dataset_file"], [8, 3, 1, "", "intermediate_training_dataset_file"], [8, 3, 1, "", "log_transform"], [8, 3, 1, "", "log_transform_base"], [8, 3, 1, "", "log_transform_negative"], [8, 3, 1, "", "log_transform_unit_conversion"], [8, 3, 1, "", "probabilistic_threshold_representation"], [8, 3, 1, "", "probabilistic_threshold_representation_std"], [8, 3, 1, "", "probabilistic_threshold_representation_threshold"], [8, 3, 1, "", "response_column"], [8, 3, 1, "", "response_type"], [8, 3, 1, "", "save_intermediate_files"], [8, 3, 1, "", "split_strategy"], [8, 3, 1, "", "test_dataset_file"], [8, 3, 1, "", "training_dataset_file"]], "optunaz.descriptors": [[8, 2, 1, "", "Avalon"], [8, 2, 1, "", "CanonicalSmiles"], [8, 2, 1, "", "CompositeDescriptor"], [8, 2, 1, "", "ECFP"], [8, 2, 1, "", "ECFP_counts"], [8, 2, 1, "", "FittedSklearnScaler"], [8, 2, 1, "", "GenericScaffold"], [8, 2, 1, "", "JazzyDescriptors"], [8, 2, 1, "", "MACCS_keys"], [8, 2, 1, "", "MolDescriptor"], [8, 5, 1, "", "NoValidSmiles"], [8, 2, 1, "", "PathFP"], [8, 2, 1, "", "PhyschemDescriptors"], [8, 2, 1, "", "PrecomputedDescriptorFromFile"], [8, 2, 1, "", "RdkitDescriptor"], [8, 2, 1, "", "Scaffold"], [8, 2, 1, "", "ScaledDescriptor"], [8, 5, 1, "", "ScalingFittingError"], [8, 2, 1, "", "SmilesAndSideInfoFromFile"], [8, 2, 1, "", "SmilesFromFile"], [8, 2, 1, "", "UnfittedSklearnScaler"], [8, 2, 1, "", "UnscaledJazzyDescriptors"], [8, 2, 1, "", "UnscaledPhyschemDescriptors"], [8, 2, 1, "", "UnscaledZScalesDescriptors"], [8, 2, 1, "", "ValidDescriptor"], [8, 2, 1, "", "ZScalesDescriptors"], [8, 1, 1, "", "descriptor_from_config"], [8, 1, 1, "", "mol_from_smi"], [8, 1, 1, "", "numpy_from_rdkit"]], "optunaz.descriptors.Avalon": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.Avalon.Parameters": [[8, 3, 1, "", "nBits"]], "optunaz.descriptors.CanonicalSmiles": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.CompositeDescriptor": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 4, 1, "", "fp_info"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.CompositeDescriptor.Parameters": [[8, 3, 1, "", "descriptors"]], "optunaz.descriptors.ECFP": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ECFP.Parameters": [[8, 3, 1, "", "nBits"], [8, 3, 1, "", "radius"], [8, 3, 1, "", "returnRdkit"]], "optunaz.descriptors.ECFP_counts": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ECFP_counts.Parameters": [[8, 3, 1, "", "nBits"], [8, 3, 1, "", "radius"], [8, 3, 1, "", "useFeatures"]], "optunaz.descriptors.FittedSklearnScaler": [[8, 4, 1, "", "get_fitted_scaler"], [8, 3, 1, "", "name"], [8, 3, 1, "", "saved_params"]], "optunaz.descriptors.GenericScaffold": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.JazzyDescriptors": [[8, 2, 1, "", "Parameters"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.JazzyDescriptors.Parameters": [[8, 3, 1, "", "descriptor"], [8, 3, 1, "", "jazzy_filters"], [8, 3, 1, "", "jazzy_names"], [8, 3, 1, "", "scaler"]], "optunaz.descriptors.MACCS_keys": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.MolDescriptor": [[8, 4, 1, "", "calculate_from_smi"], [8, 4, 1, "", "parallel_compute_descriptor"]], "optunaz.descriptors.PathFP": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.PathFP.Parameters": [[8, 3, 1, "", "fpSize"], [8, 3, 1, "", "maxPath"]], "optunaz.descriptors.PhyschemDescriptors": [[8, 2, 1, "", "Parameters"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.PhyschemDescriptors.Parameters": [[8, 3, 1, "", "descriptor"], [8, 3, 1, "", "rdkit_names"], [8, 3, 1, "", "scaler"]], "optunaz.descriptors.PrecomputedDescriptorFromFile": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.PrecomputedDescriptorFromFile.Parameters": [[8, 3, 1, "", "file"], [8, 3, 1, "", "input_column"], [8, 3, 1, "", "response_column"]], "optunaz.descriptors.RdkitDescriptor": [[8, 4, 1, "", "calculate_from_mol"], [8, 4, 1, "", "calculate_from_smi"]], "optunaz.descriptors.Scaffold": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ScaledDescriptor": [[8, 2, 1, "", "ScaledDescriptorParameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"], [8, 4, 1, "", "set_unfitted_scaler_data"]], "optunaz.descriptors.ScaledDescriptor.ScaledDescriptorParameters": [[8, 3, 1, "", "descriptor"], [8, 3, 1, "", "scaler"]], "optunaz.descriptors.SmilesAndSideInfoFromFile": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters": [[8, 2, 1, "", "Aux_Weight_Pc"], [8, 3, 1, "", "aux_weight_pc"], [8, 3, 1, "", "file"], [8, 3, 1, "", "input_column"]], "optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters.Aux_Weight_Pc": [[8, 3, 1, "", "high"], [8, 3, 1, "", "low"], [8, 3, 1, "", "q"]], "optunaz.descriptors.SmilesFromFile": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.UnfittedSklearnScaler": [[8, 2, 1, "", "MolData"], [8, 4, 1, "", "get_fitted_scaler_for_fp"], [8, 3, 1, "", "mol_data"], [8, 3, 1, "", "name"]], "optunaz.descriptors.UnfittedSklearnScaler.MolData": [[8, 3, 1, "", "file_path"], [8, 3, 1, "", "smiles_column"]], "optunaz.descriptors.UnscaledJazzyDescriptors": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.UnscaledJazzyDescriptors.Parameters": [[8, 3, 1, "", "jazzy_filters"], [8, 3, 1, "", "jazzy_names"]], "optunaz.descriptors.UnscaledPhyschemDescriptors": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.UnscaledPhyschemDescriptors.Parameters": [[8, 3, 1, "", "rdkit_names"]], "optunaz.descriptors.UnscaledZScalesDescriptors": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ValidDescriptor": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ZScalesDescriptors": [[8, 2, 1, "", "Parameters"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ZScalesDescriptors.Parameters": [[8, 3, 1, "", "descriptor"], [8, 3, 1, "", "scaler"]], "optunaz.evaluate": [[8, 1, 1, "", "get_merged_train_score"], [8, 1, 1, "", "get_scores"], [8, 1, 1, "", "get_train_test_scores"], [8, 1, 1, "", "score_all"], [8, 1, 1, "", "score_all_smiles"]], "optunaz.explainability": [[8, 1, 1, "", "ExplainPreds"], [8, 1, 1, "", "ShapExplainer"], [8, 1, 1, "", "explain_ECFP"], [8, 1, 1, "", "get_ecfp_fpinfo"], [8, 1, 1, "", "get_ecfpcount_fpinfo"], [8, 1, 1, "", "get_fp_info"], [8, 1, 1, "", "runShap"]], "optunaz.metircs": [[8, 1, 1, "", "auc_pr_cal"], [8, 1, 1, "", "bedroc_score"], [8, 1, 1, "", "concordance_index"], [8, 1, 1, "", "validate_cls_input"]], "optunaz.model_writer": [[8, 2, 1, "", "Predictor"], [8, 2, 1, "", "QSARtunaModel"], [8, 1, 1, "", "get_metadata"], [8, 1, 1, "", "get_transform"], [8, 1, 1, "", "perform_ptr"], [8, 1, 1, "", "save_model"], [8, 1, 1, "", "wrap_model"]], "optunaz.model_writer.Predictor": [[8, 4, 1, "", "explain"], [8, 4, 1, "", "predict"], [8, 4, 1, "", "predict_proba"], [8, 4, 1, "", "predict_uncert"]], "optunaz.model_writer.QSARtunaModel": [[8, 3, 1, "", "aux_transform"], [8, 3, 1, "", "descriptor"], [8, 3, 1, "", "metadata"], [8, 3, 1, "", "mode"], [8, 4, 1, "", "predict_from_smiles"], [8, 3, 1, "", "predictor"], [8, 3, 1, "", "transform"]], "optunaz.objective": [[8, 5, 1, "", "NoValidDescriptors"], [8, 2, 1, "", "Objective"], [8, 1, 1, "", "null_scores"]], "optunaz.objective.Objective": [[8, 3, 1, "", "cache"], [8, 3, 1, "", "optconfig"], [8, 3, 1, "", "train_aux"], [8, 3, 1, "", "train_smiles"], [8, 3, 1, "", "train_y"]], "optunaz.optbuild": [[8, 1, 1, "", "main"], [8, 1, 1, "", "predict_pls"]], "optunaz.predict": [[8, 5, 1, "", "ArgsError"], [8, 5, 1, "", "AuxCovariateMissing"], [8, 5, 1, "", "PrecomputedError"], [8, 5, 1, "", "UncertaintyError"], [8, 1, 1, "", "check_precomp_args"], [8, 1, 1, "", "main"], [8, 1, 1, "", "validate_args"], [8, 1, 1, "", "validate_aux"], [8, 1, 1, "", "validate_set_precomputed"], [8, 1, 1, "", "validate_uncertainty"]], "optunaz.schemagen": [[8, 1, 1, "", "doctitle"], [8, 1, 1, "", "main"], [8, 1, 1, "", "patch_schema_generic"], [8, 1, 1, "", "patch_schema_optunaz"], [8, 1, 1, "", "type_base_schema"]], "optunaz.three_step_opt_build_merge": [[8, 1, 1, "", "base_chemprop_params"], [8, 1, 1, "", "build_best"], [8, 1, 1, "", "build_merged"], [8, 1, 1, "", "buildconfig_best"], [8, 1, 1, "", "log_scores"], [8, 1, 1, "", "optimize"], [8, 1, 1, "", "run_study"], [8, 1, 1, "", "split_optimize"]], "optunaz.utils": [[11, 0, 0, "-", "enums"], [10, 0, 0, "-", "files_paths"], [10, 1, 1, "", "load_df_from_file"], [10, 0, 0, "-", "load_json"], [10, 1, 1, "", "md5_hash"], [10, 1, 1, "", "mkdict"], [10, 0, 0, "-", "mlflow"], [12, 0, 0, "-", "preprocessing"], [10, 1, 1, "", "remove_failed_idx"], [10, 0, 0, "-", "schema"], [10, 0, 0, "-", "tracking"]], "optunaz.utils.enums": [[11, 2, 1, "", "MlflowLogParams"], [11, 2, 1, "", "StudyUserAttrs"], [11, 2, 1, "", "TrialParams"], [11, 2, 1, "", "TrialUserAttrs"], [11, 0, 0, "-", "building_configuration_enum"], [11, 0, 0, "-", "configuration_enum"], [11, 0, 0, "-", "interface_enum"], [11, 0, 0, "-", "model_runner_enum"], [11, 0, 0, "-", "objective_enum"], [11, 0, 0, "-", "optimization_configuration_enum"], [11, 0, 0, "-", "prediction_configuration_enum"], [11, 0, 0, "-", "return_values_enum"], [11, 0, 0, "-", "visualization_enum"]], "optunaz.utils.enums.MlflowLogParams": [[11, 3, 1, "", "TRIAL_NUMBER"]], "optunaz.utils.enums.StudyUserAttrs": [[11, 3, 1, "", "OPTCONFIG"]], "optunaz.utils.enums.TrialParams": [[11, 3, 1, "", "ALGORITHM_HASH"], [11, 3, 1, "", "ALGORITHM_NAME"], [11, 3, 1, "", "DESCRIPTOR"]], "optunaz.utils.enums.TrialUserAttrs": [[11, 3, 1, "", "TEST_SCORES"], [11, 3, 1, "", "TRAIN_SCORES"]], "optunaz.utils.enums.building_configuration_enum": [[11, 2, 1, "", "BuildingConfigurationEnum"]], "optunaz.utils.enums.building_configuration_enum.BuildingConfigurationEnum": [[11, 3, 1, "", "GENERAL_CLASSIFIER"], [11, 3, 1, "", "GENERAL_HYPERPARAMETERS"], [11, 3, 1, "", "GENERAL_REGRESSOR"], [11, 3, 1, "", "METADATA"], [11, 3, 1, "", "METADATA_BESTTRIAL"], [11, 3, 1, "", "METADATA_BESTVALUE"]], "optunaz.utils.enums.configuration_enum": [[11, 2, 1, "", "ConfigurationEnum"]], "optunaz.utils.enums.configuration_enum.ConfigurationEnum": [[11, 3, 1, "", "ALGORITHMS"], [11, 3, 1, "", "ALGORITHMS_ADABOOSTCLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_ADABOOSTCLASSIFIER_LEARNING_RATE"], [11, 3, 1, "", "ALGORITHMS_ADABOOSTCLASSIFIER_N_ESTIMATORS"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_ENSEMBLE"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_ESTIMATOR"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_METHOD"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_N_FOLDS"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_PARAMS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_ACTIVATION"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_AGGREGATION"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_AGGREGATION_NORM"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_BATCH_SIZE"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_CLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_DEPTH"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_DROPOUT"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_ENSEMBLE_SIZE"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_EPOCHS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FEATURES_GENERATOR"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FFN_HIDDEN_SIZE"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FFN_NUM_LAYERS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FINAL_LR_RATIO_EXP"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FRZN"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_HIDDEN_SIZE"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_HYPEROPT_CLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_HYPEROPT_REGRESSOR"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_INIT_LR_RATIO_EXP"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_MAX_LR_EXP"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_NUM_ITERS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_PRETRAINED_MODEL"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_REGRESSOR"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_SEARCH_PARAMETER_LEVEL"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_STARTUP_RANDOM_ITERS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_WARMUP_EPOCHS_RATIO"], [11, 3, 1, "", "ALGORITHMS_HIGH"], [11, 3, 1, "", "ALGORITHMS_INTERFACE_SKLEARN"], [11, 3, 1, "", "ALGORITHMS_INTERFACE_XGBOOST"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORSCLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORSREGRESSOR"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORS_METRIC"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORS_N_NEIGHBORS"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORS_WEIGHTS"], [11, 3, 1, "", "ALGORITHMS_LASSO"], [11, 3, 1, "", "ALGORITHMS_LASSO_ALPHA"], [11, 3, 1, "", "ALGORITHMS_LOGISTICREGRESSION"], [11, 3, 1, "", "ALGORITHMS_LOGISTICREGRESSION_C"], [11, 3, 1, "", "ALGORITHMS_LOGISTICREGRESSION_SOLVER"], [11, 3, 1, "", "ALGORITHMS_LOW"], [11, 3, 1, "", "ALGORITHMS_MAPIE"], [11, 3, 1, "", "ALGORITHMS_MAPIE_ALPHA"], [11, 3, 1, "", "ALGORITHMS_PLSREGRESSION"], [11, 3, 1, "", "ALGORITHMS_PLSREGRESSION_N_COMPONENTS"], [11, 3, 1, "", "ALGORITHMS_PRF"], [11, 3, 1, "", "ALGORITHMS_PRF_MAX_DEPTH"], [11, 3, 1, "", "ALGORITHMS_PRF_MAX_FEATURES"], [11, 3, 1, "", "ALGORITHMS_PRF_MINPYSUMLEAF"], [11, 3, 1, "", "ALGORITHMS_PRF_N_ESTIMATORS"], [11, 3, 1, "", "ALGORITHMS_PRF_USE_PY_GINI"], [11, 3, 1, "", "ALGORITHMS_PRF_USE_PY_LEAFS"], [11, 3, 1, "", "ALGORITHMS_Q"], [11, 3, 1, "", "ALGORITHMS_RFCLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_RFREGRESSOR"], [11, 3, 1, "", "ALGORITHMS_RF_MAX_DEPTH"], [11, 3, 1, "", "ALGORITHMS_RF_MAX_FEATURES"], [11, 3, 1, "", "ALGORITHMS_RF_N_ESTIMATORS"], [11, 3, 1, "", "ALGORITHMS_RIDGE"], [11, 3, 1, "", "ALGORITHMS_RIDGE_ALPHA"], [11, 3, 1, "", "ALGORITHMS_SVC"], [11, 3, 1, "", "ALGORITHMS_SVC_C"], [11, 3, 1, "", "ALGORITHMS_SVC_GAMMA"], [11, 3, 1, "", "ALGORITHMS_SVR"], [11, 3, 1, "", "ALGORITHMS_SVR_C"], [11, 3, 1, "", "ALGORITHMS_SVR_GAMMA"], [11, 3, 1, "", "ALGORITHMS_XGBREGRESSOR"], [11, 3, 1, "", "ALGORITHMS_XGBREGRESSOR_LEARNING_RATE"], [11, 3, 1, "", "ALGORITHMS_XGBREGRESSOR_MAX_DEPTH"], [11, 3, 1, "", "ALGORITHMS_XGBREGRESSOR_N_ESTIMATORS"], [11, 3, 1, "", "DATA"], [11, 3, 1, "", "DATA_INPUTCOLUMN"], [11, 3, 1, "", "DATA_RESPONSECOLUMN"], [11, 3, 1, "", "DATA_TEST"], [11, 3, 1, "", "DATA_TRAINING"], [11, 3, 1, "", "DESCRIPTORS"], [11, 3, 1, "", "DESCRIPTORS_AVALON"], [11, 3, 1, "", "DESCRIPTORS_AVALON_NBITS"], [11, 3, 1, "", "DESCRIPTORS_COMPOSITE"], [11, 3, 1, "", "DESCRIPTORS_ECFP"], [11, 3, 1, "", "DESCRIPTORS_ECFPCOUNTS"], [11, 3, 1, "", "DESCRIPTORS_ECFPCOUNTS_RADIUS"], [11, 3, 1, "", "DESCRIPTORS_ECFPCOUNTS_USEFEATURES"], [11, 3, 1, "", "DESCRIPTORS_ECFP_NBITS"], [11, 3, 1, "", "DESCRIPTORS_ECFP_RADIUS"], [11, 3, 1, "", "DESCRIPTORS_JAZZY"], [11, 3, 1, "", "DESCRIPTORS_JAZZY_JAZZYNAMES"], [11, 3, 1, "", "DESCRIPTORS_MACCSKEYS"], [11, 3, 1, "", "DESCRIPTORS_PATHFP"], [11, 3, 1, "", "DESCRIPTORS_PATHFP_FPSIZE"], [11, 3, 1, "", "DESCRIPTORS_PATHFP_MAXPATH"], [11, 3, 1, "", "DESCRIPTORS_PHYSCHEM"], [11, 3, 1, "", "DESCRIPTORS_PHYSCHEM_RDKITNAMES"], [11, 3, 1, "", "DESCRIPTORS_PRECOMPUTED"], [11, 3, 1, "", "DESCRIPTORS_PRECOMPUTED_FILE"], [11, 3, 1, "", "DESCRIPTORS_PRECOMPUTED_INPUT_COLUMNN"], [11, 3, 1, "", "DESCRIPTORS_PRECOMPUTED_RESPONSE_COLUMN"], [11, 3, 1, "", "DESCRIPTORS_SCALED"], [11, 3, 1, "", "DESCRIPTORS_SCALED_DESCRIPTOR"], [11, 3, 1, "", "DESCRIPTORS_SCALED_DESCRIPTOR_PARAMETERS"], [11, 3, 1, "", "DESCRIPTORS_SMILES"], [11, 3, 1, "", "DESCRIPTORS_SMILES_AND_SI"], [11, 3, 1, "", "DESCRIPTORS_SMILES_AND_SI_AUX_WEIGHT_PC"], [11, 3, 1, "", "DESCRIPTORS_SMILES_AND_SI_FILE"], [11, 3, 1, "", "DESCRIPTORS_SMILES_AND_SI_INPUT_COLUMN"], [11, 3, 1, "", "DESCRIPTORS_UNSC_JAZZY"], [11, 3, 1, "", "DESCRIPTORS_UNSC_PHYSCHEM"], [11, 3, 1, "", "DESCRIPTORS_UNSC_ZSCALES"], [11, 3, 1, "", "DESCRIPTORS_ZSCALES"], [11, 3, 1, "", "GENERAL_DISABLED"], [11, 3, 1, "", "GENERAL_PARAMETERS"], [11, 3, 1, "", "SETTINGS"], [11, 3, 1, "", "SETTINGS_CROSS_VALIDATION"], [11, 3, 1, "", "SETTINGS_DIRECTION"], [11, 3, 1, "", "SETTINGS_MODE"], [11, 3, 1, "", "SETTINGS_MODE_CLASSIFICATION"], [11, 3, 1, "", "SETTINGS_MODE_REGRESSION"], [11, 3, 1, "", "SETTINGS_N_JOBS"], [11, 3, 1, "", "SETTINGS_N_TRIALS"], [11, 3, 1, "", "SETTINGS_SHUFFLE"], [11, 3, 1, "", "TASK"], [11, 3, 1, "", "TASK_BUILDING"], [11, 3, 1, "", "TASK_OPTIMIZATION"]], "optunaz.utils.enums.interface_enum": [[11, 2, 1, "", "InterfaceEnum"]], "optunaz.utils.enums.interface_enum.InterfaceEnum": [[11, 3, 1, "", "CALIBRATED_SET"], [11, 3, 1, "", "CHEMPROP_SET"], [11, 3, 1, "", "PRF_SET"], [11, 3, 1, "", "SKLEARN_SET"], [11, 3, 1, "", "XGBOOST_SET"]], "optunaz.utils.enums.model_runner_enum": [[11, 2, 1, "", "ModelRunnerDataframeEnum"]], "optunaz.utils.enums.model_runner_enum.ModelRunnerDataframeEnum": [[11, 3, 1, "", "SET"], [11, 3, 1, "", "SMILES"], [11, 3, 1, "", "TEST"], [11, 3, 1, "", "TRAIN"], [11, 3, 1, "", "Y_PRED"], [11, 3, 1, "", "Y_TRUE"]], "optunaz.utils.enums.objective_enum": [[11, 2, 1, "", "ObjectiveEnum"]], "optunaz.utils.enums.objective_enum.ObjectiveEnum": [[11, 3, 1, "", "ATTRIBUTE_TRIAL_TRAIN_SCORE"], [11, 3, 1, "", "EXTRA_COLUMN_BESTHIT"]], "optunaz.utils.enums.optimization_configuration_enum": [[11, 2, 1, "", "OptimizationConfigurationEnum"]], "optunaz.utils.enums.prediction_configuration_enum": [[11, 2, 1, "", "PredictionConfigurationEnum"]], "optunaz.utils.enums.prediction_configuration_enum.PredictionConfigurationEnum": [[11, 3, 1, "", "DATA_DATASET"]], "optunaz.utils.enums.return_values_enum": [[11, 2, 1, "", "SklearnReturnValueEnum"], [11, 2, 1, "", "XGBoostReturnValueEnum"]], "optunaz.utils.enums.return_values_enum.SklearnReturnValueEnum": [[11, 3, 1, "", "CROSS_VALIDATE_FIT_TIME"], [11, 3, 1, "", "CROSS_VALIDATE_SCORE_TIME"], [11, 3, 1, "", "CROSS_VALIDATE_TEST_SCORE"], [11, 3, 1, "", "CROSS_VALIDATE_TRAIN_SCORE"]], "optunaz.utils.enums.return_values_enum.XGBoostReturnValueEnum": [[11, 3, 1, "", "CROSS_VALIDATE_FIT_TIME"], [11, 3, 1, "", "CROSS_VALIDATE_SCORE_TIME"], [11, 3, 1, "", "CROSS_VALIDATE_TEST_SCORE"], [11, 3, 1, "", "CROSS_VALIDATE_TRAIN_SCORE"]], "optunaz.utils.enums.visualization_enum": [[11, 2, 1, "", "VisualizationEnum"]], "optunaz.utils.enums.visualization_enum.VisualizationEnum": [[11, 3, 1, "", "OPTUNA_SYSTEM_ATTRS_INTERMEDIATE_VALUES"], [11, 3, 1, "", "OPTUNA_SYSTEM_ATTRS_NUMBER"], [11, 3, 1, "", "OPTUNA_SYSTEM_ATTRS_TRIAL_ID"], [11, 3, 1, "", "VISUALIZATION"], [11, 3, 1, "", "VISUALIZATION_CLASSIFIER"], [11, 3, 1, "", "VISUALIZATION_FILE_FORMAT"], [11, 3, 1, "", "VISUALIZATION_OUTPUT_FOLDER"], [11, 3, 1, "", "VISUALIZATION_PLOTS"], [11, 3, 1, "", "VISUALIZATION_PLOTS_CONTOUR"], [11, 3, 1, "", "VISUALIZATION_PLOTS_HISTORY"], [11, 3, 1, "", "VISUALIZATION_PLOTS_PARALLEL_COORDINATE"], [11, 3, 1, "", "VISUALIZATION_PLOTS_SLICE"], [11, 3, 1, "", "VISUALIZATION_REGRESSOR"], [11, 3, 1, "", "VISUALIZATION_USE_XVFB"]], "optunaz.utils.files_paths": [[10, 1, 1, "", "attach_root_path"], [10, 1, 1, "", "move_up_directory"]], "optunaz.utils.load_json": [[10, 1, 1, "", "loadJSON"]], "optunaz.utils.mlflow": [[10, 2, 1, "", "MLflowCallback"], [10, 1, 1, "", "add_ellipsis"], [10, 1, 1, "", "shorten_names"]], "optunaz.utils.mlflow.MLflowCallback": [[10, 3, 1, "", "optconfig"], [10, 4, 1, "", "prepare_tags"], [10, 4, 1, "", "tmp_buildconfig"], [10, 3, 1, "", "tracking_uri"], [10, 3, 1, "", "trial_number_offset"]], "optunaz.utils.preprocessing": [[12, 0, 0, "-", "deduplicator"], [12, 0, 0, "-", "splitter"], [12, 0, 0, "-", "transform"]], "optunaz.utils.preprocessing.deduplicator": [[12, 2, 1, "", "Deduplicator"], [12, 2, 1, "", "KeepAllNoDeduplication"], [12, 2, 1, "", "KeepAvg"], [12, 2, 1, "", "KeepFirst"], [12, 2, 1, "", "KeepLast"], [12, 2, 1, "", "KeepMax"], [12, 2, 1, "", "KeepMedian"], [12, 2, 1, "", "KeepMin"], [12, 2, 1, "", "KeepRandom"]], "optunaz.utils.preprocessing.deduplicator.Deduplicator": [[12, 4, 1, "", "dedup"]], "optunaz.utils.preprocessing.deduplicator.KeepAllNoDeduplication": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepAvg": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepFirst": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepLast": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepMax": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepMedian": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepMin": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepRandom": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"], [12, 3, 1, "", "seed"]], "optunaz.utils.preprocessing.splitter": [[12, 2, 1, "", "GroupingSplitter"], [12, 2, 1, "", "HistogramStratifiedShuffleSplit"], [12, 2, 1, "", "KFold"], [12, 2, 1, "", "NoSplitting"], [13, 2, 1, "", "Predefined"], [13, 2, 1, "", "Random"], [13, 2, 1, "", "ScaffoldSplit"], [12, 2, 1, "", "SklearnSplitter"], [12, 2, 1, "", "Splitter"], [13, 2, 1, "", "Stratified"], [13, 2, 1, "", "Temporal"], [12, 1, 1, "", "butina_cluster"], [12, 1, 1, "", "fd_bin"], [12, 1, 1, "", "stratify"]], "optunaz.utils.preprocessing.splitter.GroupingSplitter": [[12, 4, 1, "", "groups"]], "optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit": [[12, 3, 1, "", "bins"], [12, 4, 1, "", "get_n_splits"], [12, 3, 1, "", "n_splits"], [12, 3, 1, "", "random_state"], [12, 4, 1, "", "split"], [12, 3, 1, "", "test_fraction"]], "optunaz.utils.preprocessing.splitter.KFold": [[12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [12, 3, 1, "", "random_state"], [12, 3, 1, "", "shuffle"], [12, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.NoSplitting": [[12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [12, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.Predefined": [[12, 3, 1, "", "column_name"], [12, 4, 1, "", "get_sklearn_splitter"], [12, 4, 1, "", "groups"], [12, 3, 1, "", "name"], [13, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.Random": [[12, 3, 1, "", "fraction"], [12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [12, 3, 1, "", "seed"]], "optunaz.utils.preprocessing.splitter.ScaffoldSplit": [[12, 3, 1, "", "bins"], [12, 3, 1, "", "butina_cluster"], [12, 4, 1, "", "get_n_splits"], [12, 4, 1, "", "get_sklearn_splitter"], [13, 4, 1, "", "groups"], [12, 3, 1, "", "make_scaffold_generic"], [12, 3, 1, "", "name"], [12, 3, 1, "", "random_state"], [13, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.SklearnSplitter": [[12, 4, 1, "", "get_n_splits"], [12, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.Splitter": [[12, 4, 1, "", "get_sklearn_splitter"], [12, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.Stratified": [[12, 3, 1, "", "bins"], [12, 3, 1, "", "fraction"], [12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [12, 3, 1, "", "seed"]], "optunaz.utils.preprocessing.splitter.Temporal": [[12, 3, 1, "", "fraction"], [12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [13, 4, 1, "", "split"]], "optunaz.utils.preprocessing.transform": [[12, 2, 1, "", "AuxTransformer"], [12, 2, 1, "", "DataTransform"], [12, 2, 1, "", "LogBase"], [12, 2, 1, "", "LogNegative"], [14, 2, 1, "", "ModelDataTransform"], [14, 2, 1, "", "PTRTransform"], [14, 2, 1, "", "VectorFromColumn"], [14, 2, 1, "", "ZScales"]], "optunaz.utils.preprocessing.transform.AuxTransformer": [[12, 4, 1, "", "transform"]], "optunaz.utils.preprocessing.transform.DataTransform": [[12, 4, 1, "", "transform"]], "optunaz.utils.preprocessing.transform.LogBase": [[12, 3, 1, "", "LOG"], [12, 3, 1, "", "LOG10"], [12, 3, 1, "", "LOG2"]], "optunaz.utils.preprocessing.transform.LogNegative": [[12, 3, 1, "", "FALSE"], [12, 3, 1, "", "TRUE"]], "optunaz.utils.preprocessing.transform.ModelDataTransform": [[14, 2, 1, "", "Parameters"], [12, 3, 1, "", "base_dict"], [12, 3, 1, "", "base_negation"], [12, 3, 1, "", "name"], [12, 3, 1, "", "parameters"], [12, 3, 1, "", "reverse_dict"], [12, 4, 1, "", "reverse_transform"], [12, 4, 1, "", "reverse_transform_df"], [12, 4, 1, "", "reverse_transform_one"], [12, 4, 1, "", "transform"], [12, 4, 1, "", "transform_df"], [12, 4, 1, "", "transform_one"]], "optunaz.utils.preprocessing.transform.ModelDataTransform.Parameters": [[12, 3, 1, "", "base"], [12, 3, 1, "", "conversion"], [12, 3, 1, "", "negation"]], "optunaz.utils.preprocessing.transform.PTRTransform": [[14, 2, 1, "", "Parameters"], [12, 3, 1, "", "name"], [12, 3, 1, "", "parameters"], [12, 4, 1, "", "reverse_transform"], [12, 4, 1, "", "transform"]], "optunaz.utils.preprocessing.transform.PTRTransform.Parameters": [[12, 3, 1, "", "std"], [12, 3, 1, "", "threshold"]], "optunaz.utils.preprocessing.transform.VectorFromColumn": [[14, 2, 1, "", "Parameters"], [12, 3, 1, "", "name"], [12, 3, 1, "", "parameters"], [12, 4, 1, "", "transform"]], "optunaz.utils.preprocessing.transform.VectorFromColumn.Parameters": [[12, 3, 1, "", "delimiter"]], "optunaz.utils.preprocessing.transform.ZScales": [[14, 2, 1, "", "Parameters"], [12, 3, 1, "", "name"], [12, 3, 1, "", "parameters"], [12, 4, 1, "", "transform"]], "optunaz.utils.schema": [[10, 1, 1, "", "add_boolean_guards_for_schema_properties"], [10, 1, 1, "", "addsibling"], [10, 1, 1, "", "addtitles"], [10, 1, 1, "", "copytitle"], [10, 1, 1, "", "create_dependency"], [10, 1, 1, "", "delsibling"], [10, 1, 1, "", "getref"], [10, 1, 1, "", "remove_schema_properties"], [10, 1, 1, "", "replaceenum"], [10, 1, 1, "", "replacekey"], [10, 1, 1, "", "replacevalue"]], "optunaz.utils.tracking": [[10, 2, 1, "", "BuildTrackingData"], [10, 2, 1, "", "Datapoint"], [10, 2, 1, "", "InternalTrackingCallback"], [10, 2, 1, "", "TrackingData"], [10, 1, 1, "", "get_authorization_header"], [10, 1, 1, "", "removeprefix"], [10, 1, 1, "", "round_scores"], [10, 1, 1, "", "track_build"]], "optunaz.utils.tracking.BuildTrackingData": [[10, 3, 1, "", "response_column_name"], [10, 3, 1, "", "test_points"], [10, 3, 1, "", "test_scores"]], "optunaz.utils.tracking.Datapoint": [[10, 3, 1, "", "expected"], [10, 3, 1, "", "predicted"], [10, 3, 1, "", "smiles"]], "optunaz.utils.tracking.InternalTrackingCallback": [[10, 3, 1, "", "optconfig"], [10, 3, 1, "", "trial_number_offset"]], "optunaz.utils.tracking.TrackingData": [[10, 3, 1, "", "all_cv_test_scores"], [10, 3, 1, "", "buildconfig"], [10, 3, 1, "", "scoring"], [10, 3, 1, "", "trial_number"], [10, 3, 1, "", "trial_state"], [10, 3, 1, "", "trial_value"]], "optunaz.visualizer": [[8, 2, 1, "", "Visualizer"]], "optunaz.visualizer.Visualizer": [[8, 4, 1, "", "plot_by_configuration"], [8, 4, 1, "", "plot_contour"], [8, 4, 1, "", "plot_history"], [8, 4, 1, "", "plot_parallel_coordinate"], [8, 4, 1, "", "plot_slice"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method", "5": "py:exception"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"], "5": ["py", "exception", "Python exception"]}, "titleterms": {"qsartuna": [0, 4, 6, 7], "\ud80c\udd9b": 0, "qsar": 0, "us": 0, "optim": [0, 6], "hyperparamet": 0, "tune": 0, "formerli": 0, "optuna": 0, "az": 0, "qptuna": 0, "background": [0, 6], "The": [0, 6], "three": [0, 6], "step": [0, 6], "process": [0, 6], "json": 0, "base": [0, 7], "command": 0, "line": 0, "interfac": 0, "configur": [0, 6], "file": [0, 6], "run": [0, 6], "via": 0, "singulart": 0, "submit": 0, "slurm": 0, "model": [0, 6], "option": [0, 6], "inspect": 0, "from": [0, 6, 7], "python": 0, "jupyt": 0, "notebook": 0, "avail": [1, 2, 3, 13, 14], "algorithm": [1, 6], "adaboostclassifi": 1, "lasso": 1, "kneighborsclassifi": 1, "kneighborsregressor": 1, "logisticregress": 1, "plsregress": 1, "randomforestclassifi": 1, "randomforestregressor": 1, "ridg": 1, "svc": 1, "svr": 1, "xgbregressor": 1, "prfclassifi": 1, "chempropregressor": 1, "chempropclassifi": 1, "chemprophyperoptclassifi": 1, "chemprophyperoptregressor": 1, "chemprophyperoptregressorpretrain": 1, "calibratedclassifiercvwithva": 1, "mapi": [1, 6], "dedupl": [2, 7, 12], "keepfirst": 2, "keeplast": 2, "keeprandom": 2, "keepmin": 2, "keepmax": 2, "keepavg": 2, "keepmedian": 2, "keepkeepallnodedupl": 2, "descriptor": [3, 6, 8], "avalon": 3, "ecfp": 3, "ecfp_count": 3, "pathfp": 3, "maccs_kei": 3, "unscaledphyschemdescriptor": 3, "unscaledjazzydescriptor": 3, "unscaledzscalesdescriptor": 3, "physchemdescriptor": 3, "jazzydescriptor": 3, "precomputeddescriptorfromfil": 3, "zscale": [3, 14], "smilesfromfil": 3, "smilesandsideinfofromfil": 3, "scaleddescriptor": 3, "compositedescriptor": 3, "welcom": 4, "document": 4, "develop": 4, "optunaz": [5, 8, 9, 10, 11, 12], "cli": 6, "tutori": 6, "thi": 6, "prepar": 6, "regress": 6, "exampl": 6, "creat": 6, "visual": [6, 8], "progress": 6, "pick": 6, "best": [6, 7], "trial": 6, "build": 6, "merg": 6, "preprocess": [6, 7, 12], "split": [6, 7], "data": [6, 7], "train": 6, "test": 6, "set": 6, "remov": 6, "duplic": [6, 7], "dataset": 6, "choos": 6, "score": 6, "function": 6, "advanc": 6, "functoinail": 6, "probabilist": [6, 7], "random": [6, 7, 13], "forest": 6, "prf": 6, "interlud": [6, 7], "cautionari": 6, "advic": 6, "y": 6, "respons": 6, "column": 6, "valid": 6, "chemprop": 6, "simpl": 6, "separ": 6, "shallow": 6, "method": 6, "default": 6, "behavior": 6, "turn": 6, "hyperopt": 6, "within": [6, 7], "functionail": 6, "veri": 6, "larg": 6, "comput": 6, "cost": 6, "A": 6, "note": 6, "mpnn": 6, "search": 6, "space": 6, "side": 6, "inform": 6, "multi": 6, "task": 6, "learn": 6, "mtl": 6, "combin": 6, "onli": 6, "recommend": 6, "long": 6, "time": 6, "pre": 6, "adapt": 6, "transfer": 6, "fingerprint": 6, "encod": 6, "latent": 6, "represent": [6, 7], "probabl": 6, "calibr": 6, "classif": 6, "uncertainti": 6, "estim": 6, "vennab": 6, "ensembl": 6, "dropout": 6, "explain": [6, 8], "shap": 6, "interpret": 6, "log": [6, 7], "transform": [6, 7, 12, 14], "covari": 6, "one": 6, "e": 6, "g": 6, "dose": 6, "point": 6, "co": 6, "variat": 6, "proteochemometr": 6, "pcm": 6, "more": 6, "vectorfromsmil": 6, "z": 6, "scale": 6, "object": [6, 8], "priorit": 6, "perform": [6, 7], "standard": 6, "deviat": 6, "further": 6, "precomput": 6, "introduct": 7, "translat": 7, "sdf": 7, "csv": 7, "need": 7, "deal": 7, "compar": 7, "differ": 7, "unif": 7, "strategi": 7, "tempor": [7, 13], "stratifi": [7, 13], "scaffold": 7, "input": 7, "user": 7, "import": 7, "logarithm": 7, "dataread": [7, 8], "threshold": 7, "ptr": [7, 14], "experiment": 7, "error": 7, "definit": 7, "implement": 7, "conclus": 7, "calcul": 7, "evalu": [7, 8], "reproduc": 7, "practic": 7, "packag": [8, 9, 10, 11, 12], "subpackag": [8, 10], "submodul": [8, 9, 10, 11, 12], "builder": 8, "modul": [8, 9, 10, 11, 12], "metirc": 8, "model_writ": 8, "optbuild": 8, "predict": 8, "schemagen": 8, "three_step_opt_build_merg": 8, "content": [8, 9, 10, 11, 12], "config": 9, "build_from_opt": 9, "buildconfig": 9, "optconfig": 9, "util": [10, 11, 12], "files_path": 10, "load_json": 10, "mlflow": 10, "schema": 10, "track": 10, "enum": 11, "building_configuration_enum": 11, "configuration_enum": 11, "interface_enum": 11, "model_runner_enum": 11, "objective_enum": 11, "optimization_configuration_enum": 11, "prediction_configuration_enum": 11, "return_values_enum": 11, "visualization_enum": 11, "splitter": [12, 13], "predefin": 13, "scaffoldsplit": 13, "modeldatatransform": 14, "vectorfromcolumn": 14}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "nbsphinx": 4, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 56}})
\ No newline at end of file
+Search.setIndex({"docnames": ["README", "algorithms", "deduplicator", "descriptors", "index", "modules", "notebooks/QSARtuna_Tutorial", "notebooks/preprocess_data", "optunaz", "optunaz.config", "optunaz.utils", "optunaz.utils.enums", "optunaz.utils.preprocessing", "splitters", "transform"], "filenames": ["README.md", "algorithms.rst", "deduplicator.rst", "descriptors.rst", "index.rst", "modules.rst", "notebooks/QSARtuna_Tutorial.ipynb", "notebooks/preprocess_data.ipynb", "optunaz.rst", "optunaz.config.rst", "optunaz.utils.rst", "optunaz.utils.enums.rst", "optunaz.utils.preprocessing.rst", "splitters.rst", "transform.rst"], "titles": ["QSARtuna \ud80c\udd9b: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ and QPTUNA)", "Available algorithms", "Available deduplicators", "Available descriptors", "Welcome to QSARtuna Documentation!", "optunaz", "QSARtuna CLI Tutorial", "Preprocessing data for QSARtuna", "optunaz package", "optunaz.config package", "optunaz.utils package", "optunaz.utils.enums package", "optunaz.utils.preprocessing package", "Available splitters", "Available transform"], "terms": {"build": [0, 4, 8, 9, 10, 11], "predict": [0, 1, 3, 5, 6, 7, 9, 10, 11], "compchem": 0, "develop": [0, 3, 8], "uncertainti": [0, 1, 4, 7, 8, 9, 12, 14], "quantif": 0, "explain": [0, 1, 4, 5, 9], "mind": 0, "thi": [0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13], "librari": [0, 7], "search": [0, 1, 3, 8, 9], "best": [0, 1, 8, 9], "ml": [0, 4, 9], "algorithm": [0, 3, 4, 7, 8, 9, 10, 11, 12, 13], "molecular": [0, 1, 3, 4, 6, 7, 8, 9], "descriptor": [0, 4, 5, 9, 11], "given": [0, 1, 3, 6, 7, 8, 9, 10], "data": [0, 1, 3, 4, 8, 9, 11, 12, 13, 14], "itself": [0, 6], "done": [0, 6], "emploi": [0, 3, 6, 7, 8], "latest": [0, 9], "state": [0, 6, 12], "art": [0, 6], "estim": [0, 1, 3, 4, 7, 8, 9, 11], "packag": [0, 1, 3, 5, 6, 7], "further": [0, 9], "document": [0, 6, 7], "github": [0, 6, 8, 12], "page": 0, "here": [0, 3, 6, 7, 8, 9, 12, 13], "public": [0, 1, 3, 4, 6, 8, 9], "avail": [0, 4, 6, 7, 8], "structur": [0, 1, 3, 6, 7, 8, 9], "around": [0, 6, 7], "train": [0, 1, 3, 4, 7, 8, 9, 11, 12, 13], "mani": [0, 1, 6, 9], "differ": [0, 1, 3, 6, 8, 9, 12], "paramet": [0, 1, 3, 6, 7, 8, 9, 11, 12, 13, 14], "onli": [0, 1, 3, 7, 8, 9, 12, 13], "dataset": [0, 1, 7, 8, 9, 11, 12], "usual": [0, 1, 6, 7, 9], "cross": [0, 1, 6, 9, 12], "valid": [0, 1, 3, 7, 8, 9, 11, 12], "pick": 0, "evalu": [0, 4, 5, 6], "its": [0, 1, 6, 9, 11], "perform": [0, 3, 8, 11, 12, 14], "test": [0, 1, 4, 7, 8, 9, 11, 12, 13], "prod": [0, 6], "re": [0, 6, 8], "merg": [0, 7, 8, 12], "ha": [0, 1, 6, 7, 8, 9, 12], "drawback": [0, 6], "left": [0, 6, 7], "result": [0, 1, 3, 6, 7, 8, 9], "big": [0, 6], "benefit": [0, 6], "final": [0, 1, 6, 9], "all": [0, 1, 3, 6, 7, 8, 9, 11, 12], "let": [0, 6, 7], "s": [0, 6, 7], "look": [0, 1, 6, 7, 9], "trivial": 0, "exampl": [0, 3, 7, 8, 9], "weight": [0, 1, 3, 6, 8, 9, 11], "set": [0, 3, 4, 7, 8, 9, 10, 11, 12, 13], "50": [0, 1, 3, 6, 8, 9], "molecul": [0, 1, 3, 6, 7, 8, 9], "we": [0, 3, 6, 7, 8, 9, 12, 13], "start": [0, 4, 6, 7], "format": [0, 3, 6, 7, 8, 10], "It": [0, 1, 3, 6, 7, 8, 9], "contain": [0, 3, 6, 8], "four": 0, "main": [0, 3, 6, 7, 8], "section": [0, 6, 7], "locat": [0, 6], "column": [0, 3, 7, 8, 11, 12, 13, 14], "detail": [0, 3, 6, 7, 8, 9, 10], "about": [0, 6, 7], "which": [0, 1, 3, 6, 7, 8, 9, 12], "below": [0, 3, 6, 7, 8], "task": [0, 3, 7, 8, 9, 11], "training_dataset_fil": [0, 6, 7, 8], "drd2": [0, 6], "subset": [0, 1, 6, 7, 9], "csv": [0, 3, 4, 6, 8], "input_column": [0, 3, 6, 7, 8, 11], "canon": [0, 6, 8, 12], "response_column": [0, 3, 6, 7, 8, 11], "molwt": [0, 6], "mode": [0, 6, 8, 9, 11], "regress": [0, 1, 7, 9, 11, 12], "cross_valid": [0, 6, 9, 11, 12], "5": [0, 1, 3, 6, 7, 8, 9, 12], "direct": [0, 1, 6, 9, 11], "maxim": [0, 1, 6, 9], "n_trial": [0, 6, 8, 9, 11], "100": [0, 1, 3, 6, 7, 8, 9, 10], "n_startup_tri": [0, 6, 8, 9], "30": [0, 1, 6, 7, 9], "name": [0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14], "ecfp": [0, 4, 6, 8, 9, 11], "radiu": [0, 3, 6, 8, 11], "3": [0, 1, 3, 4, 6, 7, 8, 9], "nbit": [0, 3, 6, 8, 9, 11], "2048": [0, 3, 6, 8], "maccs_kei": [0, 4, 6, 8, 11], "randomforestregressor": [0, 4, 6, 9, 11], "max_depth": [0, 1, 9, 11], "low": [0, 1, 3, 6, 7, 8, 9, 11], "2": [0, 1, 3, 6, 7, 8, 9, 12, 13], "high": [0, 1, 3, 6, 8, 9, 11], "32": [0, 1, 6, 9], "n_estim": [0, 1, 6, 9, 11], "10": [0, 1, 3, 6, 7, 8, 9, 12], "250": [0, 1, 6, 9], "max_featur": [0, 1, 9, 11], "auto": [0, 1, 6, 8, 9], "ridg": [0, 4, 6, 9, 11], "alpha": [0, 1, 6, 7, 8, 9, 11], "0": [0, 1, 3, 4, 6, 7, 8, 9, 12, 13], "lasso": [0, 4, 6, 9, 11], "xgbregressor": [0, 4, 6, 9, 11], "learning_r": [0, 1, 9, 11], "1": [0, 1, 3, 4, 6, 7, 8, 9, 10, 12, 13], "specifi": [0, 1, 6, 7, 8, 9, 11], "In": [0, 1, 3, 6, 7, 8, 9], "rel": [0, 6], "path": [0, 1, 3, 6, 7, 8, 9, 10], "folder": [0, 6, 7], "ar": [0, 1, 3, 6, 7, 8, 9, 11, 12, 13], "want": [0, 6, 7], "fold": [0, 1, 6, 7, 9, 12, 13], "valu": [0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14], "object": [0, 1, 5, 7, 9, 10, 11, 12], "function": [0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 14], "standard": [0, 1, 7, 9, 12, 14], "scikit": [0, 6, 8, 12, 13], "learn": [0, 1, 3, 7, 8, 9, 12, 13], "have": [0, 3, 6, 7, 8, 9, 12], "total": [0, 6, 7], "trial": [0, 1, 9, 10, 11], "first": [0, 1, 3, 6, 7, 8, 9, 12], "startup": [0, 6], "should": [0, 1, 3, 6, 7, 8, 9, 12], "random": [0, 1, 4, 9, 12], "explor": [0, 6], "get": [0, 6, 7, 8], "stuck": 0, "earli": [0, 1, 6, 8, 9], "one": [0, 3, 7, 8, 9, 12, 13], "local": [0, 6], "minimum": [0, 1, 3, 8, 9, 12, 13], "two": [0, 1, 6, 7, 9, 12, 13], "free": [0, 3, 8], "pair": [0, 6], "ani": [0, 3, 6, 7, 8, 9, 12], "when": [0, 1, 6, 7, 8, 9, 12, 13], "our": [0, 6, 7], "time": [0, 1, 3, 7, 8, 9], "can": [0, 1, 3, 6, 7, 8, 9, 12, 13], "deploi": 0, "singular": [0, 6], "To": [0, 6, 7], "insid": [0, 8], "follow": [0, 3, 6, 7, 8, 9], "syntax": 0, "exec": 0, "sif": 0, "project": [0, 1, 9], "cc": [0, 6, 7], "mai": [0, 1, 3, 6, 7, 8, 9], "qsartuna_latest": 0, "opt": 0, "venv": [0, 6], "bin": [0, 6, 7, 12, 13], "config": [0, 1, 5, 6, 8], "regression_drd2_50": 0, "buildconfig": [0, 5, 6, 8, 10], "outpath": 0, "target": [0, 1, 6, 7, 9, 12, 14], "pkl": [0, 1, 6, 9], "sinc": [0, 3, 6, 7, 8, 12], "long": [0, 7], "avoid": [0, 6, 12], "login": 0, "node": 0, "queue": 0, "instead": [0, 1, 3, 6, 7, 8, 9, 12], "script": 0, "give": [0, 6], "sbatch": 0, "sh": 0, "ntask": 0, "cpu": 0, "per": [0, 1, 7, 9], "mem": 0, "4g": 0, "partit": 0, "core": [0, 7, 9], "illustr": [0, 6, 7], "how": [0, 1, 3, 6, 7, 8, 9], "chose": 0, "chang": [0, 6], "directori": [0, 6, 10], "cd": 0, "project_fold": 0, "optunaaz": 0, "version": [0, 7, 9], "optunaaz_latest": 0, "complet": [0, 3, 6, 8], "creat": [0, 7, 10], "pickl": [0, 6], "your": [0, 6, 7], "home": 0, "under": [0, 6], "built": [0, 3, 7, 8, 9], "infer": [0, 6, 7, 8], "input": [0, 1, 3, 4, 6, 8, 9, 12, 13, 14], "smile": [0, 3, 6, 7, 8, 10, 11, 12, 13], "output": [0, 1, 6, 7, 8, 9, 12, 14], "note": [0, 1, 3, 7, 8, 9, 11, 12, 13], "_": [0, 6], "point": [0, 1, 7, 9, 12, 13], "most": [0, 6, 7], "recent": [0, 6], "legaci": 0, "requir": [0, 3, 6, 7, 8], "same": [0, 1, 6, 7, 9], "modifi": [0, 8], "abov": [0, 6, 7], "suppli": [0, 1, 3, 6, 7, 8, 9], "qsartuna_": 0, "replac": [0, 6, 10], "e": [0, 1, 3, 7, 8, 9, 12, 14], "g": [0, 3, 7, 8, 12, 14], "qsartuna_2": 0, "1_model": 0, "would": [0, 3, 6, 7, 8], "gener": [0, 1, 3, 6, 7, 8, 9, 12, 13], "tri": 0, "dure": [0, 1, 3, 6, 7, 8, 9], "mlflow": [0, 5, 8, 11], "track": [0, 3, 5, 8, 9], "ui": 0, "modul": [0, 5, 6], "load": [0, 1, 6, 7, 9], "Then": 0, "open": [0, 1, 6, 9], "link": 0, "browser": 0, "If": [0, 1, 3, 6, 8, 9, 12, 13], "you": [0, 1, 6, 7, 9], "scp": 0, "forward": [0, 1, 9], "port": 0, "separ": [0, 3, 7, 8], "ssh": 0, "session": 0, "non": [0, 1, 3, 6, 7, 8, 9], "machin": [0, 1, 3, 6, 7, 8, 9], "n": [0, 1, 6, 7, 9, 10], "l": 0, "localhost": 0, "5000": 0, "user": [0, 1, 3, 4, 6, 8, 9, 11, 12, 13, 14], "intranet": 0, "net": 0, "just": [0, 6], "execut": 0, "select": [0, 1, 3, 6, 7, 8, 9], "experi": [0, 7, 10], "after": [0, 1, 3, 6, 7, 8, 9, 10], "choos": [0, 4], "compar": [0, 6], "comparison": [0, 6, 7], "show": [0, 6, 7], "call": [0, 1, 3, 6, 8, 9, 12], "well": [0, 6, 7], "metric": [0, 1, 6, 8, 9, 11], "At": 0, "bottom": 0, "plot": [0, 6, 7, 9, 11], "For": [0, 1, 3, 6, 7, 8, 9, 12], "x": [0, 1, 3, 6, 7, 8, 9, 12, 13], "axi": [0, 6, 7], "number": [0, 1, 3, 6, 7, 8, 9, 10], "y": [0, 1, 7, 8, 9, 12, 13], "cvmean": 0, "r2": [0, 6, 7, 9], "more": [0, 1, 3, 7, 8, 9, 10], "click": 0, "individu": [0, 1, 6, 7, 9], "There": [0, 1, 6, 7, 9], "access": [0, 3, 8], "conda": 0, "environ": [0, 3, 6, 8], "instal": [0, 6], "purg": 0, "miniconda3": 0, "my_env_with_qsartuna": 0, "pip": [0, 6], "activ": [0, 1, 6, 7, 9, 11, 12, 14], "case": [0, 1, 6, 7, 8, 9], "check": [0, 6, 8, 11, 12], "m": [0, 6, 8], "http": [0, 3, 6, 7, 8, 9, 12], "com": [0, 6, 7, 8, 12], "molecularai": [0, 6], "releas": [0, 4, 6, 7], "download": [0, 6], "tar": [0, 6], "gz": [0, 6], "three_step_opt_build_merg": [0, 5, 6], "import": [0, 6], "buildconfig_best": [0, 6, 8], "build_best": [0, 6, 8], "build_merg": [0, 6, 8], "modelmod": [0, 6, 8, 9], "optimizationdirect": [0, 6, 9], "optconfig": [0, 1, 5, 6, 8, 10, 11], "optimizationconfig": [0, 6, 8, 9], "svr": [0, 4, 6, 9, 11], "randomforest": 0, "pl": [0, 1, 9], "dataread": [0, 5, 6], "ecfp_count": [0, 4, 6, 8, 11], "prepar": [0, 4, 7], "new": [0, 1, 6, 7, 9], "studi": [0, 3, 6, 8, 9, 10, 11], "study_nam": [0, 6, 8], "my_studi": [0, 6], "make": [0, 1, 6, 7, 9, 12, 13, 14], "write": [0, 6], "out": [0, 1, 6, 7, 9], "print": [0, 6, 7], "dump": [0, 6], "indent": [0, 6], "save": [0, 6], "class": [1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14], "optunaz": [1, 3, 6, 7, 13, 14], "sourc": [1, 3, 8, 9, 10, 11, 12, 13, 14], "adaboost": [1, 9], "classifi": [1, 6, 8, 9, 11], "an": [1, 3, 6, 7, 8, 9, 10, 12, 13], "meta": [1, 6, 9], "begin": [1, 6, 7, 9, 12, 13], "fit": [1, 3, 6, 7, 8, 9], "origin": [1, 3, 6, 7, 8, 9, 12], "addit": [1, 6, 9], "copi": [1, 7, 9, 10], "where": [1, 6, 7, 9], "incorrectli": [1, 9], "instanc": [1, 6, 7, 9], "adjust": [1, 9], "subsequ": [1, 9], "focu": [1, 9], "difficult": [1, 6, 9], "adaboostclassifierparametersnestim": [1, 9], "adaboostclassifierparameterslearningr": [1, 9], "The": [1, 3, 7, 8, 9, 10, 12, 14], "maximum": [1, 3, 6, 7, 8, 9, 12, 13], "boost": [1, 3, 8, 9], "termin": [1, 9], "perfect": [1, 9], "procedur": [1, 3, 7, 8, 9], "stop": [1, 6, 9], "titl": [1, 3, 6, 7, 8, 9, 10, 12, 13, 14], "appli": [1, 3, 6, 7, 8, 9, 12, 13, 14], "each": [1, 3, 6, 7, 8, 9, 12], "classifierat": [1, 9], "iter": [1, 6, 9, 12, 13], "A": [1, 3, 7, 8, 9], "higher": [1, 6, 9], "rateincreas": [1, 9], "contribut": [1, 3, 6, 8, 9], "trade": [1, 9], "off": [1, 6, 7, 9, 12, 13], "between": [1, 6, 7, 9], "learning_rateand": [1, 9], "int": [1, 3, 8, 9, 12, 13], "float": [1, 6, 7, 9, 10, 12, 13, 14], "linear": [1, 7, 9], "model": [1, 3, 4, 7, 8, 9, 10, 12, 13, 14], "l1": [1, 9], "prior": [1, 7, 9], "regular": [1, 6, 9], "spars": [1, 9], "coeffici": [1, 9], "tend": [1, 9], "prefer": [1, 9], "solut": [1, 6, 9], "fewer": [1, 9], "zero": [1, 3, 8, 9], "effect": [1, 6, 7, 9, 12], "reduc": [1, 6, 9], "featur": [1, 3, 6, 8, 9], "upon": [1, 6, 9], "depend": [1, 6, 7, 9], "lassoparametersalpha": [1, 9], "constant": [1, 9], "multipli": [1, 9], "term": [1, 6, 9], "control": [1, 6, 7, 9, 12], "strength": [1, 3, 8, 9], "must": [1, 6, 9], "neg": [1, 6, 7, 9], "i": [1, 3, 6, 7, 8, 9], "inf": [1, 6, 8, 9], "equival": [1, 9], "ordinari": [1, 9], "least": [1, 6, 9], "squar": [1, 6, 9], "solv": [1, 6, 9], "linearregress": [1, 9], "numer": [1, 7, 9], "reason": [1, 7, 9], "us": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14], "advis": [1, 6, 7, 9], "implement": [1, 3, 6, 8, 9, 12], "k": [1, 6, 7, 9, 12, 13], "nearest": [1, 6, 9], "neighbor": [1, 6, 9, 12, 13], "vote": [1, 9], "principl": [1, 9], "behind": [1, 9], "method": [1, 3, 7, 8, 9, 11, 12], "find": [1, 6, 9], "predefin": [1, 4, 9, 12, 14], "sampl": [1, 6, 9, 12, 13], "closest": [1, 9], "distanc": [1, 6, 9], "label": [1, 6, 7, 8, 9, 12, 13], "from": [1, 3, 4, 8, 9, 10, 12, 13, 14], "defin": [1, 3, 6, 7, 8, 9, 10, 12], "despit": [1, 6, 9], "simplic": [1, 9], "success": [1, 6, 9], "larg": [1, 7, 9], "classif": [1, 4, 7, 8, 9, 11, 12], "problem": [1, 6, 7, 8, 9], "n_neighbor": [1, 9, 11], "kneighborsclassifierparametersn_neighbor": [1, 9], "default": [1, 7, 8, 9, 12, 13], "kneighbor": [1, 9], "queri": [1, 6, 7, 9], "list": [1, 3, 4, 6, 7, 8, 9, 12, 14], "comput": [1, 3, 7, 8, 9, 12], "minkowski": [1, 6, 9], "euclidean": [1, 9], "regressor": [1, 6, 8, 9, 11], "kneighborsregressorparametersn_neighbor": [1, 9], "logist": [1, 9], "rather": [1, 3, 6, 7, 8, 9], "than": [1, 3, 6, 7, 8, 9], "also": [1, 3, 6, 7, 8, 9, 12], "known": [1, 3, 6, 7, 8, 9], "literatur": [1, 9], "logit": [1, 9], "entropi": [1, 7, 9], "maxent": [1, 9], "log": [1, 4, 9, 10, 11, 12, 14], "probabl": [1, 4, 7, 9], "describ": [1, 3, 6, 8, 9, 12], "possibl": [1, 6, 7, 9, 12, 13], "outcom": [1, 9], "singl": [1, 6, 9], "solver": [1, 9, 11], "c": [1, 3, 6, 7, 8, 9, 11], "logisticregressionparametersparameterc": [1, 9], "try": [1, 6, 7, 9], "sag": [1, 9], "saga": [1, 9], "fast": [1, 6, 9], "converg": [1, 6, 9], "guarante": [1, 9], "approxim": [1, 6, 9], "scale": [1, 3, 7, 8, 9, 12, 14], "preprocess": [1, 4, 8, 9, 10, 13, 14], "scaler": [1, 3, 8, 9], "invers": [1, 9], "posit": [1, 3, 6, 8, 9], "like": [1, 3, 6, 7, 8, 9], "support": [1, 6, 8, 9], "vector": [1, 3, 6, 8, 9, 12, 14], "smaller": [1, 6, 9], "stronger": [1, 9], "decomposit": [1, 9], "partial": [1, 6, 9], "form": [1, 3, 6, 7, 8, 9, 12], "compon": [1, 3, 6, 8, 9], "fundament": [1, 9], "relat": [1, 3, 6, 7, 8, 9], "matric": [1, 9], "thei": [1, 3, 6, 7, 8, 9], "latent": [1, 9], "variabl": [1, 6, 7, 9], "approach": [1, 3, 6, 7, 8, 9], "covari": [1, 4, 8, 9], "space": [1, 7, 9, 12, 13], "multidimension": [1, 9], "varianc": [1, 6, 7, 9], "other": [1, 6, 7, 9, 12], "word": [1, 6, 9], "both": [1, 6, 7, 9], "lower": [1, 6, 9], "dimension": [1, 9], "subspac": [1, 6, 8, 9], "transform": [1, 4, 8, 9, 10], "n_compon": [1, 9, 11], "ncompon": [1, 9], "keep": [1, 6, 7, 9, 12], "min": [1, 6, 7, 9, 12], "n_sampl": [1, 9], "n_featur": [1, 9], "n_target": [1, 9], "forest": [1, 4, 7, 9], "decis": [1, 6, 7, 9, 12, 14], "tree": [1, 6, 9], "variou": [1, 6, 8, 9], "sub": [1, 6, 9], "averag": [1, 3, 6, 7, 8, 9, 12], "improv": [1, 3, 6, 8, 9], "accuraci": [1, 6, 9], "over": [1, 6, 9], "randomforestclassifierparametersmaxdepth": [1, 9], "randomforestclassifierparametersnestim": [1, 6, 9], "depth": [1, 6, 9, 11], "considerwhen": [1, 9], "split": [1, 4, 8, 9, 12, 13, 14], "thenconsid": [1, 9], "sqrt": [1, 6, 7, 9], "log2": [1, 7, 9, 12, 14], "randomforestregressorparametersmaxdepth": [1, 9], "randomforestregressorparametersnestim": [1, 9], "l2": [1, 9], "loss": [1, 3, 6, 8, 9], "norm": [1, 7, 9], "tikhonov": [1, 9], "base": [1, 3, 4, 6, 8, 9, 10, 11, 12, 13, 14], "libsvm": [1, 9], "quadrat": [1, 9], "impract": [1, 9], "beyond": [1, 9], "ten": [1, 9], "thousand": [1, 9], "svcparametersparameterc": [1, 9], "1e": [1, 9], "gamma": [1, 9, 11], "0001": [1, 9], "proport": [1, 6, 9], "strictli": [1, 9], "penalti": [1, 9], "kernel": [1, 9], "epsilon": [1, 9], "complex": [1, 6, 9], "hard": [1, 3, 8, 9], "coupl": [1, 9], "10000": [1, 9], "svrparametersparameterc": [1, 9], "svrparametersgamma": [1, 9], "maxdepth": [1, 9], "nestim": [1, 9], "learningr": [1, 9], "xgboost": [1, 9, 11], "gradient": [1, 9], "stand": [1, 9], "extrem": [1, 6, 9], "paper": [1, 3, 6, 8, 9], "greedi": [1, 9], "friedman": [1, 9], "learner": [1, 9], "round": [1, 6, 7, 9], "prf": [1, 4, 7, 9], "probabilist": [1, 4, 9], "seen": [1, 6, 7, 9], "hybrid": [1, 6, 9], "similar": [1, 3, 6, 7, 8, 9, 12, 13], "take": [1, 3, 6, 7, 8, 9, 12], "real": [1, 6, 7, 9, 12, 13], "threshold": [1, 3, 4, 6, 8, 9, 12, 13, 14], "represent": [1, 3, 4, 8, 9], "ptr": [1, 4, 6, 9, 12], "howev": [1, 3, 6, 7, 8, 9], "belong": [1, 3, 6, 7, 8, 9], "inact": [1, 6, 7, 9, 12, 14], "use_py_gini": [1, 9, 11], "use_py_leaf": [1, 9, 11], "prfclassifierparametersmaxdepth": [1, 9], "prfclassifierparametersnestim": [1, 9], "min_py_sum_leaf": [1, 9, 11], "prfclassifierparametersminpysumleaf": [1, 9], "gini": [1, 9], "true": [1, 3, 6, 7, 8, 9, 12, 13], "py": [1, 6, 7, 9], "leav": [1, 9], "leaf": [1, 9], "allow": [1, 3, 6, 7, 8, 9], "prune": [1, 6, 9], "propag": [1, 9], "small": [1, 7, 9], "thu": [1, 6, 9], "pth": [1, 9], "scheme": [1, 9], "noisi": [1, 9], "chemprop": [1, 3, 4, 8, 9], "deep": [1, 6, 9], "properti": [1, 3, 6, 7, 8, 9, 10], "network": [1, 3, 6, 8, 9], "messag": [1, 6, 9], "pass": [1, 3, 6, 7, 8, 9, 12], "neural": [1, 6, 8, 9], "d": [1, 3, 6, 8, 9], "mpnn": [1, 9], "encod": [1, 9], "graph": [1, 3, 6, 8, 9], "feed": [1, 9], "ffnn": [1, 9], "multi": [1, 3, 8, 9], "layer": [1, 3, 6, 8, 9], "perceptron": [1, 9], "wa": [1, 3, 6, 7, 8, 9], "present": [1, 6, 7, 9], "analyz": [1, 6, 9], "optuna": [1, 4, 6, 8, 9, 10, 11], "optims": [1, 9], "hyperopt": [1, 9], "ensemble_s": [1, 6, 9, 11], "epoch": [1, 6, 9, 11], "aggreg": [1, 6, 7, 9, 11, 12, 13], "aggregation_norm": [1, 6, 9, 11], "chempropparametersaggregation_norm": [1, 9], "200": [1, 6, 9], "q": [1, 3, 6, 8, 9, 11], "batch_siz": [1, 6, 9, 11], "chempropparametersbatch_s": [1, 9], "chempropparametersdepth": [1, 9], "6": [1, 6, 7, 9], "dropout": [1, 9, 11], "chempropparametersdropout": [1, 9], "4": [1, 3, 6, 7, 8, 9, 12, 13], "04": [1, 6, 9], "features_gener": [1, 6, 9, 11], "ffn_hidden_s": [1, 6, 9, 11], "chempropparametersffn_hidden_s": [1, 9], "300": [1, 6, 9], "2400": [1, 9], "ffn_num_lay": [1, 6, 9, 11], "chempropparametersffn_num_lay": [1, 9], "final_lr_ratio_exp": [1, 6, 9, 11], "chempropparametersfinal_lr_ratio_exp": [1, 9], "hidden_s": [1, 6, 9, 11], "chempropparametershidden_s": [1, 9], "init_lr_ratio_exp": [1, 6, 9, 11], "chempropparametersinit_lr_ratio_exp": [1, 9], "max_lr_exp": [1, 6, 9, 11], "chempropparametersmax_lr_exp": [1, 9], "warmup_epochs_ratio": [1, 6, 9, 11], "chempropparameterswarmup_epochs_ratio": [1, 9], "ensembl": [1, 9, 11], "initialis": [1, 6, 9], "provid": [1, 3, 6, 7, 8, 9, 12], "size": [1, 3, 6, 7, 8, 9], "run": [1, 3, 4, 7, 8, 9, 10], "increas": [1, 6, 7, 9, 12, 13], "400": [1, 9], "sum": [1, 6, 9], "atom": [1, 3, 6, 8, 9, 12, 13], "divid": [1, 6, 9], "up": [1, 3, 6, 8, 9, 10], "batch": [1, 9, 12], "step": [1, 7, 8, 9], "visibl": [1, 9], "randomli": [1, 6, 7, 9], "some": [1, 3, 6, 7, 8, 9], "element": [1, 9, 12, 13], "tensor": [1, 9], "p": [1, 3, 8, 9], "bernoulli": [1, 9], "distribut": [1, 6, 7, 9], "channel": [1, 9], "independ": [1, 7, 9], "everi": [1, 6, 9], "proven": [1, 9], "techniqu": [1, 7, 9], "prevent": [1, 6, 9], "co": [1, 7, 9], "adapt": [1, 3, 8, 9], "neuron": [1, 9], "hidden": [1, 6, 9], "ffn": [1, 6, 9], "exponenti": [1, 7, 9], "rate": [1, 9], "bond": [1, 3, 8, 9], "ratio": [1, 9], "linearli": [1, 9], "init_lr": [1, 9], "max_lr": [1, 9], "afterward": [1, 7, 9], "decreas": [1, 7, 9], "final_lr": [1, 9], "without": [1, 6, 9, 12], "within": [1, 3, 8, 9, 12, 13], "hyperparamet": [1, 4, 6, 8, 9], "side": [1, 3, 8, 9], "inform": [1, 3, 8, 9, 10], "nb": [1, 3, 6, 7, 8, 9], "quick": [1, 4, 9], "simpl": [1, 7, 9], "sensibl": [1, 6, 7, 8, 9], "author": [1, 6, 8, 9], "do": [1, 6, 7, 9, 12], "num_it": [1, 6, 9, 11], "search_parameter_level": [1, 6, 9, 11], "dictat": [1, 9], "larger": [1, 3, 6, 7, 8, 9], "pretrin": [1, 9], "pretrain": [1, 6, 9], "carri": [1, 9], "previous": [1, 9], "qsartuna": [1, 9], "chempropparametersepoch": [1, 6, 9], "frzn": [1, 9, 11], "pretrained_model": [1, 6, 9, 11], "none": [1, 3, 6, 8, 9, 10, 12, 13, 14], "fine": [1, 9], "tune": [1, 3, 4, 6, 8, 9], "decid": [1, 9], "freez": [1, 9], "transfer": [1, 9], "frozen": [1, 9], "str": [1, 3, 6, 8, 9, 10, 11, 12, 13, 14], "calibr": [1, 4, 8, 9], "isoton": [1, 6, 9], "vennab": [1, 9], "cv": [1, 6, 9], "With": [1, 3, 8, 9], "across": [1, 6, 7, 9, 12], "fals": [1, 3, 6, 7, 8, 9, 12], "obtain": [1, 6, 7, 9], "unbias": [1, 9], "offer": [1, 3, 6, 8, 9], "p0": [1, 6, 9], "vs": [1, 6, 7, 9], "p1": [1, 6, 9], "discord": [1, 6, 9], "type": [1, 3, 6, 7, 8, 9, 12], "union": [1, 3, 8, 9], "calibratedclassifiercvensembl": [1, 9], "calibratedclassifiercvmethod": [1, 9], "n_fold": [1, 6, 9, 11], "whether": [1, 3, 7, 8, 9, 12, 14], "agnost": [1, 6, 9], "interv": [1, 6, 9], "encompass": [1, 9], "aleator": [1, 9], "epistem": [1, 9], "back": [1, 6, 9], "strong": [1, 9], "theoret": [1, 6, 9], "thank": [1, 9], "conform": [1, 9], "mapie_alpha": [1, 6, 9, 11], "05": [1, 6, 7, 9], "01": [1, 6, 9], "99": [1, 6, 9], "see": [3, 6, 7, 8, 9, 12, 13], "gedeck": [3, 8], "et": [3, 7, 8], "al": [3, 7, 8], "qsar": [3, 4, 6, 7, 8], "good": [3, 6, 7, 8], "practic": [3, 8], "fingerprint": [3, 8, 9], "wai": [3, 6, 7, 8], "daylight": [3, 8], "enumer": [3, 6, 8, 9], "custom": [3, 6, 8], "ref": [3, 8, 10], "16": [3, 6, 7, 8], "hash": [3, 6, 8, 9, 10], "code": [3, 6, 7, 8], "style": [3, 6, 7, 8], "implicitli": [3, 8], "largest": [3, 6, 8], "refer": [3, 6, 8, 10, 11], "toward": [3, 6, 7, 8], "binari": [3, 6, 8, 9], "extend": [3, 6, 7, 8], "connect": [3, 6, 8], "roger": [3, 8], "circular": [3, 8], "morgan": [3, 8, 9], "invari": [3, 8], "getmorganfingerprintasbitvect": [3, 8], "rdkit": [3, 6, 7, 8, 9], "systemat": [3, 8], "record": [3, 6, 7, 8], "neighborhood": [3, 8, 9], "h": [3, 6, 7, 8], "multipl": [3, 6, 8, 12, 13], "runtim": [3, 8], "substructur": [3, 6, 8], "map": [3, 6, 7, 8], "integ": [3, 7, 8, 12, 13], "length": [3, 6, 8], "identifi": [3, 6, 7, 8], "diamet": [3, 8], "append": [3, 6, 7, 8, 9], "ecfp4": [3, 8], "correspond": [3, 6, 7, 8, 9], "returnrdkit": [3, 6, 8], "consid": [3, 6, 8, 12, 13], "while": [3, 6, 7, 8, 12], "bit": [3, 6, 8], "sometim": [3, 6, 7, 8], "bool": [3, 8, 9, 12, 13], "calculate_from_mol": [3, 8], "mol": [3, 6, 7, 8], "return": [3, 6, 7, 8, 10, 11, 12, 13], "numpi": [3, 6, 7, 8, 12, 13], "arrai": [3, 6, 8, 12, 13], "count": [3, 6, 8, 9], "gethashedmorganfingerprint": [3, 8], "appear": [3, 8, 11], "usefeatur": [3, 6, 8, 11], "fcfp": [3, 8], "normal": [3, 6, 7, 8, 9], "ones": [3, 6, 8], "definit": [3, 8, 12], "gobbi": [3, 8], "popping": [3, 8], "biotechnolog": [3, 8], "bioengin": [3, 8], "61": [3, 6, 8], "47": [3, 6, 8], "54": [3, 6, 8], "1998": [3, 6, 8], "lead": [3, 7, 8], "score": [3, 4, 8, 9, 10, 12, 14], "fp": [3, 6, 8], "maxpath": [3, 6, 8, 11], "fpsize": [3, 6, 8, 11], "macc": [3, 6, 8], "system": [3, 7, 8], "often": [3, 6, 8], "mdl": [3, 8], "kei": [3, 6, 7, 8, 10, 11], "compani": [3, 8], "calcul": [3, 6, 8, 12, 13, 14], "keyset": [3, 8], "construct": [3, 8, 11], "optim": [3, 4, 7, 8, 9, 11], "durant": [3, 8], "reoptim": [3, 8], "drug": [3, 8], "discoveri": [3, 8], "166": [3, 6, 8], "2d": [3, 8, 9], "essenti": [3, 7, 8], "answer": [3, 8], "fragment": [3, 8], "question": [3, 8], "explicitli": [3, 6, 7, 8], "exist": [3, 8], "sens": [3, 8], "matter": [3, 8], "becaus": [3, 6, 7, 8], "address": [3, 8], "specif": [3, 6, 7, 8, 11], "repres": [3, 6, 7, 8], "9": [3, 6, 7, 8], "1049": [3, 8], "distinct": [3, 6, 7, 8, 9], "rdkit_nam": [3, 6, 8, 11], "unscal": [3, 8], "These": [3, 6, 7, 8, 12], "physchem": [3, 6, 8], "caution": [3, 7, 8], "208": [3, 6, 8], "includ": [3, 6, 7, 8], "clogp": [3, 6, 8], "mw": [3, 6, 8], "ring": [3, 7, 8], "rotat": [3, 8], "fraction": [3, 6, 7, 8, 12, 13], "sp3": [3, 8], "kier": [3, 8], "indic": [3, 6, 7, 8, 12, 13], "etc": [3, 6, 8], "tpsa": [3, 6, 8], "slogp": [3, 8], "group": [3, 7, 8, 12, 13], "vsa": [3, 8], "moe": [3, 8], "charg": [3, 8], "www": [3, 8], "org": [3, 6, 8], "doc": [3, 6, 8], "gettingstartedinpython": [3, 8], "html": [3, 6, 7, 8, 9], "whose": [3, 8], "been": [3, 6, 7, 8], "level": [3, 6, 7, 8, 9], "One": [3, 7, 8], "advantag": [3, 8], "interpret": [3, 8], "mean": [3, 6, 7, 8, 9, 12], "physicochem": [3, 8], "intuit": [3, 8], "understood": [3, 8], "option": [3, 4, 7, 8, 9, 11, 12, 13, 14], "jazzy_nam": [3, 6, 8, 11], "jazzy_filt": [3, 6, 8], "jazzi": [3, 8], "hydrat": [3, 8], "energi": [3, 8], "hydrogen": [3, 8], "acceptor": [3, 6, 8], "donor": [3, 6, 8], "found": [3, 6, 8], "doi": [3, 6, 8], "1038": [3, 8], "s41598": [3, 8], "023": [3, 8], "30089": [3, 8], "mmff94": [3, 8], "minimis": [3, 8], "1000da": [3, 8], "compound": [3, 6, 7, 8, 12, 13], "dict": [3, 8, 9, 10, 11], "calculate_from_smi": [3, 6, 8], "smi": [3, 8, 10], "string": [3, 6, 7, 8, 11, 12, 13, 14], "ndarrai": [3, 8], "z": [3, 8, 12, 14], "peptid": [3, 6, 8, 12, 14], "unfittedsklearnscal": [3, 8], "mol_data": [3, 8], "moldata": [3, 8], "file_path": [3, 8], "smiles_column": [3, 8], "fittedsklearnscal": [3, 8], "alia": [3, 8, 9], "precomput": [3, 7, 8], "file": [3, 7, 8, 10, 11, 12, 13], "header": [3, 8], "line": [3, 4, 6, 7, 8, 10], "row": [3, 6, 7, 8], "comma": [3, 6, 7, 8], "respons": [3, 7, 8], "pre": [3, 7, 8], "zscalesdescriptor": [3, 8, 11], "were": [3, 6, 7, 8], "propos": [3, 8], "sandberg": [3, 8], "proteogen": [3, 8], "amino": [3, 6, 8], "acid": [3, 6, 8], "nmr": [3, 8], "thin": [3, 8], "chromatographi": [3, 8], "tlc": [3, 8], "1021": [3, 6, 8], "jm9700575": [3, 8], "captur": [3, 6, 7, 8], "lipophil": [3, 8], "steric": [3, 8], "bulk": [3, 8], "polariz": [3, 8], "electron": [3, 8], "polar": [3, 8], "electroneg": [3, 8], "heat": [3, 8], "electrophil": [3, 8], "anoth": [3, 6, 8], "optimis": [3, 6, 8, 9, 10], "either": [3, 7, 8, 9], "through": [3, 6, 8], "_and_": [3, 8], "auxiliari": [3, 6, 8, 12, 14], "continu": [3, 6, 8], "learnt": [3, 6, 8], "manner": [3, 6, 8], "intent": [3, 6, 8], "much": [3, 8], "remain": [3, 7, 8, 12], "deriv": [3, 6, 7, 8], "cautiou": [3, 8], "upload": [3, 8], "_all_": [3, 8], "ruder": [3, 8], "io": [3, 6, 8, 9], "index": [3, 6, 7, 8], "auxiliarytask": [3, 8], "aux_weight_pc": [3, 6, 8, 9, 11], "20": [3, 6, 7, 8], "info": [3, 6, 8], "percentag": [3, 8], "wrap": [3, 6, 8], "certain": [3, 6, 7, 8], "rang": [3, 6, 7, 8, 12, 13], "scaleddescriptorparamet": [3, 8], "cach": [3, 6, 7, 8, 9], "composit": [3, 6, 8], "concaten": [3, 8], "button": [3, 8], "pleas": [3, 6, 7, 8, 10], "compat": [3, 6, 8], "intro": 4, "background": 4, "json": [4, 6, 9, 11], "command": [4, 6], "interfac": [4, 6, 8, 11, 12], "python": [4, 6, 8, 12], "jupyt": [4, 6], "notebook": [4, 6], "introduct": 4, "translat": [4, 6], "sdf": [4, 6, 8], "need": 4, "deal": [4, 12], "duplic": [4, 8, 9, 12], "dedupl": [4, 6, 8, 10], "experiment": [4, 6, 12, 14], "error": [4, 6], "cli": 4, "tutori": 4, "remov": [4, 7, 8, 9, 12, 13], "advanc": [4, 7, 8], "functoinail": 4, "adaboostclassifi": [4, 6, 9, 11], "kneighborsclassifi": [4, 6, 9, 11], "kneighborsregressor": [4, 6, 9, 11], "logisticregress": [4, 6, 9, 11], "plsregress": [4, 6, 9, 11], "randomforestclassifi": [4, 6, 9, 11], "svc": [4, 6, 9, 11], "prfclassifi": [4, 6, 9, 11], "chempropregressor": [4, 6, 9, 11], "chempropclassifi": [4, 6, 9, 11], "chemprophyperoptclassifi": [4, 6, 9, 11], "chemprophyperoptregressor": [4, 6, 9, 11], "chempropregressorpretrain": [4, 6, 9], "calibratedclassifiercvwithva": [4, 6, 9, 11], "mapi": [4, 9, 11], "avalon": [4, 8, 9, 11], "pathfp": [4, 6, 8, 11], "unscaledphyschemdescriptor": [4, 6, 8, 11], "unscaledjazzydescriptor": [4, 6, 8, 11], "unscaledzscalesdescriptor": [4, 8, 11], "physchemdescriptor": [4, 8, 11], "jazzydescriptor": [4, 8, 11], "precomputeddescriptorfromfil": [4, 6, 8, 11], "zscale": [4, 6, 8, 12], "smilesfromfil": [4, 6, 8, 11], "smilesandsideinfofromfil": [4, 6, 8, 11], "scaleddescriptor": [4, 8, 11], "compositedescriptor": [4, 6, 8, 11], "tempor": [4, 6, 12], "stratifi": [4, 6, 12], "scaffoldsplit": [4, 7, 12], "modeldatatransform": [4, 6, 7, 8, 12], "vectorfromcolumn": [4, 6, 8, 12], "keepfirst": [4, 7, 12], "keeplast": [4, 7, 12], "keeprandom": [4, 7, 12], "keepmin": [4, 7, 12], "keepmax": [4, 7, 12], "keepavg": [4, 7, 12], "keepmedian": [4, 6, 7, 12], "keepkeepallnodedupl": 4, "report": [4, 6, 7], "coverag": 4, "subpackag": 5, "submodul": 5, "build_from_opt": [5, 8], "content": 5, "util": [5, 6, 7, 8, 13, 14], "files_path": [5, 8], "load_json": [5, 8], "schema": [5, 8, 11], "builder": 5, "metirc": 5, "model_writ": 5, "optbuild": 5, "schemagen": 5, "visual": [5, 9, 11], "intend": 6, "necessari": 6, "gui": 6, "autom": [6, 7], "reinvent": 6, "varieti": 6, "them": [6, 7, 9], "so": [6, 7, 9], "hyper": [6, 9], "influenc": [6, 7, 9], "automat": [6, 7], "idea": [6, 7], "read": [6, 7, 8], "otherwis": [6, 12], "might": [6, 7, 12], "skip": [6, 7], "toi": 6, "chosen": 6, "whole": [6, 7], "less": [6, 7], "minut": 6, "holdout": [6, 7], "readi": 6, "next": [6, 7], "few": [6, 7], "head": [6, 7], "molwt_gt_330": 6, "cc1cc": 6, "nc": [6, 7], "o": [6, 7], "c2cccc": 6, "coc3ccc": 6, "br": [6, 7], "cc3": [6, 7], "c2": [6, 7], "no1": 6, "387": 6, "233": 6, "nc1ccc": 6, "f": [6, 7, 12], "cc1f": 6, "nc1sccc1": 6, "c1nc2ccccc2s1": 6, "4360000000001": 6, "coc": 6, "c1ccccc1nc": 6, "c1cc": 6, "nn1cc1ccccc1": 6, "380": 6, "36000000000007": 6, "ccoc": 6, "sc1nc": 6, "c2ccccc2": 6, "ccc1c": 6, "312": 6, "39400000000006": 6, "ccc": [6, 7], "c1nn": [6, 7], "cc2ccccc2": 6, "c2ccccc12": 6, "349": 6, "4340000000001": 6, "brc1ccccc1occcoc1cccc2cccnc12": 6, "358": 6, "235": 6, "ccccn1c": 6, "coc2cccc": 6, "oc": 6, "nc2ccccc21": 6, "310": 6, "39700000000005": 6, "ccoc1cccc": 6, "c2sc3nc": 6, "c4ccc": 6, "cc4": 6, "ccc3c2n": 6, "c1": [6, 7], "407": 6, "4700000000001": 6, "coc1ccc": 6, "nc2ccc": 6, "cc2": 6, "c2ccc": 6, "cc1oc": 6, "454": 6, "54800000000023": 6, "sy": [6, 7], "sklearn": [6, 11], "kljk345": [6, 7], "pycharmproject": 6, "public_qptuna": 6, "lib": [6, 7], "python3": [6, 7], "site": [6, 7], "tqdm": 6, "21": [6, 7], "tqdmwarn": 6, "iprogress": 6, "updat": [6, 7], "ipywidget": 6, "readthedoc": [6, 9], "en": [6, 9], "stabl": [6, 8], "user_instal": 6, "autonotebook": 6, "notebook_tqdm": 6, "typic": [6, 7], "test_dataset_fil": [6, 8], "random_se": [6, 9], "42": [6, 7, 12, 13], "seed": [6, 7, 8, 12, 13], "reproduc": [6, 12, 14], "setup": [6, 9], "basic": [6, 8, 9], "importlib": 6, "reload": 6, "basicconfig": 6, "getlogg": 6, "disabl": [6, 7, 11], "np": [6, 7], "seterr": 6, "ignor": 6, "warn": [6, 7], "filterwarn": 6, "categori": 6, "futurewarn": 6, "runtimewarn": 6, "functool": 6, "partialmethod": 6, "__init__": [6, 9], "flood": 6, "decpreci": 6, "simplefilt": 6, "def": [6, 7, 9], "arg": [6, 8, 9], "kwarg": [6, 9], "stderr": 6, "render": [6, 7], "red": 6, "2024": 6, "07": 6, "02": 6, "13": [6, 7], "17": [6, 7], "26": [6, 7], "561": 6, "memori": [6, 8], "714": 6, "study_name_0": 6, "27": [6, 7], "022": 6, "finish": 6, "3594": 6, "2228073972638": 6, "39": [6, 7], "algorithm_nam": [6, 11], "randomforestregressor_algorithm_hash": 6, "f1ac01e1bba332215ccbd0c29c9ac3c3": 6, "max_depth__f1ac01e1bba332215ccbd0c29c9ac3c3": 6, "n_estimators__f1ac01e1bba332215ccbd0c29c9ac3c3": 6, "max_features__f1ac01e1bba332215ccbd0c29c9ac3c3": 6, "lt": [6, 7], "randomforestmaxfeatur": [6, 9], "gt": [6, 7], "34": [6, 7], "171": 6, "5029": 6, "734616310275": 6, "svr_algorithm_hash": 6, "ea7ccc7ef4a9329af0d4e39eb6184933": 6, "gamma__ea7ccc7ef4a9329af0d4e39eb6184933": 6, "039054412752107935": 6, "c__ea7ccc7ef4a9329af0d4e39eb6184933": 6, "1242780840717016e": 6, "429": 6, "4242": 6, "092751193529": 6, "579": 6, "3393": 6, "577488426015": 6, "ridge_algorithm_hash": 6, "cfa1990d5153c8812982f034d788d7e": 6, "alpha__cfa1990d5153c8812982f034d788d7e": 6, "06877704223043679": 6, "644": 6, "427": 6, "45250420148204": 6, "lasso_algorithm_hash": 6, "5457f609662e44f04dcc9423066d2f58": 6, "alpha__5457f609662e44f04dcc9423066d2f58": 6, "7896547008552977": 6, "698": 6, "3387": 6, "245629616474": 6, "plsregression_algorithm_hash": 6, "9f2f76e479633c0bf18cf2912fed9eda": 6, "n_components__9f2f76e479633c0bf18cf2912fed9eda": 6, "853": 6, "734620250011": 6, "3661540064603184": 6, "1799882524170321": 6, "28": [6, 7], "029": 6, "7": [6, 7, 9], "9650": 6, "026568221794": 6, "kneighborsregressor_algorithm_hash": 6, "1709d2c39117ae29f6c9debe7241287b": 6, "metric__1709d2c39117ae29f6c9debe7241287b": 6, "kneighborsmetr": [6, 9], "n_neighbors__1709d2c39117ae29f6c9debe7241287b": 6, "weights__1709d2c39117ae29f6c9debe7241287b": 6, "kneighborsweight": [6, 9], "uniform": [6, 9], "070": 6, "8": [6, 7, 9], "5437": 6, "151635569594": 6, "05083825348819038": 6, "336": 6, "2669": 6, "8534551928174": 6, "373": 6, "4341": 6, "586120152291": 6, "7921825998469865": 6, "532": 6, "11": [6, 7], "5514": 6, "404088878843": 6, "680": 6, "12": [6, 7], "5431": 6, "634989239215": 6, "722": 6, "3530": 6, "5496618991288": 6, "765": 6, "14": [6, 7], "3497": 6, "6833185436312": 6, "793": 6, "15": [6, 7], "4382": 6, "16208862162": 6, "831": 6, "734620031822": 6, "002825619931800395": 6, "309885135051862e": 6, "09": 6, "870": 6, "679": 6, "3109044887755": 6, "16827992999009767": 6, "932": 6, "18": [6, 7], "2550": 6, "114129318373": 6, "974": 6, "19": [6, 7], "4847": 6, "085792360169": 6, "735431606118867": 6, "29": 6, "016": 6, "268760278916": 6, "0014840820994557746": 6, "04671166881768783": 6, "096": 6, "4783": 6, "0470154796785": 6, "135": 6, "22": [6, 7], "3905": 6, "0064899852296": 6, "259": 6, "23": [6, 7], "4030": 6, "45773791647": 6, "340": 6, "24": [6, 7], "4681": 6, "602145939593": 6, "381": 6, "25": [6, 7], "4398": 6, "544034028325": 6, "6452011213193165": 6, "474": 6, "4454": 6, "143979828408": 6, "503": 6, "533": 6, "600": 6, "4397": 6, "330360587512": 6, "617": 6, "682": 6, "31": [6, 7], "2602": 6, "7561184287083": 6, "715": 6, "5267": 6, "388279961089": 6, "2015560027548533": 6, "794": 6, "33": 6, "4863": 6, "581760751052": 6, "836": 6, "388": 6, "96473594016675": 6, "5528259214839937": 6, "906": 6, "35": 6, "5539": 6, "698232987626": 6, "6400992020612235": 6, "962": 6, "36": 6, "5180": 6, "5533034102455": 6, "8968910439566395": 6, "005": 6, "37": 6, "4989": 6, "929984864281": 6, "04458440839692226": 6, "492108041427977": 6, "034": 6, "38": [6, 7], "103": 6, "6528": 6, "215066535042": 6, "16700143339733753": 6, "240": 6, "40": [6, 7], "4168": 6, "7955967552625": 6, "311": 6, "41": 6, "6177": 6, "060727800014": 6, "401": 6, "3963": 6, "906954658343": 6, "435": 6, "43": 6, "6805334166565": 6, "013186009009851564": 6, "001008958590140135": 6, "501": 6, "44": 6, "9300": 6, "86840721566": 6, "547": 6, "45": [6, 7], "83": 6, "87968210939489": 6, "382674443425525e": 6, "565": 6, "46": 6, "594": 6, "626": 6, "48": 6, "717": 6, "49": 6, "3660": 6, "9359502556": 6, "767": 6, "688": 6, "5244070398325": 6, "5267860995545326": 6, "813": 6, "51": 6, "690": 6, "6494438072099": 6, "8458809314722497": 6, "848": 6, "52": 6, "691": 6, "1197058420935": 6, "9167866889210807": 6, "898": 6, "53": 6, "3111710449325": 6, "945685900574672": 6, "934": 6, "9665592812149": 6, "8936837761725833": 6, "970": 6, "55": 6, "4682747008223": 6, "5183865279530455": 6, "030": 6, "56": 6, "687": 6, "5230947231512": 6, "3771771681361766": 6, "078": 6, "57": 6, "4503442069594": 6, "3663259819415374": 6, "127": 6, "58": 6, "686": 6, "9553733616618": 6, "2925652230875628": 6, "174": 6, "59": 6, "370": 6, "2038330506566": 6, "3962903248948568": 6, "222": 6, "60": 6, "377": 6, "25988028857313": 6, "45237513161879": 6, "270": 6, "379": 6, "8933285317637": 6, "4741161933311207": 6, "319": 6, "62": 6, "374": 6, "50897467366013": 6, "4290962207409417": 6, "356": 6, "63": [6, 7], "376": 6, "5588572940058": 6, "4464295711264585": 6, "416": 6, "64": 6, "237448916406": 6, "4687500034684213": 6, "65": 6, "375": 6, "7474776359051": 6, "4395650011783436": 6, "504": 6, "66": 6, "362": 6, "2834906299732": 6, "3326755354190032": 6, "542": 6, "67": 6, "357": 6, "3474880122588": 6, "2887212943233457": 6, "591": 6, "68": 6, "354": 6, "279045046449": 6, "2577677164664005": 6, "642": 6, "69": 6, "347": 6, "36894395697703": 6, "1672928587680225": 6, "706": 6, "70": 6, "345": 6, "17697390093394": 6, "1242367255308854": 6, "757": 6, "71": 6, "74610809299037": 6, "1728352983905301": 6, "807": 6, "72": 6, "23464281634324": 6, "1265380781508565": 6, "856": 6, "73": 6, "344": 6, "6848312222365": 6, "0829896313820404": 6, "902": 6, "74": [6, 7], "9111966504334": 6, "1070414661080543": 6, "966": 6, "75": 6, "70116419828565": 6, "0875643695329498": 6, "026": 6, "76": 6, "62647974688133": 6, "0716281620790837": 6, "089": 6, "77": 6, "6759429204596": 6, "0456289319914898": 6, "141": 6, "78": 6, "343": 6, "58131497761616": 6, "0010195360522613": 6, "193": 6, "79": 6, "342": 6, "7290581014813": 6, "9073210715005748": 6, "254": 6, "80": [6, 7], "67866114080107": 6, "9166305667100072": 6, "317": 6, "81": 6, "6440308445311": 6, "9248722692093634": 6, "367": 6, "82": 6, "02085648448934": 6, "8776928646870886": 6, "1662266300702": 6, "867592364677856": 6, "457": 6, "84": 6, "30158716569775": 6, "8599491178327108": 6, "497": 6, "85": 6, "2803074848341": 6, "8396948389352923": 6, "86": 6, "28301101884045": 6, "8396651775801683": 6, "587": 6, "87": 6, "6781906268143": 6, "8356021935129933": 6, "639": 6, "88": 6, "0405418264898": 6, "7430046191126949": 6, "677": 6, "89": 6, "77203208258476": 6, "9015965341429055": 6, "90": 6, "363": 6, "1622720320929": 6, "6746575663752555": 6, "91": 6, "7403796626193": 6, "9057564666836629": 6, "797": 6, "92": 6, "63579667712696": 6, "9332275205203372": 6, "93": [6, 7], "6886425884964": 6, "9433063264508291": 6, "94": 6, "9341048659705": 6, "884739221967487": 6, "935": 6, "95": [6, 7], "63507445779743": 6, "9381000493689634": 6, "986": 6, "96": 6, "06021011302374": 6, "963138023068903": 6, "97": 6, "9990546212019": 6, "9601651093867907": 6, "066": 6, "98": 6, "3821": 6, "2267845437514": 6, "117": 6, "6786067133016": 6, "721603508336166": 6, "seaborn": [6, 7], "sn": [6, 7], "set_them": 6, "darkgrid": 6, "default_reg_scor": 6, "ax": [6, 7], "scatterplot": 6, "trials_datafram": 6, "xlabel": [6, 7], "ylabel": [6, 7], "ojbect": 6, "interest": [6, 7], "neg_mean_squared_error": [6, 9], "highlight": 6, "color": [6, 7], "cv_test": 6, "user_attrs_test_scor": 6, "lambda": [6, 12], "item": [6, 10], "idx": [6, 7], "v": 6, "hue": 6, "palett": 6, "set1": 6, "inspect": 6, "apischema": [6, 8], "buildconfig_as_dict": 6, "serial": 6, "response_typ": [6, 7, 8], "deduplication_strategi": [6, 7, 8], "split_strategi": [6, 7, 8], "nosplit": [6, 12], "save_intermediate_fil": [6, 8], "log_transform": [6, 7, 8], "log_transform_bas": [6, 7, 8], "null": 6, "log_transform_neg": [6, 7, 8], "log_transform_unit_convers": [6, 7, 8], "probabilistic_threshold_represent": [6, 7, 8], "probabilistic_threshold_representation_threshold": [6, 7, 8], "probabilistic_threshold_representation_std": [6, 7, 8], "metadata": [6, 8, 9, 10, 11], "shuffl": [6, 9, 11, 12, 13], "best_trial": [6, 9, 11], "best_valu": [6, 9, 11], "tracking_rest_endpoint": [6, 9], "best_build": 6, "rb": 6, "predict_from_smil": [6, 8], "cc1": [6, 7], "43103985": 6, "177": 6, "99850936": 6, "now": [6, 7, 9], "panda": [6, 7], "pd": [6, 7], "df": [6, 12, 13], "read_csv": 6, "expect": [6, 7, 10], "matplotlib": [6, 7], "pyplot": [6, 7], "plt": [6, 7], "scatter": 6, "lim": 6, "max": [6, 7, 12], "diagon": 6, "r2_score": 6, "mean_squared_error": 6, "mean_absolute_error": 6, "y_true": [6, 8, 11], "y_pred": [6, 8, 11], "rmse": 6, "ad": [6, 7, 12, 13], "mae": 6, "absolut": 6, "8566354978126369": 6, "204909888075044": 6, "298453946973815": 6, "accept": [6, 7], "again": 6, "hopefulli": [6, 7], "littl": 6, "better": [6, 7, 8, 12], "send": 6, "strategi": [6, 8], "current": 6, "observ": [6, 7], "last": [6, 7, 12], "alreadi": [6, 7], "sort": [6, 7, 12, 13], "oldest": [6, 7, 12, 13], "newest": [6, 7, 12, 13], "end": [6, 7, 12, 13], "extern": 6, "tool": 6, "excel": 6, "ensur": [6, 7, 8, 9], "unballanc": 6, "work": [6, 7], "come": [6, 7], "measur": [6, 7], "fact": 6, "disregard": 6, "stereochemistri": [6, 7], "even": [6, 7], "sever": 6, "median": [6, 7, 12], "factor": [6, 7], "replic": [6, 7], "robust": [6, 7], "outlier": [6, 7], "acorss": 6, "trust": 6, "kept": 6, "splitter": [6, 7, 8, 10], "track_to_mlflow": [6, 9], "my_study_stratified_split": 6, "922": 6, "963": 6, "046": 6, "1856": 6, "4459752935309": 6, "123": 6, "1692": 6, "0451328577294": 6, "2918844591266672": 6, "592": 6, "1378": 6, "9731014410709": 6, "471164936778079": 6, "2658": 6, "13214897931": 6, "804": 6, "2059": 6, "3079659969176": 6, "330": [6, 7], "280": 6, "17777558722315": 6, "7001901522391756": 6, "422": 6, "3551": 6, "475476217507": 6, "466": 6, "2124": 6, "9660426577593": 6, "509": 6, "1686": 6, "5737716985532": 6, "9841058851292832": 6, "552": 6, "1702": 6, "174704715547": 6, "861494545249233": 6, "578": 6, "621": 6, "1204": 6, "636967895143": 6, "5238298142840006": 6, "676": 6, "228": 6, "44505332657158": 6, "9836853549192415": 6, "729": 6, "3949": 6, "499774068696": 6, "04535826280986047": 6, "012999584021838e": 6, "829": 6, "2856": 6, "917927507731": 6, "linear_model": 6, "_coordinate_desc": 6, "678": 6, "convergencewarn": 6, "did": 6, "regularis": 6, "dualiti": 6, "gap": 6, "306e": 6, "toler": 6, "824e": 6, "cd_fast": 6, "enet_coordinate_desc": 6, "882": 6, "2554": 6, "2079198900733": 6, "10588223712643852": 6, "1261": 6, "484274761188": 6, "0950442632698256": 6, "965": 6, "282": 6, "6478019258886": 6, "2920636100136971": 6, "004": 6, "1814": 6, "6019641143478": 6, "048": 6, "1284": 6, "7430070920798": 6, "1729012287538991": 6, "237": 6, "98783693000647": 6, "1721667984096773": 6, "192": 6, "2129": 6, "55317061882": 6, "4997740833423": 6, "779895470793612": 6, "260941957410989e": 6, "279": 6, "1740": 6, "8894369939983": 6, "02841448247455669": 6, "698e": 6, "280e": 6, "820e": 6, "352e": 6, "770e": 6, "3317": 6, "417858905051": 6, "003050380617617421": 6, "404": 6, "448": 6, "1256": 6, "7270466276807": 6, "1594144041655936": 6, "491": 6, "1245": 6, "1399766270456": 6, "336730512398918": 6, "583": 6, "2908": 6, "3563960057677": 6, "628": 6, "1775": 6, "55204856041": 6, "721": 6, "1257": 6, "9288888831513": 6, "1441514794000534": 6, "808": 6, "98174313112844": 6, "1939105579414777": 6, "900": 6, "3054": 6, "7066202193805": 6, "944": 6, "1227": 6, "082986184029": 6, "909508127148669": 6, "988": 6, "1676": 6, "7481962719485": 6, "4307837873914335": 6, "079": 6, "307965996918": 6, "168": 6, "3441": 6, "9109103644514": 6, "211": 6, "1670": 6, "5213862925175": 6, "07945856808433427": 6, "264": 6, "2756": 6, "046839500092": 6, "320": 6, "4997735530674": 6, "022099719935614482": 6, "4657380646234507e": 6, "08": 6, "0862402902634642": 6, "12519632281925502": 6, "467": 6, "3438": 6, "566583971217": 6, "524": 6, "4422556954731": 6, "19967589906728334": 6, "016e": 6, "618": 6, "359": [6, 7], "7639743940817": 6, "059252880514551576": 6, "662": 6, "1246": 6, "7813032646238": 6, "3074782262329858": 6, "755": 6, "2224": 6, "3845873049813": 6, "810": 6, "1673": 6, "9639799911165": 6, "2737740844660712": 6, "896": 6, "3163": 6, "129883232068": 6, "987": 6, "2753": 6, "414173913392": 6, "057": 6, "263": 6, "1352845182604": 6, "627030918721665": 6, "105": 6, "271": 6, "2979718788249": 6, "8548903728617034": 6, "165": 6, "277": 6, "86441431259567": 6, "9605867591283856": 6, "227": 6, "4329099850367": 6, "9537398361705693": 6, "274": 6, "3838070241422": 6, "9045589309769144": 6, "334": 6, "260": 6, "4460398258507": 6, "5589021326002044": 6, "383": 6, "257": 6, "95032410206767": 6, "5053759377103249": 6, "444": 6, "256": 6, "5958038666581": 6, "4789082433356577": 6, "495": 6, "253": 6, "4269973575198": 6, "4281024602273042": 6, "560": 6, "249": 6, "40822811603962": 6, "3546313579812586": 6, "620": 6, "245": 6, "71101688809983": 6, "2913960369109012": 6, "675": 6, "247": 6, "88538215472033": 6, "3274897484709072": 6, "737": 6, "244": 6, "23847775159297": 6, "2647865635312279": 6, "803": 6, "59033004585282": 6, "3228443521984092": 6, "863": 6, "243": 6, "40694430653753": 6, "2489205103047292": 6, "928": 6, "223": 6, "85145692792733": 6, "8934822741396387": 6, "990": [6, 7], "221": 6, "94026043724057": 6, "8552798675517863": 6, "219": 6, "60947928367543": 6, "8149866573467666": 6, "108": 6, "84441955310717": 6, "8531301788095305": 6, "170": 6, "24134912135943": 6, "8418420411160932": 6, "232": 6, "34805357903284": 6, "883998932301903": 6, "293": 6, "99342925522842": 6, "8564564664338091": 6, "353": 6, "50886633416462": 6, "8672069097403997": 6, "415": 6, "61235541906441": 6, "8482856353268698": 6, "479": 6, "217": 6, "7749814513912": 6, "7823980442129331": 6, "538": 6, "216": 6, "00225784039503": 6, "7113129125761161": 6, "601": 6, "8736767409489": 6, "6250904023479531": 6, "666": 6, "94414119442342": 6, "6227757503715069": 6, "731": 6, "45936690929625": 6, "6343056785694773": 6, "63861804615567": 6, "6302707941523814": 6, "860": 6, "1969": 6, "3749442111905": 6, "00019861806798724335": 6, "586529041453": 6, "923": 6, "215": 6, "82051598778696": 6, "6518244359516081": 6, "06387687700067": 6, "6440087841656821": 6, "041": 6, "24994687849525": 6, "6393212787552464": 6, "106": 6, "92984604804667": 6, "6232144947646524": 6, "25506613319246": 6, "603388647930941": 6, "2733": 6, "5772576431627": 6, "287": 6, "29854648789728": 6, "5873312673596333": 6, "16592450348784": 6, "4337907998582289": 6, "410": 6, "68514116107337": 6, "6695836226711808": 6, "475": 6, "220": 6, "8939514172608": 6, "4420925048614356": 6, "535": 6, "72299797702155": 6, "6960582933068138": 6, "69285146262294": 6, "69078828949453": 6, "665": 6, "0538787714827": 6, "7144357045239296": 6, "728": 6, "4213281391621": 6, "7353090312302926": 6, "74724725664498": 6, "92653950485437e": 6, "858": 6, "12287184152592": 6, "7183304951103088": 6, "22186485689846": 6, "7234233661662641": 6, "977": 6, "2720": 6, "793752592223": 6, "042": 6, "3855763846717": 6, "4726201914486088": 6, "By": 6, "roc_auc": [6, 9], "model_evalu": 6, "amongst": 6, "regression_scor": 6, "classification_scor": 6, "explained_vari": [6, 9], "max_error": [6, 9], "neg_mean_absolute_error": [6, 9], "neg_median_absolute_error": [6, 9], "average_precis": [6, 9], "balanced_accuraci": [6, 9], "f1": [6, 9], "f1_macro": [6, 9], "f1_micro": [6, 9], "f1_weight": [6, 9], "jaccard": [6, 9], "jaccard_macro": [6, 9], "jaccard_micro": [6, 9], "jaccard_weight": [6, 9], "neg_brier_scor": [6, 9], "precis": [6, 7, 9], "precision_macro": [6, 9], "precision_micro": [6, 9], "precision_weight": [6, 9], "recal": [6, 9], "recall_macro": [6, 9], "recall_micro": [6, 9], "recall_weight": [6, 9], "auc_pr_cal": [6, 8, 9], "bedroc": [6, 8, 9], "concordance_index": [6, 8, 9], "my_study_r2": 6, "945": 6, "947": 6, "072": 6, "011171868665159623": 6, "197": 6, "08689402230378174": 6, "283": 6, "12553701248394863": 6, "141096648805748": 6, "4893466963980463e": 6, "3039309544203818": 6, "20182749628697164": 6, "485": 6, "8187194367176578": 6, "558": 6, "4647239019719945": 6, "6574750183038587": 6, "611": 6, "8614818478547979": 6, "3974313630683448": 6, "705": 6, "12769795082909816": 6, "773": 6, "8639946428338224": 6, "2391884918766034": 6, "838": 6, "12553701248377633": 6, "00044396482429275296": 6, "3831436879125245e": 6, "892": 6, "12553700871203702": 6, "00028965395242758657": 6, "99928292425642e": 6, "2935582042429075": 6, "976": 6, "18476333152695587": 6, "8190707459213998": 6, "4060379177903557": 6, "118": 6, "12206148974315871": 6, "3105263811279067": 6, "344271094811757": 6, "3562469062424869": 6, "670604991178476": 6, "316": [6, 7], "045959695906983344": 6, "8583939656024446": 6, "5158832554303112": 6, "433": 6, "3062574078515544": 6, "487": 6, "11657354998283716": 6, "0009327650919528738": 6, "062479210472502": 6, "586": 6, "629": 6, "8498478905829554": 6, "1366172066709432": 6, "733": 6, "1276979508290982": 6, "786": 6, "13519830637607919": 6, "92901911959232": 6, "999026012594694": 6, "839": 6, "8198078293055633": 6, "5888977841391714": 6, "878": 6, "8201573964824842": 6, "19435298754153707": 6, "958": 6, "013": 6, "6285506249643193": 6, "35441495011256785": 6, "11934070343348298": 6, "145": 6, "4374125584543907": 6, "2457809516380005": 6, "213": 6, "3625576518621392": 6, "6459129458824919": 6, "36175556871883746": 6, "8179058888285398": 6, "285": 6, "8202473217121523": 6, "0920052840435055": 6, "372": 6, "3672927879319306": 6, "8677032984759461": 6, "402": 6, "445": 6, "40076792599874356": 6, "2865764368847064": 6, "26560316846701765": 6, "632": 6, "41215254857081174": 6, "671": 6, "763": 6, "00461414372160085": 6, "27282533524183633": 6, "919": 6, "10220127407364991": 6, "975": 6, "30323404130582854": 6, "3044553805553568": 6, "6437201185807124": 6, "076": 6, "41502276709562": 6, "10978379088847677": 6, "120": 6, "36160209098547913": 6, "022707289534838138": 6, "175": 6, "2916101445983833": 6, "936e": 6, "782e": 6, "434e": 6, "977e": 6, "276": 6, "8609413020928532": 6, "04987590926279814": 6, "794e": 6, "830e": 6, "906e": 6, "578e": 6, "8610289662757457": 6, "019211413400468974": 6, "754e": 6, "843e": 6, "507e": 6, "493": 6, "8610070549049179": 6, "018492644772509947": 6, "840e": 6, "513e": 6, "924e": 6, "8569771623635769": 6, "008783442408928633": 6, "243e": 6, "014e": 6, "700": 6, "8624781673814641": 6, "05782221001517797": 6, "113e": 6, "935e": 6, "122e": 6, "798": 6, "8618589507037001": 6, "02487072255316275": 6, "886": 6, "864754359721037": 6, "2079910754941946": 6, "946": 6, "8622236413326235": 6, "333215560931422": 6, "009": 6, "861832165638517": 6, "3628098560209365": 6, "068": 6, "8620108533993581": 6, "34240779695521706": 6, "142": 6, "8638540565650902": 6, "26493714991266293": 6, "8629799500771645": 6, "30596394512914815": 6, "8621408609583922": 6, "33648829357762355": 6, "351": 6, "8638132124078156": 6, "2679814646317183": 6, "424": 6, "863983758876634": 6, "24062119162159595": 6, "500": 6, "8627356047945115": 6, "3141728910335158": 6, "8639203054085788": 6, "23391390640786494": 6, "8570103863991635": 6, "6124885145996103": 6, "742": 6, "8647961976727571": 6, "2059976546070975": 6, "830": 6, "8648312544921793": 6, "20266060662750784": 6, "926": 6, "8648431452862716": 6, "20027647978240445": 6, "010": 6, "8648491459660418": 6, "1968919999787333": 6, "8650873115156988": 6, "174598921162764": 6, "204": 6, "8650350577921149": 6, "16468002989641095": 6, "8649412283687147": 6, "1606717091615047": 6, "986e": 6, "396": [6, 7], "8649537211609554": 6, "14694925097689848": 6, "506": 6, "8649734575435447": 6, "147612713300643": 6, "446e": 6, "8648761002838515": 6, "14440434705706803": 6, "398e": 6, "775": 6, "8639826593122782": 6, "1265357179513065": 6, "690e": 6, "875": 6, "864435565531768": 6, "1374245525868926": 6, "938": 6, "8590221951825531": 6, "49890830155012533": 6, "8649098880804443": 6, "1573428812070292": 6, "405e": 6, "864536410656637": 6, "13886104722511608": 6, "8597401050431873": 6, "47746341180045787": 6, "8537465461603838": 6, "050e": 6, "8642643827090003": 6, "13446778921611002": 6, "175e": 6, "8641621818665252": 6, "1286796719653316": 6, "625": 6, "864182755916388": 6, "13303218726548235": 6, "693": 6, "1255357440899417": 6, "021711452917433944": 6, "559714273835951e": 6, "758": 6, "8604596648091501": 6, "43644874418279245": 6, "463e": 6, "861": 6, "8635689909135862": 6, "10940922083495383": 6, "951": 6, "8648544336551733": 6, "1912756875742137": 6, "8648496595672595": 6, "19628449928540487": 6, "8452625121122099": 6, "4324661283995224": 6, "149": 6, "8378670635846416": 6, "839206620815206": 6, "002e": 6, "082e": 6, "8649365368153895": 6, "07270781179126021": 6, "8875676754699953": 6, "0006995169897945908": 6, "586e": 6, "618e": 6, "234e": 6, "484": 6, "8730555131061773": 6, "0018186269840273495": 6, "12553508835019533": 6, "04867556317570456": 6, "0011658455138452": 6, "284e": 6, "177e": 6, "664": 6, "8586292788613132": 6, "005078762921098462": 6, "anyalgorithm": 6, "__args__": 6, "consider": [6, 7], "modif": [6, 12], "establish": 6, "rf": 6, "account": [6, 7, 8], "though": 6, "treat": [6, 7], "pdf": [6, 9], "denot": [6, 12, 13], "determinist": [6, 7], "quantiti": 6, "tradit": [6, 7], "discret": 6, "discretis": [6, 12, 14], "bioactiv": [6, 7], "integr": 6, "afford": [6, 7], "particularli": 6, "liklihood": 6, "membership": [6, 7], "iopscienc": 6, "iop": 6, "articl": [6, 7], "3847": 6, "1538": 6, "3881": 6, "aaf101": 6, "pxc50": [6, 7], "p24863": 6, "enabl": [6, 7], "alwai": [6, 7], "734": 6, "joblib": [6, 8], "577": 6, "joblibcollisionwarn": 6, "collis": 6, "180": 6, "self": [6, 9], "_cached_cal": 6, "shelv": 6, "00": 6, "764": 6, "08099580623289632": 6, "prfclassifier_algorithm_hash": 6, "efe0ba9870529a6cde0dd3ad22447cbb": 6, "max_depth__efe0ba9870529a6cde0dd3ad22447cbb": 6, "n_estimators__efe0ba9870529a6cde0dd3ad22447cbb": 6, "max_features__efe0ba9870529a6cde0dd3ad22447cbb": 6, "prfclassifiermaxfeatur": [6, 9], "min_py_sum_leaf__efe0ba9870529a6cde0dd3ad22447cbb": 6, "use_py_gini__efe0ba9870529a6cde0dd3ad22447cbb": 6, "use_py_leafs__efe0ba9870529a6cde0dd3ad22447cbb": 6, "408": [6, 7], "07261454017489567": 6, "780": 6, "08791063872794351": 6, "911": 6, "07114663955819509": 6, "879": 6, "06537440628140882": 6, "446": 6, "05680450487193368": 6, "968": 6, "543": 6, "0656836821774901": 6, "333": 6, "07863564862376404": 6, "329": 6, "0648840199215795": 6, "014": 6, "07861037073288182": 6, "608": 6, "06669924317660021": 6, "997": 6, "06734611679947522": 6, "526": 6, "06810559387741143": 6, "0528189695245453": 6, "best_built": 6, "demonstr": [6, 7], "purpos": [6, 7], "transduct": 6, "example_smil": 6, "get_set": [6, 7, 8], "b": [6, 7], "outsid": [6, 7, 8], "likelihood": 6, "problemat": 6, "except": [6, 8], "valueerror": 6, "As": [6, 7], "raw": [6, 7, 8, 12], "760": 6, "800": 6, "w": 6, "801": 6, "fail": 6, "traceback": 6, "_optim": 6, "196": 6, "_run_trial": 6, "value_or_valu": 6, "func": 6, "128": 6, "__call__": 6, "_validate_algo": 6, "rais": [6, 8], "summaris": 6, "handl": 6, "via": [6, 7, 12], "convent": [6, 7], "classic": 6, "relev": 6, "cutoff": [6, 7, 12], "ouput": 6, "reflect": [6, 7], "arguabl": 6, "mpo": 6, "pub": 6, "ac": 6, "full": [6, 9], "jcim": 6, "9b00237": 6, "slide": 6, "googl": 6, "14pbd9ltxzfpsjhyxykflxnk8q80lhvnjimg8a3wqcrm": 6, "edit": 6, "calcault": 6, "directli": [6, 7], "later": [6, 7], "smilesbaseddescriptor": 6, "architectur": [6, 7], "quickli": 6, "867": 6, "868": 6, "root": [6, 9, 10], "enqueu": [6, 8], "manual": 6, "activation__668a7428ff5cdb271b01c0925e8fea45": 6, "relu": [6, 9], "aggregation__668a7428ff5cdb271b01c0925e8fea45": 6, "aggregation_norm__668a7428ff5cdb271b01c0925e8fea45": 6, "batch_size__668a7428ff5cdb271b01c0925e8fea45": 6, "depth__668a7428ff5cdb271b01c0925e8fea45": 6, "dropout__668a7428ff5cdb271b01c0925e8fea45": 6, "features_generator__668a7428ff5cdb271b01c0925e8fea45": 6, "ffn_hidden_size__668a7428ff5cdb271b01c0925e8fea45": 6, "ffn_num_layers__668a7428ff5cdb271b01c0925e8fea45": 6, "final_lr_ratio_exp__668a7428ff5cdb271b01c0925e8fea45": 6, "hidden_size__668a7428ff5cdb271b01c0925e8fea45": 6, "init_lr_ratio_exp__668a7428ff5cdb271b01c0925e8fea45": 6, "max_lr_exp__668a7428ff5cdb271b01c0925e8fea45": 6, "warmup_epochs_ratio__668a7428ff5cdb271b01c0925e8fea45": 6, "chempropregressor_algorithm_hash": 6, "668a7428ff5cdb271b01c0925e8fea45": 6, "301": 6, "6833": 6, "034983241957": 6, "chempropactiv": [6, 9], "chempropaggreg": [6, 9], "ensemble_size__668a7428ff5cdb271b01c0925e8fea45": 6, "epochs__668a7428ff5cdb271b01c0925e8fea45": 6, "chempropfeatures_gener": [6, 9], "6445": 6, "608102397302": 6, "1700": 6, "2300": 6, "safe": 6, "nan": [6, 8, 12, 13], "prompt": 6, "due": [6, 7, 8], "deactiv": 6, "own": 6, "still": 6, "commun": 6, "facilit": [6, 7, 9], "preset": 6, "enqu": 6, "bayesian": 6, "suggest": 6, "split_chemprop": [6, 9], "flag": [6, 7, 12, 13], "n_chemprop_tri": [6, 9], "desir": 6, "undirect": 6, "shown": [6, 7], "aspect": [6, 8], "princip": [6, 7], "expand": 6, "differnt": 6, "rememb": 6, "unless": 6, "alter": [6, 9], "characterist": [6, 7], "too": [6, 9], "limit": [6, 7, 9], "vice": [6, 9], "versa": [6, 9], "extens": [6, 9], "trail": [6, 9], "applic": [6, 7, 9], "chanc": 6, "help": 6, "caruana": 6, "particular": 6, "achiev": [6, 7], "st": 6, "figur": [6, 7], "signal": 6, "aka": 6, "could": [6, 7], "share": [6, 12, 13], "until": [6, 9], "longer": [6, 7], "mt": 6, "onc": [6, 7, 12], "knowledg": 6, "order": [6, 7, 9, 12], "earlier": [6, 7], "accompi": 6, "train_side_info": 6, "clog": 6, "surfac": 6, "area": [6, 7], "psa": 6, "265": 6, "22475": 6, "8088": 6, "883": 6, "32297": 6, "6237": 6, "835": 6, "33334": 6, "2804": 6, "314": 6, "26075": 6, "2533": 6, "498": 6, "278": 6, "18917": 6, "5102": 6, "694": 6, "246": 6, "12575": 6, "7244": 6, "255": 6, "14831": 6, "4338": 6, "895": 6, "302": 6, "26838": 6, "2041": 6, "22298": 6, "match": 6, "train_side_info_cl": 6, "clogp_gt2": 6, "clogs_gt": 6, "acceptors_gt5": 6, "donors_gt0": 6, "area_gt250": 6, "psa_lt0": 6, "aux": [6, 8, 10], "03": 6, "350": 6, "443": 6, "5817": 6, "944008002311": 6, "chemprophyperoptregressor_algorithm_hash": 6, "db9e60f9b8f0a43eff4b41917b6293d9": 6, "ensemble_size__db9e60f9b8f0a43eff4b41917b6293d9": 6, "epochs__db9e60f9b8f0a43eff4b41917b6293d9": 6, "features_generator__db9e60f9b8f0a43eff4b41917b6293d9": 6, "num_iters__db9e60f9b8f0a43eff4b41917b6293d9": 6, "search_parameter_level__db9e60f9b8f0a43eff4b41917b6293d9": 6, "chempropsearch_parameter_level": [6, 9], "aux_weight_pc__db9e60f9b8f0a43eff4b41917b6293d9": 6, "5796": 6, "34392897437": 6, "439": 6, "5795": 6, "086720713623": 6, "470": 6, "241": 6, "5820": 6, "227555999914": 6, "322": 6, "5852": 6, "160071204277": 6, "inlfuenc": 6, "henc": [6, 7], "percent": 6, "product": 6, "user_attrs_trial_ran": 6, "drop": [6, 7, 8], "erron": 6, "__": 6, "params_aux_weight_pc": 6, "conclud": [6, 7], "produc": 6, "overrid": [6, 9], "situat": [6, 7], "along": 6, "potenti": [6, 7], "compris": 6, "incompat": 6, "whilst": [6, 7], "desciptor": 6, "grei": [6, 7], "tial": 6, "what": 6, "design": 6, "unpromis": 6, "why": [6, 7], "poor": 6, "sampler": 6, "incompta": 6, "repeatedli": 6, "hyerparamet": 6, "ident": 6, "9525489095524835": 6, "aux_weight_pc__cfa1990d5153c8812982f034d788d7e": 6, "777": 6, "4824": 6, "686269039228": 6, "7731425652872588": 6, "819": 6, "849": 6, "4409": 6, "946844928445": 6, "791002332112292": 6, "021": [6, 7], "167": 6, "329624779366306": 6, "00015024763718638216": 6, "269": 6, "523": 6, "4396": 6, "722635068717": 6, "559": 6, "753": 6, "4577379164707": 6, "790": 6, "960": 6, "consult": 6, "incompitbl": 6, "algo": [6, 9], "occur": 6, "assign": [6, 7], "doe": [6, 7, 8, 9, 12], "params_algorithm_nam": 6, "move_legend": 6, "upper": [6, 7], "bbox_to_anchor": [6, 7], "overview": 6, "never": 6, "successfulli": 6, "absenc": 6, "8th": 6, "miss": [6, 8, 12, 13], "associ": [6, 7], "asid": 6, "mitig": 6, "overal": [6, 7], "serv": [6, 11], "argument": [6, 8], "tl": 6, "wider": 6, "activation__e0d3a442222d4b38f3aa1434851320db": 6, "aggregation__e0d3a442222d4b38f3aa1434851320db": 6, "aggregation_norm__e0d3a442222d4b38f3aa1434851320db": 6, "batch_size__e0d3a442222d4b38f3aa1434851320db": 6, "depth__e0d3a442222d4b38f3aa1434851320db": 6, "dropout__e0d3a442222d4b38f3aa1434851320db": 6, "features_generator__e0d3a442222d4b38f3aa1434851320db": 6, "ffn_hidden_size__e0d3a442222d4b38f3aa1434851320db": 6, "ffn_num_layers__e0d3a442222d4b38f3aa1434851320db": 6, "final_lr_ratio_exp__e0d3a442222d4b38f3aa1434851320db": 6, "hidden_size__e0d3a442222d4b38f3aa1434851320db": 6, "init_lr_ratio_exp__e0d3a442222d4b38f3aa1434851320db": 6, "max_lr_exp__e0d3a442222d4b38f3aa1434851320db": 6, "warmup_epochs_ratio__e0d3a442222d4b38f3aa1434851320db": 6, "e0d3a442222d4b38f3aa1434851320db": 6, "4937": 6, "540075659691": 6, "ensemble_size__e0d3a442222d4b38f3aa1434851320db": 6, "epochs__e0d3a442222d4b38f3aa1434851320db": 6, "retrain": 6, "954": 6, "043": 6, "5114": 6, "7131239123555": 6, "chempropregressorpretrained_algorithm_hash": 6, "dfc518a76317f23d95e5aa5a3eac77f0": 6, "frzn__dfc518a76317f23d95e5aa5a3eac77f0": 6, "chempropfrzn": [6, 9], "epochs__dfc518a76317f23d95e5aa5a3eac77f0": 6, "cover": 6, "global": 6, "job": [6, 7], "fair": 6, "1545": 6, "tl_studi": 6, "loc": [6, 7], "params_epoch": 6, "fillna": 6, "astyp": [6, 7], "agg": 6, "join": [6, 7], "params_chempropregressor_algorithm_hash": 6, "isna": 6, "annot": 6, "172": 6, "5891": 6, "7552821093905": 6, "140": 6, "5890": 6, "94653501547": 6, "77dfc8230317e08504ed5e643243fbc2": 6, "frzn__77dfc8230317e08504ed5e643243fbc2": 6, "epochs__77dfc8230317e08504ed5e643243fbc2": 6, "181": 6, "right": [6, 7], "ncol": 6, "world": [6, 7, 12, 13], "penultim": [6, 9], "chemprop_model": 6, "heatmap": 6, "predictor": [6, 8], "chemprop_fingerprint": 6, "fingerprint_typ": 6, "mpn": 6, "cbar_kw": 6, "semi": 6, "supervis": 6, "altern": [6, 7], "last_ffn": 6, "howeev": 6, "respect": [6, 7], "kind": [6, 7, 12], "confid": 6, "calibratedclassifiercv": 6, "understand": 6, "predict_proba": [6, 8], "among": 6, "gave": 6, "close": [6, 7], "actual": [6, 7], "topic": 6, "sigmoid": [6, 9], "review": 6, "those": [6, 7, 8], "calibration_curv": 6, "collect": 6, "defaultdict": 6, "precision_scor": 6, "recall_scor": 6, "f1_score": 6, "brier_score_loss": 6, "log_loss": 6, "roc_auc_scor": 6, "n_job": [6, 9, 11], "calibrated_rf": 6, "calibrated_model": 6, "173": 6, "110": 6, "8353535353535354": 6, "calibratedclassifiercvwithva_algorithm_hash": 6, "e788dfbfc5075967acb5ddf9d971ea20": 6, "n_folds__e788dfbfc5075967acb5ddf9d971ea20": 6, "max_depth__e788dfbfc5075967acb5ddf9d971ea20": 6, "n_estimators__e788dfbfc5075967acb5ddf9d971ea20": 6, "max_features__e788dfbfc5075967acb5ddf9d971ea20": 6, "uncalibr": 6, "uncalibrated_rf": 6, "uncalibrated_model": 6, "566": 6, "915": 6, "8185858585858585": 6, "randomforestclassifier_algorithm_hash": 6, "167e1e88dd2a80133e317c78f009bdc9": 6, "max_depth__167e1e88dd2a80133e317c78f009bdc9": 6, "n_estimators__167e1e88dd2a80133e317c78f009bdc9": 6, "max_features__167e1e88dd2a80133e317c78f009bdc9": 6, "conserv": 6, "1000": [6, 7], "random_st": [6, 12, 13], "calibrated_predict": 6, "uncalibrated_predict": 6, "cal_df": 6, "datafram": [6, 7, 8, 11, 12], "boxplot": 6, "melt": 6, "set_ylabel": [6, 7], "behaviour": [6, 7], "curv": [6, 7], "reliabl": 6, "diagram": 6, "against": 6, "figsiz": [6, 7], "ax1": 6, "subplot2grid": 6, "rowspan": 6, "ax2": 6, "perfectli": [6, 7], "pred": 6, "fraction_of_posit": 6, "mean_predicted_valu": 6, "n_bin": 6, "brier": 6, "2f": 6, "hist": 6, "histtyp": 6, "lw": 6, "set_ylim": 6, "legend": [6, 7], "set_titl": 6, "set_xlabel": [6, 7], "center": [6, 7], "tight_layout": [6, 7], "compos": 6, "refin": 6, "notic": 6, "significantli": 6, "cell": 6, "accur": 6, "alloc": 6, "y_prob": 6, "ye": 6, "score_nam": 6, "__name__": 6, "capit": 6, "score_df": 6, "set_index": 6, "decim": 6, "roc": 6, "auc": [6, 8], "184705": 6, "547129": 6, "830565": 6, "744048": 6, "784929": 6, "716536": 6, "175297": 6, "529474": 6, "811209": 6, "818452": 6, "814815": 6, "714104": 6, "va": 6, "multipoint": 6, "0c00476": 6, "margin": [6, 7], "bounari": 6, "548": 6, "537": 6, "8213131313131313": 6, "79765fbec1586f3c917ff30de274fdb4": 6, "n_folds__79765fbec1586f3c917ff30de274fdb4": 6, "max_depth__79765fbec1586f3c917ff30de274fdb4": 6, "n_estimators__79765fbec1586f3c917ff30de274fdb4": 6, "max_features__79765fbec1586f3c917ff30de274fdb4": 6, "uncert": [6, 8], "chem": [6, 7, 8], "allchem": 6, "pandastool": [6, 7], "rdconfig": 6, "datastruct": 6, "train_df": 6, "addmoleculecolumntofram": 6, "includefingerprint": 6, "getmorganfingerprint": 6, "nn": 6, "bulktanimotosimilar": 6, "add": [6, 7, 8, 10], "va_pr": 6, "va_uncert": 6, "dtm": 6, "trelli": 6, "fig": [6, 7], "subplot": [6, 7], "sharei": 6, "regplot": 6, "referenc": 6, "boundari": [6, 7, 12, 14], "neither": 6, "nor": 6, "dissimilar": 6, "cp_pred_ensembl": 6, "cp_uncert_ensembl": 6, "916": 6, "959": 6, "activation__fd833c2dde0b7147e6516ea5eebb2657": 6, "aggregation__fd833c2dde0b7147e6516ea5eebb2657": 6, "aggregation_norm__fd833c2dde0b7147e6516ea5eebb2657": 6, "batch_size__fd833c2dde0b7147e6516ea5eebb2657": 6, "depth__fd833c2dde0b7147e6516ea5eebb2657": 6, "dropout__fd833c2dde0b7147e6516ea5eebb2657": 6, "features_generator__fd833c2dde0b7147e6516ea5eebb2657": 6, "ffn_hidden_size__fd833c2dde0b7147e6516ea5eebb2657": 6, "ffn_num_layers__fd833c2dde0b7147e6516ea5eebb2657": 6, "final_lr_ratio_exp__fd833c2dde0b7147e6516ea5eebb2657": 6, "hidden_size__fd833c2dde0b7147e6516ea5eebb2657": 6, "init_lr_ratio_exp__fd833c2dde0b7147e6516ea5eebb2657": 6, "max_lr_exp__fd833c2dde0b7147e6516ea5eebb2657": 6, "warmup_epochs_ratio__fd833c2dde0b7147e6516ea5eebb2657": 6, "chempropclassifier_algorithm_hash": 6, "fd833c2dde0b7147e6516ea5eebb2657": 6, "65625": 6, "ensemble_size__fd833c2dde0b7147e6516ea5eebb2657": 6, "epochs__fd833c2dde0b7147e6516ea5eebb2657": 6, "midpoint": 6, "mont": 6, "carlo": 6, "virtual": [6, 8], "468": 6, "activation__c73885c5d5a4182168b8b002d321965a": 6, "aggregation__c73885c5d5a4182168b8b002d321965a": 6, "aggregation_norm__c73885c5d5a4182168b8b002d321965a": 6, "batch_size__c73885c5d5a4182168b8b002d321965a": 6, "depth__c73885c5d5a4182168b8b002d321965a": 6, "dropout__c73885c5d5a4182168b8b002d321965a": 6, "features_generator__c73885c5d5a4182168b8b002d321965a": 6, "ffn_hidden_size__c73885c5d5a4182168b8b002d321965a": 6, "ffn_num_layers__c73885c5d5a4182168b8b002d321965a": 6, "final_lr_ratio_exp__c73885c5d5a4182168b8b002d321965a": 6, "hidden_size__c73885c5d5a4182168b8b002d321965a": 6, "init_lr_ratio_exp__c73885c5d5a4182168b8b002d321965a": 6, "max_lr_exp__c73885c5d5a4182168b8b002d321965a": 6, "warmup_epochs_ratio__c73885c5d5a4182168b8b002d321965a": 6, "c73885c5d5a4182168b8b002d321965a": 6, "46875": 6, "ensemble_size__c73885c5d5a4182168b8b002d321965a": 6, "epochs__c73885c5d5a4182168b8b002d321965a": 6, "cp_pred_dropout": 6, "cp_uncert_dropout": 6, "previou": 6, "proabil": 6, "va_predict": 6, "correl": [6, 7], "drouput": 6, "uncertatinti": 6, "cp_uncert_delta": 6, "categor": [6, 12], "unit": [6, 7], "parsabl": 6, "date": 6, "cast": 6, "appropri": 6, "befor": [6, 7, 12], "choic": [6, 12], "822": 6, "862": 6, "4430": 6, "271946796234": 6, "mapie_algorithm_hash": 6, "976d211e4ac64e5568d369bcddd3aeb1": 6, "mapie_alpha__976d211e4ac64e5568d369bcddd3aeb1": 6, "max_depth__976d211e4ac64e5568d369bcddd3aeb1": 6, "n_estimators__976d211e4ac64e5568d369bcddd3aeb1": 6, "max_features__976d211e4ac64e5568d369bcddd3aeb1": 6, "analysi": [6, 7, 8], "perfom": 6, "post": 6, "mapie_pr": 6, "mapie_unc": 6, "bar": 6, "visualis": 6, "errorbar": 6, "yerr": 6, "ab": 6, "fmt": 6, "black": [6, 7], "ecolor": 6, "grai": 6, "elinewidth": 6, "capsiz": 6, "move": [6, 10], "analys": [6, 7], "width": 6, "alpha_impact": 6, "ma": 6, "unc_df": 6, "unc": 6, "reset_index": [6, 7], "concat": 6, "lineplot": 6, "err_styl": 6, "se": 6, "incorpor": 6, "tradition": 6, "unsupport": 6, "kernelexplain": [6, 8], "shaplei": 6, "explan": 6, "slundberg": 6, "game": 6, "credit": 6, "theori": 6, "publish": 6, "comopsit": 6, "540": 6, "_ridg": 6, "userwarn": [6, 7], "matrix": 6, "dual": 6, "34035600917066766": 6, "676421027478709": 6, "dga": 6, "dgp": 6, "dgtot": 6, "sa": 6, "sdc": 6, "sdx": 6, "numhacceptor": 6, "numhdonor": 6, "maxabsestateindex": 6, "maxestateindex": 6, "minabsestateindex": 6, "minestateindex": 6, "qed": 6, "sp": 6, "heavyatommolwt": 6, "exactmolwt": 6, "numvalenceelectron": 6, "numradicalelectron": 6, "maxpartialcharg": 6, "minpartialcharg": 6, "maxabspartialcharg": 6, "minabspartialcharg": 6, "fpdensitymorgan1": 6, "fpdensitymorgan2": 6, "fpdensitymorgan3": 6, "bcut2d_mwhi": 6, "bcut2d_mwlow": 6, "bcut2d_chghi": 6, "bcut2d_chglo": 6, "bcut2d_logphi": 6, "bcut2d_logplow": 6, "bcut2d_mrhi": 6, "bcut2d_mrlow": 6, "avgipc": 6, "balabanj": 6, "bertzct": 6, "chi0": 6, "chi0n": 6, "chi0v": 6, "chi1": 6, "chi1n": 6, "chi1v": 6, "chi2n": 6, "chi2v": 6, "chi3n": 6, "chi3v": 6, "chi4n": 6, "chi4v": 6, "hallkieralpha": 6, "ipc": 6, "kappa1": 6, "kappa2": 6, "kappa3": 6, "labuteasa": 6, "peoe_vsa1": 6, "peoe_vsa10": 6, "peoe_vsa11": 6, "peoe_vsa12": 6, "peoe_vsa13": 6, "peoe_vsa14": 6, "peoe_vsa2": 6, "peoe_vsa3": 6, "peoe_vsa4": 6, "peoe_vsa5": 6, "peoe_vsa6": 6, "peoe_vsa7": 6, "peoe_vsa8": 6, "peoe_vsa9": 6, "smr_vsa1": 6, "smr_vsa10": 6, "smr_vsa2": 6, "smr_vsa3": 6, "smr_vsa4": 6, "smr_vsa5": 6, "smr_vsa6": 6, "smr_vsa7": 6, "smr_vsa8": 6, "smr_vsa9": 6, "slogp_vsa1": 6, "slogp_vsa10": 6, "slogp_vsa11": 6, "slogp_vsa12": 6, "slogp_vsa2": 6, "slogp_vsa3": 6, "slogp_vsa4": 6, "slogp_vsa5": 6, "slogp_vsa6": 6, "slogp_vsa7": 6, "slogp_vsa8": 6, "slogp_vsa9": 6, "estate_vsa1": 6, "estate_vsa10": 6, "estate_vsa11": 6, "estate_vsa2": 6, "estate_vsa3": 6, "estate_vsa4": 6, "estate_vsa5": 6, "estate_vsa6": 6, "estate_vsa7": 6, "estate_vsa8": 6, "estate_vsa9": 6, "vsa_estate1": 6, "vsa_estate10": 6, "vsa_estate2": 6, "vsa_estate3": 6, "vsa_estate4": 6, "vsa_estate5": 6, "vsa_estate6": 6, "vsa_estate7": 6, "vsa_estate8": 6, "vsa_estate9": 6, "fractioncsp3": 6, "heavyatomcount": 6, "nhohcount": 6, "nocount": 6, "numaliphaticcarbocycl": 6, "numaliphaticheterocycl": 6, "numaliphaticr": 6, "numaromaticcarbocycl": 6, "numaromaticheterocycl": 6, "numaromaticr": 6, "numheteroatom": 6, "numrotatablebond": 6, "numsaturatedcarbocycl": 6, "numsaturatedheterocycl": 6, "numsaturatedr": 6, "ringcount": 6, "mollogp": 6, "molmr": 6, "fr_al_coo": 6, "fr_al_oh": 6, "fr_al_oh_notert": 6, "fr_arn": 6, "fr_ar_coo": 6, "fr_ar_n": 6, "fr_ar_nh": 6, "fr_ar_oh": 6, "fr_coo": 6, "fr_coo2": 6, "fr_c_o": 6, "fr_c_o_nocoo": 6, "fr_c_": 6, "fr_hoccn": 6, "fr_imin": 6, "fr_nh0": 6, "fr_nh1": 6, "fr_nh2": 6, "fr_n_o": 6, "fr_ndealkylation1": 6, "fr_ndealkylation2": 6, "fr_nhpyrrol": 6, "fr_sh": 6, "fr_aldehyd": 6, "fr_alkyl_carbam": 6, "fr_alkyl_halid": 6, "fr_allylic_oxid": 6, "fr_amid": 6, "fr_amidin": 6, "fr_anilin": 6, "fr_aryl_methyl": 6, "fr_azid": 6, "fr_azo": 6, "fr_barbitur": 6, "fr_benzen": 6, "fr_benzodiazepin": 6, "fr_bicycl": 6, "fr_diazo": 6, "fr_dihydropyridin": 6, "fr_epoxid": 6, "fr_ester": 6, "fr_ether": 6, "fr_furan": 6, "fr_guanido": 6, "fr_halogen": 6, "fr_hdrzine": 6, "fr_hdrzone": 6, "fr_imidazol": 6, "fr_imid": 6, "fr_isocyan": 6, "fr_isothiocyan": 6, "fr_keton": 6, "fr_ketone_topliss": 6, "fr_lactam": 6, "fr_lacton": 6, "fr_methoxi": 6, "fr_morpholin": 6, "fr_nitril": 6, "fr_nitro": 6, "fr_nitro_arom": 6, "fr_nitro_arom_nonortho": 6, "fr_nitroso": 6, "fr_oxazol": 6, "fr_oxim": 6, "fr_para_hydroxyl": 6, "fr_phenol": 6, "fr_phenol_noorthohbond": 6, "fr_phos_acid": 6, "fr_phos_est": 6, "fr_piperdin": 6, "fr_piperzin": 6, "fr_priamid": 6, "fr_prisulfonamd": 6, "fr_pyridin": 6, "fr_quatn": 6, "fr_sulfid": 6, "fr_sulfonamd": 6, "fr_sulfon": 6, "fr_term_acetylen": 6, "fr_tetrazol": 6, "fr_thiazol": 6, "fr_thiocyan": 6, "fr_thiophen": 6, "fr_unbrch_alkan": 6, "fr_urea": 6, "shap_valu": 6, "2227": 6, "042023e": 6, "2229": 6, "025199e": 6, "2228": 6, "802158e": 6, "2267": 6, "387276e": 6, "2230": 6, "106653e": 6, "1784": 6, "598471e": 6, "1785": 6, "584": 6, "ns": 6, "995": 6, "996": 6, "845": 6, "846": 6, "1375": 6, "1376": 6, "s1": 6, "n1c": 6, "1570": 6, "contrinubt": 6, "datset": 6, "unscaledphyschemjazzi": 6, "rank": [6, 8], "usag": 6, "978": 6, "032": 6, "818": 6, "t": [6, 7, 9], "kekul": 6, "unkekul": 6, "rational": 6, "rationale_scor": 6, "386": 6, "097": 6, "ch3": 6, "ch": 6, "389": [6, 7], "151": 6, "c1c": 6, "c1n": 6, "ch2": 6, "nh2": 6, "nn1cc1c": 6, "384": 6, "720": 6, "c1cccc": 6, "871": 6, "854": 6, "contian": 6, "second": 6, "dummi": 6, "third": 6, "smallest": 6, "made": [6, 7], "fourth": 6, "irregularli": 6, "xc50": [6, 7], "log10": [6, 7, 12, 14], "6th": 6, "convers": [6, 7, 12, 14], "logbas": [6, 7, 12, 14], "logneg": [6, 7, 12, 14], "negat": [6, 7, 12, 14], "transformed_studi": 6, "transform_exampl": 6, "028": 6, "5959493772536109": 6, "6571993250300608": 6, "169": 6, "1511102853256885": 6, "2487063317112765": 6, "288": 6, "6714912461080983": 6, "2725944467796781": 6, "369": 6, "194926264155893": 6, "395": 6, "7520919188596032": 6, "469": 6, "7803723847416691": 6, "499": 6, "6397753979196248": 6, "528": 6, "151110299986041": 6, "151110111437006": 6, "5410418750776741": 6, "612": 6, "7183231137124538": 6, "640": 6, "2721824844856162": 6, "716": 6, "1900929470222508": 6, "745": 6, "774": 6, "5585323973564646": 6, "3169218304262786": 6, "980": 6, "7974925066137679": 6, "008": 6, "218395226466336": 6, "039": 6, "1474226942497083": 6, "054": 6, "083": 6, "0239005731675412": 6, "160": 6, "191": 6, "178901060853144": 6, "27137790098830755": 6, "2710284516876423": 6, "361": 6, "6273152492418945": 6, "438": 6, "496": 6, "1907041717628215": 6, "3209075619139279": 6, "545": 6, "2709423025014604": 6, "609": 6, "3133943310851415": 6, "657": 6, "257769959239938": 6, "735": 6, "40359637945134746": 6, "817": 6, "4127882135896648": 6, "905": 6, "9246005133276612": 6, "003": 6, "8908739215746116": 6, "035": 6, "107536316777608": 6, "067": 6, "098": 6, "054360360588395": 6, "129": 6, "5428179904345867": 6, "5696273642213351": 6, "194": 6, "27099769667470536": 6, "1580741708125475": 6, "2709564785634315": 6, "10900413894771653": 6, "268": 6, "2709799905898163": 6, "13705914456987853": 6, "27097230608092054": 6, "12790870116376127": 6, "337": 6, "2709499903064464": 6, "10123180962907431": 6, "2710895886052581": 6, "26565663774320425": 6, "411": 6, "2708711012023424": 6, "005637048678674678": 6, "27092322402109364": 6, "06902647427781451": 6, "482": 6, "2712140349882": 6, "4076704953178294": 6, "515": 6, "27090080367174": 6, "04187106800188596": 6, "550": 6, "27086925247190047": 6, "003371853599610078": 6, "2708933298483799": 6, "032781796328385376": 6, "623": 6, "27087205624489635": 6, "006806773659187283": 6, "658": 6, "2708869511176179": 6, "025009489814943348": 6, "695": 6, "2711465077924297": 6, "3311125627707556": 6, "2708756855936628": 6, "011249102380159387": 6, "766": 6, "27087301924224993": 6, "007985924302396141": 6, "802": 6, "2708685399954944": 6, "00249856291483601": 6, "27121879554836553": 6, "4130244908975993": 6, "880": 6, "2708693196600531": 6, "0034541978803366022": 6, "918": 6, "27110195265802334": 6, "27994943662091765": 6, "956": 6, "2708682582859318": 6, "0021532199144365088": 6, "27087024523986086": 6, "0045884092728113585": 6, "27087351807632193": 6, "008596600952859433": 6, "2710818633795896": 6, "2567049271070902": 6, "109": 6, "27103241786565463": 6, "1990111983307052": 6, "146": 6, "2710350879598171": 6, "20214459724424078": 6, "183": 6, "2708688328221868": 6, "00285750520671645": 6, "27100832234449684": 6, "17064008990759916": 6, "258": 6, "27268613236193845": 6, "8725420109733135": 6, "296": 6, "27119617446689237": 6, "387533542012365": 6, "2708691110831552": 6, "0031985656730512953": 6, "27086852174155146": 6, "002476186542950981": 6, "27135383618835024": 6, "5626643670396761": 6, "449": 6, "2709819654433871": 6, "1394077979875128": 6, "488": [6, 8], "2718548944510965": 6, "0858347526799794": 6, "1508084699212935": 6, "03329943145150872": 6, "00025672309762227527": 6, "27249853374634975": 6, "702026434077893": 6, "604": 6, "27095660957755363": 6, "10916094511173127": 6, "643": 6, "27102160995407715": 6, "18630665884100353": 6, "681": 6, "27095708822582026": 6, "10973377642487026": 6, "27088222008661084": 6, "019235980282946118": 6, "762": 6, "2708703086029017": 6, "004666043957133775": 6, "799": 6, "27095279044622245": 6, "1045877457096882": 6, "840": 6, "2709408288690431": 6, "09023455456986404": 6, "9289218260898663": 6, "8200088368788958": 6, "917": 6, "27086675101898655": 6, "00030502148265565063": 6, "957": 6, "2710491243757999": 6, "21858260742423916": 6, "001": 6, "1491615840508995": 6, "024725853754515203": 6, "040": 6, "2709462479577586": 6, "0967427718847167": 6, "default_studi": 6, "252": 6, "332": 6, "3501": 6, "942111261296": 6, "5451": 6, "207265576796": 6, "459": 6, "1049201007814": 6, "9964": 6, "541364058234": 6, "3543": 6, "953608539901": 6, "570": 6, "6837": 6, "057544630979": 6, "613": 6, "2507": 6, "1794330606067": 6, "650": 6, "21534": 6, "719219668405": 6, "726": 6, "2899": 6, "736555614694": 6, "294e": 6, "760e": 6, "21674": 6, "445000284228": 6, "1049203123567": 6, "1049192609138": 6, "877": 6, "3630": 6, "72768093756": 6, "907": 6, "3431": 6, "942816967268": 6, "6908": 6, "462045154488": 6, "5964": 6, "65935954044": 6, "036": 6, "21070": 6, "107195348774": 6, "065": 6, "4977": 6, "068508997133": 6, "133": 6, "8873": 6, "669262669626": 6, "21387": 6, "63697424318": 6, "202": 6, "9958": 6, "573006910125": 6, "5182695600183": 6, "428": 6, "20684": 6, "56412138056": 6, "544": 6, "150": 6, "3435882510586": 6, "571": 6, "7068": 6, "705383113378": 6, "599": 6, "7150": 6, "482090052133": 6, "077": 6, "203": 6, "93637462922368": 6, "2570": 6, "5111262532305": 6, "21987": 6, "659957192194": 6, "9889": 6, "493204596083": 6, "413": 6, "7172": 6, "208490771303": 6, "9804": 6, "512701665093": 6, "555": 6, "585": 6, "9165": 6, "74081120673": 6, "0280270800017": 6, "161": 6, "1602933782954": 6, "888460860864": 6, "864": 6, "8414": 6, "932694243476": 6, "2270": 6, "540799189147": 6, "10383": 6, "79559309305": 6, "20815": 6, "025469865475": 6, "206": 6, "7560385808573": 6, "5264": 6, "4700789389035": 6, "3668": 6, "255064135424": 6, "156": 6, "12174877890536": 6, "793408178086295": 6, "99902820845678": 6, "157": 6, "371632749506": 6, "88307313087517": 6, "140915461519354": 6, "218": 6, "153": 6, "66773675231477": 6, "177324126813716": 6, "77906017834145": 6, "186": 6, "52056745848623": 6, "4565714180547": 6, "6710444346508": 6, "294": 6, "30976119334312": 6, "62916671166313": 6, "023639423189294": 6, "053696900694": 6, "914617418880486": 6, "31140591484044": 6, "201": 6, "33573874994386": 6, "569769302718845": 6, "5781354926491789": 6, "412": 6, "190": 6, "1384885119049": 6, "87666716965626": 6, "2537791489618": 6, "451": 6, "076949848299": 6, "9559574710535281": 6, "0032830967319653665": 6, "764974036324": 6, "03910427457823": 6, "406811480459925": 6, "164": 6, "4477304958181": 6, "701690847791482": 6, "819274780536123": 6, "567": 6, "87939164358104": 6, "32187661108304": 6, "660320437878754": 6, "607": 6, "01705178481896": 6, "61397716361812": 6, "603665957830847": 6, "645": 6, "155": 6, "73257312230092": 6, "759645965959294": 6, "503212714246787": 6, "684": 6, "154": 6, "46848394144124": 6, "8546740801317": 6, "35327336610912": 6, "724": 6, "20421802817864": 6, "57596974747163": 6, "84756262407801": 6, "51233215278089": 6, "3564642040401464": 6, "5034542273159819": 6, "207": 6, "68667089892196": 6, "034895878929095": 6, "03653571911285094": 6, "842": 6, "102": 6, "52277054278186": 6, "01961499216484045": 6, "670937191883546": 6, "881": 6, "28722475694815": 6, "012434370509176538": 6, "34222704431493": 6, "921": 6, "87402050281146": 6, "008452015347522093": 6, "914863578437455": 6, "38847505937936": 6, "01573542234868893": 6, "99307522974174": 6, "999": 6, "96336195786391": 6, "009845516063879428": 6, "59422914099683": 6, "19345618324213": 6, "009382525091504246": 6, "35573659237662": 6, "080": 6, "30772721342525": 6, "010579672066291478": 6, "35550323165882": 6, "23970902543148": 6, "013369359066405863": 6, "4744102498801": 6, "34331248758777": 6, "011398351701814368": 6, "54146340620301": 6, "195": 6, "104535853341": 6, "011708779850509646": 6, "682286191624579e": 6, "0653774146952": 6, "009806826677473646": 6, "90274406278985": 6, "64646042813787": 6, "0038598153381434685": 6, "20918134828555": 6, "68420472011734": 6, "0032474576673554513": 6, "35551178979624": 6, "85985201823172": 6, "003187930738019005": 6, "29431603544847": 6, "399": 6, "21583898009355": 6, "003122319313153475": 6, "83526418992966": 6, "437": 6, "34787242859676": 6, "002781955938462633": 6, "76228981520067": 6, "478": 6, "70914272129673": 6, "0023173546614751305": 6, "3000082904498813": 6, "519": 6, "10492031097328": 6, "002606064524407": 6, "7861330234653922e": 6, "1049154281806": 6, "0029210589377408366": 6, "200933937391094e": 6, "10492028002287": 6, "06431564840324226": 6, "2981641934644904e": 6, "56066541774658": 6, "0010848843623839548": 6, "151493073951163": 6, "76337597039308": 6, "004134805589645341": 6, "88115336652716": 6, "58009587759925": 6, "004763418454688096": 6, "02920758025023": 6, "113": 6, "35230417583477": 6, "0009098023238189749": 6, "57100980886017": 6, "809": 6, "30807467406214": 6, "03739791555156691": 6, "12818940557025": 6, "850": 6, "44100655116532": 6, "006380481141720477": 6, "4882351186755": 6, "891": 6, "35181001564942": 6, "0036244007454981787": 6, "608797806921866": 6, "124": 6, "3719027482892": 6, "0014198536004321608": 6, "05588994284273": 6, "28568052794907": 6, "005434972462746285": 6, "215759789700954": 6, "06": 6, "018": 6, "20325": 6, "66479442037": 6, "9696417046589247": 6, "132": 6, "21507621375022": 6, "0004528978867024753": 6, "80386923876023": 6, "85570350846885": 6, "0016948043699497222": 6, "455627755557016": 6, "contrast": [6, 7], "relplot": 6, "col": [6, 7], "facet_kw": 6, "axisgrid": [6, 7], "facetgrid": 6, "0x7fb3797f6b30": 6, "noramlis": 6, "unlog": 6, "yield": [6, 7, 12, 13], "mse": 6, "1126": 6, "56968721": 6, "20237903": 6, "revers": [6, 7, 12, 14], "onto": 6, "action": 6, "importantli": 6, "easili": [6, 7], "94824194": 6, "92008694": 6, "instruct": 6, "untransform": 6, "wish": 6, "cut": [6, 7], "10um": 6, "ptr_config_log_transform": 6, "ptr_transformed_studi": 6, "ptr_and_transform_exampl": 6, "518": 6, "002341918451736245": 6, "805": 6, "0024908979029632677": 6, "847": 6, "007901407671048116": 6, "888": 6, "00496231674623194": 6, "0026848278110363512": 6, "0010872728889471893": 6, "000": 6, "008706109201510277": 6, "027": 6, "093": 6, "002999462459688867": 6, "00825680029907454": 6, "148": 6, "007901407993550248": 6, "007901405163828307": 6, "0021653695362066753": 6, "002869169486971014": 6, "0010855652626111146": 6, "00550533804299308": 6, "002236800860454562": 6, "006105985607235417": 6, "004846526544994462": 6, "006964668794465202": 6, "670": 6, "699": 6, "008384326901042542": 6, "730": 6, "001082194093844804": 6, "761": 6, "0010807084256204563": 6, "948": 6, "005505338042993082": 6, "979": 6, "005247934991526694": 6, "0010803393728928605": 6, "005218354425190125": 6, "138": 6, "004999207507691546": 6, "0015694919308122948": 6, "326": 6, "0019757694194001384": 6, "421": 6, "002341918451736244": 6, "453": 6, "00368328296527152": 6, "521": 6, "003412828259848677": 6, "551": 6, "004412110711416997": 6, "616": 6, "647": 6, "0021743798524909573": 6, "0022761245849848527": 6, "0010805768178458735": 6, "750": 6, "001080400188305814": 6, "784": 6, "0010805009783570441": 6, "0010804680472500541": 6, "0010803723579987025": 6, "890": 6, "001080969596032512": 6, "925": 6, "0010800333715082816": 6, "0010802574700236845": 6, "0010814994986419817": 6, "037": 6, "001080161136846237": 6, "071": 6, "0010800254136811547": 6, "107": 6, "0010801290036870739": 6, "001080037482216557": 6, "179": 6, "0010801015705851358": 6, "0010812122378841013": 6, "0010800531021304936": 6, "291": 6, "00108004162698813": 6, "328": 6, "0010800223466649803": 6, "364": 6, "0010815197263834202": 6, "0010800257029027847": 6, "0010810223438672223": 6, "0010800211339555509": 6, "513": 6, "0010800296871141684": 6, "0010800437739166451": 6, "0010809366267195716": 6, "627": 6, "001080725386603206": 6, "0010807368035830652": 6, "704": 6, "0010800236072155854": 6, "741": 6, "0010806223050773966": 6, "779": 6, "0010876516369772728": 6, "00108142358144501": 6, "857": 6, "0010800248050489667": 6, "894": 6, "001080022268085466": 6, "0010820922958715991": 6, "969": 6, "0010805094397523254": 6, "007": 6, "0010841993753324146": 6, "007899735988203994": 6, "086": 6, "0010868762004637347": 6, "001080400750193767": 6, "163": 6, "0010806791616300314": 6, "0010804028029753213": 6, "0010800812188506515": 6, "0010800299598580359": 6, "0010803843696362083": 6, "001080333048974234": 6, "394": [6, 7], "432": 6, "001080014645182176": 6, "473": 6, "0010807968027851892": 6, "516": 6, "007907028395366658": 6, "553": 6, "0010803563024666294": 6, "inted": 6, "opter": 6, "probabilst": 6, "lossi": 6, "anywai": 6, "intention": 6, "clip": [6, 7], "cannot": 6, "timepoint": 6, "aux_column": [6, 8], "accord": [6, 7, 8], "aux_col_config": 6, "aux_descriptors_dataset": 6, "train_with_conc": 6, "aux1": 6, "aux_col_studi": 6, "covariate_exampl": 6, "aux1_model": 6, "323": 6, "5186": 6, "767663956718": 6, "522": 6, "4679": 6, "740824270968": 6, "575": 6, "4890": 6, "6705099499995": 6, "3803": 6, "9324375833753": 6, "667": 6, "3135": 6, "6497388676926": 6, "2518812859375": 6, "778": 6, "4309": 6, "124112370974": 6, "30159424580074": 6, "897": 6, "4357": 6, "02827013125": 6, "1437929337522": 6, "45281013": 6, "shape": [6, 7], "thrown": [6, 8], "prediciton": 6, "regardless": 6, "utilis": [6, 7], "seper": 6, "vector_covariate_config": 6, "precomputed_descriptor": 6, "train_with_fp": 6, "aux_transform": [6, 8], "vector_covariate_studi": 6, "vector_aux_exampl": 6, "vector_covariate_model": 6, "2200": 6, "6817959410578": 6, "011994365911634164": 6, "95660880078": 6, "029071783512897825": 6, "5798": 6, "564494725643": 6, "022631709120790048": 6, "2198637677605415": 6, "972": 6, "2899178898048": 6, "8916194399474267": 6, "556": 6, "3336440433073": 6, "5914093983615214": 6, "614": 6, "653": 6, "3036472748931": 6, "6201811079699818": 6, "3807": 6, "8035919667395": 6, "901e": 6, "892e": 6, "914e": 6, "752": 6, "5019": 6, "459500770764": 6, "1376436589359351": 6, "4017711284796": 6, "893": 6, "771": 6, "797115414836": 6, "74340620175102": 6, "train_smil": [6, 8], "train_i": [6, 8], "train_aux": [6, 8], "test_smil": [6, 8], "test_i": [6, 8], "test_aux": [6, 8], "512": 6, "legth": 6, "39754917": 6, "465": 6, "06352766": 6, "52031134": 6, "341": 6, "89875316": 6, "371": 6, "5516046": 6, "85042171": 6, "436": 6, "33406203": 6, "91439129": 6, "80585907": 6, "346": 6, "48565041": 6, "protein": [6, 12, 14], "alongsid": 6, "chemic": [6, 7, 12, 13], "sequenc": [6, 12, 14], "former": 6, "wherea": 6, "latter": [6, 7], "interact": 6, "basi": [6, 7], "toxinpred3": 6, "No": [6, 9, 12], "demponstr": 6, "zscale_covariate_config": 6, "zscale_covariate_studi": 6, "zscale_aux_exampl": 6, "zscale_covariate_model": 6, "458": 6, "8886986575836505": 6, "kneighborsclassifier_algorithm_hash": 6, "e51ca55089f389fc37a736adb2aa0e42": 6, "metric__e51ca55089f389fc37a736adb2aa0e42": 6, "n_neighbors__e51ca55089f389fc37a736adb2aa0e42": 6, "weights__e51ca55089f389fc37a736adb2aa0e42": 6, "unlik": 6, "21269231": 6, "91153846": 6, "29038462": 6, "69846154": 6, "22230769": 6, "99521739": 6, "59826087": 6, "34695652": 6, "03086957": 6, "13391304": 6, "08083333": 6, "6125": 6, "82916667": 6, "05083333": 6, "56083333": 6, "02178571": 6, "91785714": 6, "45392857": 6, "37642857": 6, "03107143": 6, "93357143": 6, "78964286": 6, "62928571": 6, "50857143": 6, "50107143": 6, "1232": 6, "3364": 6, "2328": 6, "1368": 6, "2304": 6, "7062": 6, "x_": 6, "vmin": 6, "vmax": 6, "cmap": 6, "spectral": 6, "248bit": 6, "128bit": 6, "minimz": 6, "consist": 6, "generaliz": 6, "minimize_std_dev": 6, "minimise_std_dev": [6, 9], "std": [6, 7, 12, 14], "dev": [6, 7], "example_multi": 6, "parameter_analysi": 6, "set_metric_nam": 6, "740": 6, "4008740644240856": 6, "9876203329634794": 6, "331": 6, "3561484909673425": 6, "9875061220991906": 6, "472": 6, "7856521165563053": 6, "21863029956806662": 6, "525": 6, "9125905675311808": 6, "7861693342190089": 6, "603": 6, "5238765412750027": 6, "2789424384877304": 6, "5348363849100434": 6, "5741725628917808": 6, "746": 6, "0072511048320134": 6, "2786318125997387": 6, "9625764609276656": 6, "27575381401822424": 6, "1114006274062536": 6, "7647766019001522": 6, "7801680863916906": 6, "2725738454485389": 6, "121": 6, "785652116470164": 6, "21863029955530786": 6, "152": 6, "785651973436432": 6, "21863032832257323": 6, "6101359993004856": 6, "3011280543457062": 6, "209": 6, "5361950698070447": 6, "23560786523195643": 6, "5356113574175657": 6, "5769721187181905": 6, "543430366921729": 6, "514747412346662": 6, "508": [6, 8], "5194661889628072": 6, "40146744515282495": 6, "659": 6, "659749443628722": 6, "6659085938841998": 6, "876": 6, "1068495306229729": 6, "24457822094737378": 6, "8604898820838102": 6, "7086875504668667": 6, "949": 6, "5919869916997383": 6, "2367498627927979": 6, "2497762395862362": 6, "10124660026536195": 6, "205": 6, "study_name_1": 6, "669": 6, "0621601907738047": 6, "2749020946925899": 6, "xxx": 6, "values_neg_mean_squared_error": 6, "values_standard": 6, "twinx": 6, "r": 6, "floor": 6, "ceil": 6, "align": 6, "set_ytick": 6, "linspac": 6, "set_xtick": 6, "text": [6, 7, 8, 12], "pareto": 6, "front": 6, "plot_pareto_front": 6, "plot_param_import": 6, "dictionari": [6, 10], "ordereddict": 6, "descend": 6, "algortihm": 6, "impact": 6, "durat": 6, "total_second": 6, "target_nam": 6, "relationship": 6, "plot_parallel_coordin": [6, 8, 9, 11], "param": [6, 7, 9, 10], "taken": [6, 7], "101": 6, "precomputed_config": 6, "precomputed_studi": 6, "precomputed_exampl": 6, "precomputed_model": 6, "785": 6, "788": 6, "3014": 6, "274803630188": 6, "471088599086": 6, "03592375122963953": 6, "511": 6, "3029": 6, "113810544919": 6, "8153295905650357": 6, "4358": 6, "575772003129": 6, "unseen": 6, "caus": 6, "111": 6, "new_molecul": 6, "112": 6, "tempfil": 6, "temp": [6, 7], "store": [6, 7, 11], "temporari": [6, 10], "extract": 6, "1st": 6, "example_fp": 6, "namedtemporaryfil": 6, "temp_fil": 6, "len": [6, 7], "to_csv": 6, "292": 6, "65709987": 6, "64327077": 6, "common": 7, "proper": 7, "optuna_az": 7, "process": [7, 8], "draw": 7, "ipythonconsol": 7, "ipython": 7, "displai": 7, "os": 7, "listdir": 7, "isfil": 7, "walk": 7, "handi": 7, "var": 7, "1v": 7, "9y_z128d7gvcp8mf8q0pz3ch0000gq": 7, "ipykernel_82497": 7, "796203442": 7, "deprecationwarn": 7, "deprec": 7, "med": 7, "titles": 7, "fontsiz": 7, "labels": 7, "xtick": 7, "ytick": 7, "rcparam": 7, "whitegrid": 7, "set_styl": 7, "white": 7, "inlin": 7, "3336016810": 7, "matplotlibdeprecationwarn": 7, "ship": 7, "v0_8": 7, "api": [7, 8], "boolean": 7, "nomin": 7, "convert": [7, 12], "conduct": 7, "primarydf": 7, "loadsdf": 7, "inchi": 7, "skeletonspher": 7, "nm": 7, "id": 7, "romol": 7, "ic50": 7, "\u00b5m": 7, "c1ccc2c": 7, "co2": 7, "004320939": 7, "1s": 7, "c8h7no2": 7, "c10": 7, "qrcgftxrxymjo": 7, "uhfffaoysa": 7, "86075": 7, "kinas": 7, "p38": 7, "rdchem": 7, "0x7fd1c0d34040": 7, "c1ccc": 7, "ccc2ccccc2occ3ccc": 7, "882397308": 7, "c22h20o3": 7, "c23": 7, "ytdaoqyeyfcini": 7, "89637": 7, "kd": 7, "retinoid": 7, "receptor": 7, "0x7fd1f8f965e0": 7, "130299026": 7, "0x7fd1f8f96650": 7, "nh": 7, "48148606": 7, "c9h7no": 7, "c11": 7, "lisfmebwquvkpj": 7, "n93": 7, "n82": 7, "n65": 7, "n36": 7, "n33": 7, "ki": 7, "nki": 7, "carbon": 7, "anhydras": 7, "xii": 7, "ncarbon": 7, "0x7fd1f8f966c0": 7, "nc1ccccn1": 7, "c7h8n2o": 7, "h2": 7, "5h": 7, "qrokotbwfzitjz": 7, "86233": 7, "nicotin": 7, "phosphoribosyltransferas": 7, "0x7fd1f8f96730": 7, "renam": 7, "conveni": [7, 8, 9, 12], "rest": 7, "moltosmil": 7, "isomericsmil": 7, "c1coc2ccccc2n1": 7, "004321": 7, "coc2ccccc2ccc2ccccc2": 7, "882397": 7, "130299": 7, "c1ccc2ccccc2": 7, "481486": 7, "stick": 7, "engin": 7, "assum": [7, 12, 13], "stage": 7, "slightli": 7, "pose": 7, "wise": 7, "uniqu": 7, "outlin": 7, "occurr": 7, "preserv": 7, "vari": 7, "recommend": 7, "abil": 7, "being": 7, "df_po": 7, "dedup": [7, 12], "df_rnd": 7, "df_max": 7, "df_avg": 7, "df_med": 7, "deduplidc": 7, "397": 7, "indici": 7, "coc1cc2ncnc": 7, "nc3ccc": 7, "scc4ccccc4": 7, "cl": 7, "c3": 7, "c2cc1oc": 7, "282579": 7, "912929": 7, "cc1cccc": 7, "nc2ncnc3ccc": 7, "c4ccccc4": 7, "cc23": 7, "n2cc": 7, "cc2c": 7, "nc2cccc": 7, "n2": 7, "065502": 7, "390": 7, "958607": 7, "392": 7, "oc2cccc": 7, "cn1nc": 7, "c2cnc": 7, "c3ccc": 7, "nc1c1": 7, "oc1nc": 7, "oc2cc": 7, "c3ccccc3": 7, "c3cccc": 7, "cn": 7, "936291": 7, "uniquify_by_posit": 7, "uniquify_randomli": 7, "essenc": 7, "uniquify_by_valu": 7, "highest": 7, "minim": [7, 9], "densiti": 7, "dpi": 7, "kdeplot": 7, "shade": 7, "orang": 7, "ndigit": 7, "blue": 7, "keepaverag": 7, "deeppink": 7, "hold": [7, 8], "assess": 7, "aim": 7, "simpli": 7, "sai": 7, "veri": 7, "intern": [7, 10], "resembl": 7, "easiest": 7, "especi": 7, "reli": 7, "stochast": 7, "initi": [7, 8, 9], "train_ran": 7, "test_ran": 7, "time_column": 7, "old": 7, "datapoint": [7, 10, 12, 13], "accru": 7, "entri": [7, 12, 13], "timestamp": 7, "top": 7, "df_med_tempor": 7, "fake": 7, "insert": 7, "nccccccoc1ccc2c": 7, "n1cc": 7, "cc1c": 7, "684240": 7, "1037": 7, "481464": 7, "1036": 7, "c1cn": 7, "n2c": 7, "nc3cccc": 7, "n3": 7, "cc3cc3": 7, "732625": 7, "1035": 7, "568332": 7, "1034": 7, "790259": 7, "1033": 7, "train_tempor": 7, "test_tempor": 7, "highli": 7, "skew": 7, "respcol": 7, "fd": [7, 12, 13], "histogram": [7, 12, 13], "determin": [7, 12, 13], "balanc": 7, "train_str": 7, "test_str": 7, "realist": 7, "deplopi": 7, "emul": [7, 12, 13], "hop": 7, "opportun": 7, "seri": 7, "push": 7, "domain": 7, "realibl": 7, "challeng": 7, "scaf_split": 7, "train_sca": 7, "test_sca": 7, "ground": 7, "df_val": 7, "roughli": [7, 9], "evid": 7, "pronounc": 7, "dodgerblu": 7, "middl": 7, "saffold": 7, "discuss": 7, "propreti": 7, "endpoint": 7, "routin": 7, "linearis": 7, "variat": 7, "gaussian": 7, "realiti": 7, "nearli": 7, "exhibit": 7, "superior": 7, "wide": 7, "xc50_data": 7, "keepallnodedupl": [7, 12], "pxc50_data": 7, "zip": 7, "jointplot": 7, "suptitl": 7, "plot_margin": 7, "rugplot": 7, "crimson": 7, "height": 7, "clip_on": 7, "jointgrid": 7, "0x7fd1f984f670": 7, "heteroscedast": 7, "homoscedast": 7, "transorm": 7, "0x7fd1eb924700": 7, "logartihm": 7, "power": [7, 12, 14], "um": 7, "dataset_transform": 7, "THe": 7, "0x7fd1db908550": 7, "had": 7, "reverse_transform": [7, 12], "0x7fd1bc05b4c0": 7, "mervin": 7, "framework": 7, "somewher": 7, "unavoid": 7, "ideal": 7, "deviat": [7, 12, 14], "\u03c3": 7, "heterogen": 7, "versu": 7, "assimil": 7, "hypothesi": 7, "degre": 7, "p_": 7, "activityt": 7, "cumul": 7, "cdf": 7, "eq": 7, "equal": [7, 9], "delta": 7, "vec": 7, "frac": 7, "erf": 7, "overrightarrow": 7, "sigma": 7, "concret": 7, "arbitrari": 7, "unknown": 7, "therefor": 7, "schemat": 7, "lookup": 7, "tabl": 7, "sd": 7, "scenario": [7, 12, 13], "philosoph": 7, "delimit": [7, 12, 14], "operand": 7, "censor": 7, "far": 7, "granular": 7, "therebi": 7, "combin": 7, "becom": 7, "jcheminf": 7, "biomedcentr": 7, "1186": 7, "s13321": 7, "00539": 7, "sec12": 7, "pxc50_threshold": 7, "pxc50_std": 7, "exmapl": 7, "ptr_data": 7, "gather": 7, "certainti": 7, "lower_reproduc": 7, "upper_reproduc": 7, "dataload": 7, "somewhat": 7, "invert": 7, "bell": 7, "kde": 7, "behav": 7, "patch": 7, "mpatch": 7, "line2d": 7, "ax_joint": 7, "axhlin": 7, "linestyl": 7, "ax_marg_x": 7, "axvlin": 7, "ax_marg_i": 7, "region": 7, "uncert_color": 7, "purpl": 7, "uncert_region": 7, "rectangl": 7, "fill": 7, "add_patch": 7, "box": 7, "nthreshold": 7, "nptr": 7, "nregion": 7, "fancybox": 7, "borderaxespad": 7, "leg": 7, "get_legend": 7, "legendhandl": 7, "set_color": 7, "set_alpha": 7, "tight": 7, "layout": 7, "subplots_adjust": 7, "set_size_inch": 7, "1725493911": 7, "attribut": 7, "minor": 7, "legend_handl": 7, "dash": 7, "histrogram": 7, "aforement": 7, "ptrtransform": [7, 12, 14], "ptr_transform": 7, "histplot": 7, "stat": 7, "scipi": 7, "resp_col": [7, 8], "pearsonr": 7, "std_df": 7, "groupbi": 7, "mdn_df": 7, "std_vs_median": 7, "suffix": 7, "_std": 7, "_median": 7, "dropna": 7, "activity_std": 7, "activity_median": 7, "088539": 7, "674782": 7, "265123": 7, "138620": 7, "157605": 7, "stdev": 7, "stat_func": 7, "plot_joint": 7, "zorder": 7, "0x7fd1def2f8b0": 7, "signific": 7, "assumpt": 7, "fulfil": 7, "ptr_train_ran": 7, "ptr_test_ran": 7, "ptr_train_str": 7, "ptr_test_str": 7, "ptr_train_tempor": 7, "ptr_test_tempor": 7, "ptr_train_sca": 7, "ptr_test_sca": 7, "xlim": 7, "pypoetri": 7, "virtualenv": 7, "_qsktrft": 7, "py3": 7, "warn_singular": 7, "msg": 7, "peak": 7, "extem": 7, "dsitribut": 7, "awai": 7, "bias": 7, "enum": [8, 9, 10, 12], "building_configuration_enum": [8, 10], "configuration_enum": [8, 10], "interface_enum": [8, 10], "model_runner_enum": [8, 10], "objective_enum": [8, 10], "optimization_configuration_enum": [8, 10], "prediction_configuration_enum": [8, 10], "return_values_enum": [8, 10], "visualization_enum": [8, 10], "merge_train_and_test_data": 8, "isvalid": 8, "read_data": 8, "filenam": [8, 10], "smiles_col": [8, 10, 12, 13], "aux_col": 8, "invalid": 8, "pars": [8, 9, 11], "tupl": [8, 12, 13], "ambigu": 8, "smiles_": 8, "y_": [8, 10, 12], "aux_": 8, "factori": [8, 9], "intermediate_training_dataset_fil": 8, "intermediate_test_dataset_fil": 8, "get_merged_set": 8, "check_set": 8, "scalingfittingerror": 8, "descriptor_str": 8, "insuffici": 8, "unfittedsklearnscla": 8, "novalidsmil": 8, "mol_from_smi": 8, "numpy_from_rdkit": 8, "dtype": [8, 12], "moldescriptor": 8, "nameparameterdataclass": [8, 9, 12], "abc": [8, 9, 12], "abstract": [8, 9, 12], "parallel_compute_descriptor": 8, "n_core": 8, "parallel": 8, "rdkitdescriptor": 8, "liter": [8, 9, 12, 13], "pathlib": 8, "get_fitted_scaler_for_fp": 8, "saved_param": 8, "get_fitted_scal": 8, "set_unfitted_scaler_data": 8, "fp_info": 8, "canonicalsmil": 8, "scaffold": [8, 12, 13], "genericscaffold": 8, "validdescriptor": 8, "descriptor_from_config": 8, "return_failed_idx": 8, "configur": [8, 9, 10, 11], "score_al": 8, "get_scor": 8, "score_all_smil": 8, "get_train_test_scor": 8, "get_merged_train_scor": 8, "get_ecfp_fpinfo": 8, "get_ecfpcount_fpinfo": 8, "explain_ecfp": 8, "len_feat": 8, "get_fp_info": 8, "exp_df": 8, "descript": [8, 9], "fp_idx": 8, "strt_idx": 8, "runshap": 8, "x_pred": 8, "shap": 8, "shapexplain": 8, "popul": 8, "explainpr": 8, "shallow": 8, "validate_cls_input": 8, "pi_zero": 8, "pr": 8, "melloddi": 8, "sparsechem": 8, "imbal": 8, "bedroc_scor": [8, 9], "truchon": 8, "j": 8, "bayli": 8, "screen": 8, "bad": 8, "recognit": 8, "2007": 8, "concord": 8, "statist": 8, "qualiti": 8, "harald": 8, "On": 8, "surviv": 8, "bound": 8, "2008": 8, "1209": 8, "1216": 8, "posterior": 8, "mark": 8, "abstractmethod": [8, 9], "predict_uncert": 8, "quantifi": 8, "qsartunamodel": 8, "nonetyp": [8, 9], "sent": 8, "get_metadata": 8, "train_scor": [8, 11], "test_scor": [8, 10, 11], "get_transform": 8, "perform_ptr": 8, "wrap_model": 8, "save_model": 8, "novaliddescriptor": 8, "null_scor": 8, "predict_pl": 8, "model_path": 8, "inference_path": 8, "argserror": 8, "issu": [8, 12], "uncertaintyerror": 8, "correctli": 8, "auxcovariatemiss": 8, "precomputederror": 8, "validate_arg": 8, "validate_uncertainti": 8, "check_precomp_arg": 8, "validate_set_precomput": 8, "validate_aux": 8, "doctitl": 8, "docstr": 8, "type_base_schema": 8, "tp": 8, "wyfo": 8, "json_schema": 8, "patch_schema_gener": 8, "patch_schema_optunaz": 8, "split_optim": 8, "base_chemprop_param": 8, "alg": [8, 9], "pop": 8, "fix": [8, 9], "run_studi": 8, "storag": [8, 11], "trial_number_offset": [8, 10], "log_scor": 8, "main_scor": 8, "outfnam": 8, "plot_by_configur": 8, "conf": 8, "plot_slic": [8, 9, 11], "folder_path": 8, "file_format": [8, 9, 11], "png": [8, 9], "plot_contour": [8, 9, 11], "static": 8, "plot_histori": [8, 9, 11], "set_build_cach": 9, "preexist": 9, "remove_algo_hash": 9, "buildconfig_from_tri": 9, "encode_nam": 9, "cenam": 9, "suggest_alg_param": 9, "suggest_aux_param": 9, "desc": 9, "check_invalid_descriptor_param": 9, "adaboostclassifierparamet": 9, "lassoparamet": 9, "kneighborsclassifierparamet": 9, "kneighborsregressorparamet": 9, "logisticregressionparamet": 9, "plsparamet": 9, "randomforestparamet": 9, "ridgeparamet": 9, "svcparamet": 9, "svrparamet": 9, "xgbregressorparamet": 9, "prfclassifierparamet": 9, "bootstrap": 9, "new_syn_data_frac": 9, "chempropregressorparamet": 9, "chempropclassifierparamet": 9, "chempropregressorpretrainedparamet": 9, "chemprophyperoptclassifierparamet": 9, "chemprophyperoptregressorparamet": 9, "calibratedclassifiercvparamet": 9, "mapieparamet": 9, "regressionscor": 9, "classificationscor": 9, "closer": 9, "greater": 9, "manhattan": 9, "trainarg": 9, "tanh": 9, "leakyrelu": 9, "prelu": 9, "selu": 9, "elu": 9, "turn": [9, 12, 13], "morgan_count": 9, "rdkit_2d": 9, "rdkit_2d_norm": 9, "mpnn_first_ffn": 9, "mpnn_last_ffn": 9, "linked_hidden_s": 9, "constrain": 9, "l3": 9, "init_lr_exp": 9, "final_lr_exp": 9, "warmup_epoch": 9, "l4": 9, "l5": 9, "l6": 9, "l7": 9, "l8": 9, "isanyof": 9, "obj": [9, 10], "detect_mode_from_alg": 9, "copy_path_for_scaled_descriptor": 9, "cv_split_strategi": 9, "use_cach": 9, "optuna_storag": 9, "set_cach": 9, "set_algo_hash": 9, "declar": 9, "pydant": 9, "don": 9, "classmethod": 9, "1024": 9, "shorter": 9, "output_fold": [9, 11], "use_xvfb": [9, 11], "imagefileformat": 9, "jpeg": 9, "jpg": 9, "svg": 9, "move_up_directori": 10, "attach_root_path": 10, "attach": 10, "loadjson": 10, "add_ellipsi": 10, "max_length": 10, "shorten_nam": 10, "mlflowcallback": 10, "tracking_uri": 10, "callback": 10, "uri": 10, "server": 10, "set_tracking_uri": 10, "prepare_tag": 10, "tag": 10, "tmp_buildconfig": 10, "create_depend": 10, "remove_schema_properti": 10, "add_boolean_guards_for_schema_properti": 10, "replacekei": 10, "input_": 10, "replacevalu": 10, "addsibl": 10, "delsibl": 10, "sibl": 10, "getref": 10, "context": 10, "recurs": 10, "nest": 10, "copytitl": 10, "oneof": 10, "replaceenum": 10, "singleton": 10, "const": 10, "addtitl": 10, "get_authorization_head": 10, "trackingdata": 10, "trial_numb": [10, 11], "trial_valu": 10, "trial_stat": 10, "all_cv_test_scor": 10, "dataclass": 10, "removeprefix": 10, "prefix": 10, "round_scor": 10, "internaltrackingcallback": 10, "progress": 10, "buildtrackingdata": 10, "response_column_nam": 10, "test_point": 10, "track_build": 10, "mkdict": 10, "load_df_from_fil": 10, "remove_failed_idx": 10, "failed_idx": 10, "md5_hash": 10, "md5": 10, "buildingconfigurationenum": 11, "configurationenum": 11, "general_hyperparamet": 11, "hyper_paramet": 11, "general_regressor": 11, "general_classifi": 11, "metadata_besttri": 11, "metadata_bestvalu": 11, "general_dis": 11, "general_paramet": 11, "task_optim": 11, "task_build": 11, "data_inputcolumn": 11, "data_responsecolumn": 11, "data_train": 11, "data_test": 11, "descriptors_avalon": 11, "descriptors_avalon_nbit": 11, "descriptors_ecfp": 11, "descriptors_ecfp_radiu": 11, "descriptors_ecfp_nbit": 11, "descriptors_ecfpcount": 11, "descriptors_ecfpcounts_radiu": 11, "descriptors_ecfpcounts_usefeatur": 11, "descriptors_pathfp": 11, "descriptors_pathfp_maxpath": 11, "descriptors_pathfp_fps": 11, "descriptors_maccskei": 11, "descriptors_unsc_physchem": 11, "descriptors_physchem": 11, "descriptors_physchem_rdkitnam": 11, "descriptors_unsc_jazzi": 11, "descriptors_jazzi": 11, "descriptors_jazzy_jazzynam": 11, "descriptors_precomput": 11, "descriptors_precomputed_fil": 11, "descriptors_precomputed_input_columnn": 11, "descriptors_precomputed_response_column": 11, "descriptors_unsc_zscal": 11, "descriptors_zscal": 11, "descriptors_smil": 11, "descriptors_smiles_and_si": 11, "descriptors_smiles_and_si_fil": 11, "descriptors_smiles_and_si_input_column": 11, "descriptors_smiles_and_si_aux_weight_pc": 11, "descriptors_sc": 11, "descriptors_scaled_descriptor": 11, "descriptors_scaled_descriptor_paramet": 11, "descriptors_composit": 11, "settings_mod": 11, "settings_mode_regress": 11, "settings_mode_classif": 11, "settings_cross_valid": 11, "settings_direct": 11, "settings_n_tri": 11, "settings_n_job": 11, "settings_shuffl": 11, "algorithms_low": 11, "algorithms_high": 11, "algorithms_q": 11, "algorithms_interface_sklearn": 11, "algorithms_interface_xgboost": 11, "algorithms_rfregressor": 11, "algorithms_rfclassifi": 11, "algorithms_rf_max_featur": 11, "algorithms_rf_max_depth": 11, "algorithms_rf_n_estim": 11, "algorithms_svr": 11, "algorithms_svr_c": 11, "algorithms_svr_gamma": 11, "algorithms_svc": 11, "algorithms_svc_c": 11, "algorithms_svc_gamma": 11, "algorithms_lasso": 11, "algorithms_lasso_alpha": 11, "algorithms_kneighborsclassifi": 11, "algorithms_kneighborsregressor": 11, "algorithms_kneighbors_n_neighbor": 11, "algorithms_kneighbors_metr": 11, "algorithms_kneighbors_weight": 11, "algorithms_ridg": 11, "algorithms_ridge_alpha": 11, "algorithms_plsregress": 11, "algorithms_plsregression_n_compon": 11, "algorithms_logisticregress": 11, "algorithms_logisticregression_solv": 11, "algorithms_logisticregression_c": 11, "algorithms_adaboostclassifi": 11, "algorithms_adaboostclassifier_n_estim": 11, "algorithms_adaboostclassifier_learning_r": 11, "algorithms_xgbregressor": 11, "algorithms_xgbregressor_max_depth": 11, "algorithms_xgbregressor_n_estim": 11, "algorithms_xgbregressor_learning_r": 11, "algorithms_prf": 11, "algorithms_prf_max_featur": 11, "algorithms_prf_max_depth": 11, "algorithms_prf_n_estim": 11, "algorithms_prf_minpysumleaf": 11, "algorithms_prf_use_py_gini": 11, "algorithms_prf_use_py_leaf": 11, "algorithms_chemprop": 11, "basechemprop": 11, "algorithms_chemprop_regressor": 11, "algorithms_chemprop_hyperopt_regressor": 11, "algorithms_chemprop_classifi": 11, "algorithms_chemprop_hyperopt_classifi": 11, "algorithms_chemprop_activ": 11, "algorithms_chemprop_aggreg": 11, "algorithms_chemprop_aggregation_norm": 11, "algorithms_chemprop_batch_s": 11, "algorithms_chemprop_depth": 11, "algorithms_chemprop_dropout": 11, "algorithms_chemprop_epoch": 11, "algorithms_chemprop_ensemble_s": 11, "algorithms_chemprop_features_gener": 11, "algorithms_chemprop_ffn_hidden_s": 11, "algorithms_chemprop_ffn_num_lay": 11, "algorithms_chemprop_frzn": 11, "algorithms_chemprop_final_lr_ratio_exp": 11, "algorithms_chemprop_hidden_s": 11, "algorithms_chemprop_num_it": 11, "algorithms_chemprop_init_lr_ratio_exp": 11, "algorithms_chemprop_max_lr_exp": 11, "algorithms_chemprop_pretrained_model": 11, "algorithms_chemprop_search_parameter_level": 11, "algorithms_chemprop_startup_random_it": 11, "startup_random_it": 11, "algorithms_chemprop_warmup_epochs_ratio": 11, "algorithms_calibratedclassifiercv": 11, "algorithms_calibratedclassifiercv_ensembl": 11, "algorithms_calibratedclassifiercv_estim": 11, "algorithms_calibratedclassifiercv_method": 11, "algorithms_calibratedclassifiercv_n_fold": 11, "algorithms_calibratedclassifiercv_param": 11, "calibrated_param": 11, "algorithms_mapi": 11, "algorithms_mapie_alpha": 11, "interfaceenum": 11, "sklearn_set": 11, "xgboost_set": 11, "chemprop_set": 11, "prf_set": 11, "calibrated_set": 11, "modelrunnerdataframeenum": 11, "modelrunn": 11, "objectiveenum": 11, "attribute_trial_train_scor": 11, "extra_column_besthit": 11, "besthit": 11, "optimizationconfigurationenum": 11, "predictionconfigurationenum": 11, "data_dataset": 11, "sklearnreturnvalueenum": 11, "cross_validate_fit_tim": 11, "fit_tim": 11, "cross_validate_score_tim": 11, "score_tim": 11, "cross_validate_test_scor": 11, "cross_validate_train_scor": 11, "xgboostreturnvalueenum": 11, "visualizationenum": 11, "visualization_regressor": 11, "visualization_classifi": 11, "visualization_use_xvfb": 11, "visualization_output_fold": 11, "visualization_file_format": 11, "visualization_plot": 11, "visualization_plots_histori": 11, "visualization_plots_contour": 11, "visualization_plots_parallel_coordin": 11, "visualization_plots_slic": 11, "optuna_system_attrs_numb": 11, "_number": 11, "optuna_system_attrs_intermediate_valu": 11, "intermediate_valu": 11, "optuna_system_attrs_trial_id": 11, "trial_id": 11, "studyuserattr": 11, "trialuserattr": 11, "trialparam": 11, "algorithm_hash": 11, "mlflowlogparam": 11, "sklearnsplitt": 12, "get_n_split": 12, "cvsplitter": 12, "although": 12, "underli": 12, "get_sklearn_splitt": 12, "n_split": 12, "repeat": [12, 13], "edg": [12, 13], "stratifiedshufflesplit": [12, 13], "revert": [12, 13], "empti": 12, "kfold": 12, "affect": 12, "consecut": 12, "fd_bin": 12, "11879": 12, "10297": 12, "adjac": 12, "downstream": 12, "nativ": 12, "histogramstratifiedshufflesplit": 12, "test_fract": 12, "groupingsplitt": 12, "column_nam": [12, 13], "butina_clust": [12, 13], "cluster": [12, 13], "butina": [12, 13], "make_scaffold_gener": [12, 13], "murcko": [12, 13], "hetero": [12, 13], "difficulti": [12, 13], "novel": [12, 13], "datatransform": 12, "logarithm": [12, 14], "base_dict": 12, "ufunc": 12, "base_neg": 12, "reverse_dict": 12, "exp": 12, "transform_df": 12, "transform_on": 12, "reverse_transform_df": 12, "reverse_transform_on": 12, "auxtransform": 12, "transfor": 12, "auxiliary_data": 12, "usabl": [12, 14]}, "objects": {"": [[8, 0, 0, "-", "optunaz"]], "optunaz": [[8, 0, 0, "-", "builder"], [9, 0, 0, "-", "config"], [8, 0, 0, "-", "datareader"], [8, 0, 0, "-", "descriptors"], [8, 0, 0, "-", "evaluate"], [8, 0, 0, "-", "explainability"], [8, 0, 0, "-", "metircs"], [8, 0, 0, "-", "model_writer"], [8, 0, 0, "-", "objective"], [8, 0, 0, "-", "optbuild"], [8, 0, 0, "-", "predict"], [8, 0, 0, "-", "schemagen"], [8, 0, 0, "-", "three_step_opt_build_merge"], [10, 0, 0, "-", "utils"], [8, 0, 0, "-", "visualizer"]], "optunaz.builder": [[8, 1, 1, "", "build"]], "optunaz.config": [[9, 2, 1, "", "Algorithm"], [9, 2, 1, "", "ModelMode"], [9, 2, 1, "", "NameParameterDataclass"], [9, 2, 1, "", "OptimizationDirection"], [9, 2, 1, "", "Task"], [9, 2, 1, "", "Visualization"], [9, 0, 0, "-", "build_from_opt"], [9, 0, 0, "-", "buildconfig"], [9, 0, 0, "-", "optconfig"]], "optunaz.config.ModelMode": [[9, 3, 1, "", "CLASSIFICATION"], [9, 3, 1, "", "REGRESSION"]], "optunaz.config.NameParameterDataclass": [[9, 4, 1, "", "new"]], "optunaz.config.OptimizationDirection": [[9, 3, 1, "", "MAXIMIZATION"], [9, 3, 1, "", "MINIMIZATION"]], "optunaz.config.Task": [[9, 3, 1, "", "BUILDING"], [9, 3, 1, "", "OPTIMIZATION"], [9, 3, 1, "", "PREDICTION"]], "optunaz.config.Visualization": [[9, 2, 1, "", "ImageFileFormat"], [9, 2, 1, "", "Plots"], [9, 3, 1, "", "file_format"], [9, 3, 1, "", "output_folder"], [9, 3, 1, "", "plots"], [9, 3, 1, "", "use_xvfb"]], "optunaz.config.Visualization.ImageFileFormat": [[9, 3, 1, "", "JPEG"], [9, 3, 1, "", "JPG"], [9, 3, 1, "", "PDF"], [9, 3, 1, "", "PNG"], [9, 3, 1, "", "SVG"]], "optunaz.config.Visualization.Plots": [[9, 3, 1, "", "plot_contour"], [9, 3, 1, "", "plot_history"], [9, 3, 1, "", "plot_parallel_coordinate"], [9, 3, 1, "", "plot_slice"]], "optunaz.config.build_from_opt": [[9, 1, 1, "", "buildconfig_from_trial"], [9, 1, 1, "", "check_invalid_descriptor_param"], [9, 1, 1, "", "encode_name"], [9, 1, 1, "", "remove_algo_hash"], [9, 1, 1, "", "set_build_cache"], [9, 1, 1, "", "suggest_alg_params"], [9, 1, 1, "", "suggest_aux_params"]], "optunaz.config.buildconfig": [[9, 2, 1, "", "AdaBoostClassifier"], [9, 2, 1, "", "Algorithm"], [9, 2, 1, "", "BuildConfig"], [9, 2, 1, "", "CalibratedClassifierCVWithVA"], [9, 2, 1, "", "ChemPropClassifier"], [9, 2, 1, "", "ChemPropHyperoptClassifier"], [9, 2, 1, "", "ChemPropHyperoptRegressor"], [9, 2, 1, "", "ChemPropRegressor"], [9, 2, 1, "", "ChemPropRegressorPretrained"], [9, 2, 1, "", "KNeighborsClassifier"], [9, 2, 1, "", "KNeighborsRegressor"], [9, 2, 1, "", "Lasso"], [9, 2, 1, "", "LogisticRegression"], [9, 2, 1, "", "Mapie"], [9, 2, 1, "", "PLSRegression"], [9, 2, 1, "", "PRFClassifier"], [9, 2, 1, "", "RandomForestClassifier"], [9, 2, 1, "", "RandomForestRegressor"], [9, 2, 1, "", "Ridge"], [9, 2, 1, "", "SVC"], [9, 2, 1, "", "SVR"], [9, 2, 1, "", "XGBRegressor"]], "optunaz.config.buildconfig.AdaBoostClassifier": [[9, 2, 1, "", "AdaBoostClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.AdaBoostClassifier.AdaBoostClassifierParameters": [[9, 3, 1, "", "learning_rate"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.buildconfig.Algorithm": [[9, 4, 1, "", "estimator"]], "optunaz.config.buildconfig.BuildConfig": [[9, 2, 1, "", "Metadata"], [9, 2, 1, "", "Settings"], [9, 3, 1, "", "algorithm"], [9, 3, 1, "", "data"], [9, 3, 1, "", "descriptor"], [9, 3, 1, "", "metadata"], [9, 3, 1, "", "settings"], [9, 3, 1, "", "task"]], "optunaz.config.buildconfig.BuildConfig.Metadata": [[9, 3, 1, "", "best_trial"], [9, 3, 1, "", "best_value"], [9, 3, 1, "", "cross_validation"], [9, 3, 1, "", "n_trials"], [9, 3, 1, "", "name"], [9, 3, 1, "", "shuffle"], [9, 3, 1, "", "visualization"]], "optunaz.config.buildconfig.BuildConfig.Settings": [[9, 3, 1, "", "direction"], [9, 3, 1, "", "mode"], [9, 3, 1, "", "n_trials"], [9, 3, 1, "", "scoring"], [9, 3, 1, "", "tracking_rest_endpoint"]], "optunaz.config.buildconfig.CalibratedClassifierCVWithVA": [[9, 2, 1, "", "CalibratedClassifierCVParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.CalibratedClassifierCVWithVA.CalibratedClassifierCVParameters": [[9, 3, 1, "", "ensemble"], [9, 3, 1, "", "estimator"], [9, 3, 1, "", "method"], [9, 3, 1, "", "n_folds"]], "optunaz.config.buildconfig.ChemPropClassifier": [[9, 2, 1, "", "ChemPropClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropClassifier.ChemPropClassifierParameters": [[9, 3, 1, "", "activation"], [9, 3, 1, "", "aggregation"], [9, 3, 1, "", "aggregation_norm"], [9, 3, 1, "", "aux_weight_pc"], [9, 3, 1, "", "batch_size"], [9, 3, 1, "", "depth"], [9, 3, 1, "", "dropout"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "ffn_hidden_size"], [9, 3, 1, "", "ffn_num_layers"], [9, 3, 1, "", "final_lr_ratio_exp"], [9, 3, 1, "", "hidden_size"], [9, 3, 1, "", "init_lr_ratio_exp"], [9, 3, 1, "", "max_lr_exp"], [9, 3, 1, "", "warmup_epochs_ratio"]], "optunaz.config.buildconfig.ChemPropHyperoptClassifier": [[9, 2, 1, "", "ChemPropHyperoptClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropHyperoptClassifier.ChemPropHyperoptClassifierParameters": [[9, 3, 1, "", "aux_weight_pc"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "num_iters"], [9, 3, 1, "", "search_parameter_level"]], "optunaz.config.buildconfig.ChemPropHyperoptRegressor": [[9, 2, 1, "", "ChemPropHyperoptRegressorParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropHyperoptRegressor.ChemPropHyperoptRegressorParameters": [[9, 3, 1, "", "aux_weight_pc"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "num_iters"], [9, 3, 1, "", "search_parameter_level"]], "optunaz.config.buildconfig.ChemPropRegressor": [[9, 2, 1, "", "ChemPropRegressorParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropRegressor.ChemPropRegressorParameters": [[9, 3, 1, "", "activation"], [9, 3, 1, "", "aggregation"], [9, 3, 1, "", "aggregation_norm"], [9, 3, 1, "", "aux_weight_pc"], [9, 3, 1, "", "batch_size"], [9, 3, 1, "", "depth"], [9, 3, 1, "", "dropout"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "ffn_hidden_size"], [9, 3, 1, "", "ffn_num_layers"], [9, 3, 1, "", "final_lr_ratio_exp"], [9, 3, 1, "", "hidden_size"], [9, 3, 1, "", "init_lr_ratio_exp"], [9, 3, 1, "", "max_lr_exp"], [9, 3, 1, "", "warmup_epochs_ratio"]], "optunaz.config.buildconfig.ChemPropRegressorPretrained": [[9, 2, 1, "", "ChemPropRegressorPretrainedParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.ChemPropRegressorPretrained.ChemPropRegressorPretrainedParameters": [[9, 3, 1, "", "epochs"], [9, 3, 1, "", "frzn"], [9, 3, 1, "", "pretrained_model"]], "optunaz.config.buildconfig.KNeighborsClassifier": [[9, 2, 1, "", "KNeighborsClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.KNeighborsClassifier.KNeighborsClassifierParameters": [[9, 3, 1, "", "metric"], [9, 3, 1, "", "n_neighbors"], [9, 3, 1, "", "weights"]], "optunaz.config.buildconfig.KNeighborsRegressor": [[9, 2, 1, "", "KNeighborsRegressorParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.KNeighborsRegressor.KNeighborsRegressorParameters": [[9, 3, 1, "", "metric"], [9, 3, 1, "", "n_neighbors"], [9, 3, 1, "", "weights"]], "optunaz.config.buildconfig.Lasso": [[9, 2, 1, "", "LassoParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.Lasso.LassoParameters": [[9, 3, 1, "", "alpha"]], "optunaz.config.buildconfig.LogisticRegression": [[9, 2, 1, "", "LogisticRegressionParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.LogisticRegression.LogisticRegressionParameters": [[9, 3, 1, "", "C"], [9, 3, 1, "", "solver"]], "optunaz.config.buildconfig.Mapie": [[9, 2, 1, "", "MapieParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.Mapie.MapieParameters": [[9, 3, 1, "", "estimator"], [9, 3, 1, "", "mapie_alpha"]], "optunaz.config.buildconfig.PLSRegression": [[9, 2, 1, "", "PLSParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.PLSRegression.PLSParameters": [[9, 3, 1, "", "n_components"]], "optunaz.config.buildconfig.PRFClassifier": [[9, 2, 1, "", "PRFClassifierParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.PRFClassifier.PRFClassifierParameters": [[9, 3, 1, "", "bootstrap"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "min_py_sum_leaf"], [9, 3, 1, "", "n_estimators"], [9, 3, 1, "", "new_syn_data_frac"], [9, 3, 1, "", "use_py_gini"], [9, 3, 1, "", "use_py_leafs"]], "optunaz.config.buildconfig.RandomForestClassifier": [[9, 2, 1, "", "RandomForestParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.RandomForestClassifier.RandomForestParameters": [[9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.buildconfig.RandomForestRegressor": [[9, 2, 1, "", "RandomForestParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.RandomForestRegressor.RandomForestParameters": [[9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.buildconfig.Ridge": [[9, 2, 1, "", "RidgeParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.Ridge.RidgeParameters": [[9, 3, 1, "", "alpha"]], "optunaz.config.buildconfig.SVC": [[9, 2, 1, "", "SVCParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.SVC.SVCParameters": [[9, 3, 1, "", "C"], [9, 3, 1, "", "gamma"]], "optunaz.config.buildconfig.SVR": [[9, 2, 1, "", "SVRParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.SVR.SVRParameters": [[9, 3, 1, "", "C"], [9, 3, 1, "", "gamma"]], "optunaz.config.buildconfig.XGBRegressor": [[9, 2, 1, "", "XGBRegressorParameters"], [9, 4, 1, "", "estimator"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.buildconfig.XGBRegressor.XGBRegressorParameters": [[9, 3, 1, "", "learning_rate"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig": [[9, 2, 1, "", "AdaBoostClassifier"], [9, 2, 1, "", "Algorithm"], [9, 2, 1, "", "CalibratedClassifierCVEnsemble"], [9, 2, 1, "", "CalibratedClassifierCVMethod"], [9, 2, 1, "", "CalibratedClassifierCVWithVA"], [9, 2, 1, "", "ChemPropActivation"], [9, 2, 1, "", "ChemPropAggregation"], [9, 2, 1, "", "ChemPropClassifier"], [9, 2, 1, "", "ChemPropFeatures_Generator"], [9, 2, 1, "", "ChemPropFrzn"], [9, 2, 1, "", "ChemPropHyperoptClassifier"], [9, 2, 1, "", "ChemPropHyperoptRegressor"], [9, 2, 1, "", "ChemPropRegressor"], [9, 2, 1, "", "ChemPropRegressorPretrained"], [9, 2, 1, "", "ChemPropSearch_Parameter_Level"], [9, 2, 1, "", "ClassificationScore"], [9, 2, 1, "", "KNeighborsClassifier"], [9, 2, 1, "", "KNeighborsMetric"], [9, 2, 1, "", "KNeighborsRegressor"], [9, 2, 1, "", "KNeighborsWeights"], [9, 2, 1, "", "Lasso"], [9, 2, 1, "", "LogisticRegression"], [9, 2, 1, "", "Mapie"], [9, 2, 1, "", "OptimizationConfig"], [9, 2, 1, "", "PLSRegression"], [9, 2, 1, "", "PRFClassifier"], [9, 2, 1, "", "PRFClassifierMaxFeatures"], [9, 2, 1, "", "RandomForestClassifier"], [9, 2, 1, "", "RandomForestMaxFeatures"], [9, 2, 1, "", "RandomForestRegressor"], [9, 2, 1, "", "RegressionScore"], [9, 2, 1, "", "Ridge"], [9, 2, 1, "", "SVC"], [9, 2, 1, "", "SVR"], [9, 2, 1, "", "XGBRegressor"], [9, 1, 1, "", "copy_path_for_scaled_descriptor"], [9, 1, 1, "", "detect_mode_from_algs"], [9, 1, 1, "", "isanyof"]], "optunaz.config.optconfig.AdaBoostClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.AdaBoostClassifier.Parameters": [[9, 2, 1, "", "AdaBoostClassifierParametersLearningRate"], [9, 2, 1, "", "AdaBoostClassifierParametersNEstimators"], [9, 3, 1, "", "learning_rate"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig.AdaBoostClassifier.Parameters.AdaBoostClassifierParametersLearningRate": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.AdaBoostClassifier.Parameters.AdaBoostClassifierParametersNEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.CalibratedClassifierCVEnsemble": [[9, 3, 1, "", "FALSE"], [9, 3, 1, "", "TRUE"]], "optunaz.config.optconfig.CalibratedClassifierCVMethod": [[9, 3, 1, "", "ISOTONIC"], [9, 3, 1, "", "SIGMOID"], [9, 3, 1, "", "VENNABERS"]], "optunaz.config.optconfig.CalibratedClassifierCVWithVA": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.CalibratedClassifierCVWithVA.Parameters": [[9, 3, 1, "", "ensemble"], [9, 3, 1, "", "estimator"], [9, 3, 1, "", "method"], [9, 3, 1, "", "n_folds"]], "optunaz.config.optconfig.ChemPropActivation": [[9, 3, 1, "", "ELU"], [9, 3, 1, "", "LEAKYRELU"], [9, 3, 1, "", "PRELU"], [9, 3, 1, "", "RELU"], [9, 3, 1, "", "SELU"], [9, 3, 1, "", "TANH"]], "optunaz.config.optconfig.ChemPropAggregation": [[9, 3, 1, "", "MEAN"], [9, 3, 1, "", "NORM"], [9, 3, 1, "", "SUM"]], "optunaz.config.optconfig.ChemPropClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters": [[9, 2, 1, "", "ChemPropParametersAggregation_Norm"], [9, 2, 1, "", "ChemPropParametersBatch_Size"], [9, 2, 1, "", "ChemPropParametersDepth"], [9, 2, 1, "", "ChemPropParametersDropout"], [9, 2, 1, "", "ChemPropParametersFFN_Hidden_Size"], [9, 2, 1, "", "ChemPropParametersFFN_Num_Layers"], [9, 2, 1, "", "ChemPropParametersFinal_Lr_Ratio_Exp"], [9, 2, 1, "", "ChemPropParametersHidden_Size"], [9, 2, 1, "", "ChemPropParametersInit_Lr_Ratio_Exp"], [9, 2, 1, "", "ChemPropParametersMax_Lr_Exp"], [9, 2, 1, "", "ChemPropParametersWarmup_Epochs_Ratio"], [9, 3, 1, "", "activation"], [9, 3, 1, "", "aggregation"], [9, 3, 1, "", "aggregation_norm"], [9, 3, 1, "", "batch_size"], [9, 3, 1, "", "depth"], [9, 3, 1, "", "dropout"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "ffn_hidden_size"], [9, 3, 1, "", "ffn_num_layers"], [9, 3, 1, "", "final_lr_ratio_exp"], [9, 3, 1, "", "hidden_size"], [9, 3, 1, "", "init_lr_ratio_exp"], [9, 3, 1, "", "max_lr_exp"], [9, 3, 1, "", "warmup_epochs_ratio"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersAggregation_Norm": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersBatch_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersDropout": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Hidden_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFFN_Num_Layers": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersHidden_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersInit_Lr_Ratio_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersMax_Lr_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropClassifier.Parameters.ChemPropParametersWarmup_Epochs_Ratio": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropFeatures_Generator": [[9, 3, 1, "", "MORGAN"], [9, 3, 1, "", "MORGAN_COUNT"], [9, 3, 1, "", "NONE"], [9, 3, 1, "", "RDKIT_2D"], [9, 3, 1, "", "RDKIT_2D_NORMALIZED"]], "optunaz.config.optconfig.ChemPropFrzn": [[9, 3, 1, "", "MPNN"], [9, 3, 1, "", "MPNN_FIRST_FFN"], [9, 3, 1, "", "MPNN_LAST_FFN"], [9, 3, 1, "", "NONE"]], "optunaz.config.optconfig.ChemPropHyperoptClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropHyperoptClassifier.Parameters": [[9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "num_iters"], [9, 3, 1, "", "search_parameter_level"]], "optunaz.config.optconfig.ChemPropHyperoptRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropHyperoptRegressor.Parameters": [[9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "num_iters"], [9, 3, 1, "", "search_parameter_level"]], "optunaz.config.optconfig.ChemPropRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters": [[9, 2, 1, "", "ChemPropParametersAggregation_Norm"], [9, 2, 1, "", "ChemPropParametersBatch_Size"], [9, 2, 1, "", "ChemPropParametersDepth"], [9, 2, 1, "", "ChemPropParametersDropout"], [9, 2, 1, "", "ChemPropParametersFFN_Hidden_Size"], [9, 2, 1, "", "ChemPropParametersFFN_Num_Layers"], [9, 2, 1, "", "ChemPropParametersFinal_Lr_Ratio_Exp"], [9, 2, 1, "", "ChemPropParametersHidden_Size"], [9, 2, 1, "", "ChemPropParametersInit_Lr_Ratio_Exp"], [9, 2, 1, "", "ChemPropParametersMax_Lr_Exp"], [9, 2, 1, "", "ChemPropParametersWarmup_Epochs_Ratio"], [9, 3, 1, "", "activation"], [9, 3, 1, "", "aggregation"], [9, 3, 1, "", "aggregation_norm"], [9, 3, 1, "", "batch_size"], [9, 3, 1, "", "depth"], [9, 3, 1, "", "dropout"], [9, 3, 1, "", "ensemble_size"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "features_generator"], [9, 3, 1, "", "ffn_hidden_size"], [9, 3, 1, "", "ffn_num_layers"], [9, 3, 1, "", "final_lr_ratio_exp"], [9, 3, 1, "", "hidden_size"], [9, 3, 1, "", "init_lr_ratio_exp"], [9, 3, 1, "", "max_lr_exp"], [9, 3, 1, "", "warmup_epochs_ratio"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersAggregation_Norm": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersBatch_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersDropout": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Hidden_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFFN_Num_Layers": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersFinal_Lr_Ratio_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersHidden_Size": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersInit_Lr_Ratio_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersMax_Lr_Exp": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.ChemPropRegressor.Parameters.ChemPropParametersWarmup_Epochs_Ratio": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropRegressorPretrained": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters": [[9, 2, 1, "", "ChemPropParametersEpochs"], [9, 3, 1, "", "epochs"], [9, 3, 1, "", "frzn"], [9, 3, 1, "", "pretrained_model"]], "optunaz.config.optconfig.ChemPropRegressorPretrained.Parameters.ChemPropParametersEpochs": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"], [9, 3, 1, "", "q"]], "optunaz.config.optconfig.ChemPropSearch_Parameter_Level": [[9, 3, 1, "", "AUTO"], [9, 3, 1, "", "L1"], [9, 3, 1, "", "L2"], [9, 3, 1, "", "L3"], [9, 3, 1, "", "L4"], [9, 3, 1, "", "L5"], [9, 3, 1, "", "L6"], [9, 3, 1, "", "L7"], [9, 3, 1, "", "L8"]], "optunaz.config.optconfig.ClassificationScore": [[9, 3, 1, "", "ACCURACY"], [9, 3, 1, "", "AUC_PR_CAL"], [9, 3, 1, "", "AVERAGE_PRECISION"], [9, 3, 1, "", "BALANCED_ACCURACY"], [9, 3, 1, "", "BEDROC"], [9, 3, 1, "", "CONCORDANCE_INDEX"], [9, 3, 1, "", "F1"], [9, 3, 1, "", "F1_MACRO"], [9, 3, 1, "", "F1_MICRO"], [9, 3, 1, "", "F1_WEIGHTED"], [9, 3, 1, "", "JACCARD"], [9, 3, 1, "", "JACCARD_MACRO"], [9, 3, 1, "", "JACCARD_MICRO"], [9, 3, 1, "", "JACCARD_WEIGHTED"], [9, 3, 1, "", "NEG_BRIER_SCORE"], [9, 3, 1, "", "PRECISION"], [9, 3, 1, "", "PRECISION_MACRO"], [9, 3, 1, "", "PRECISION_MICRO"], [9, 3, 1, "", "PRECISION_WEIGHTED"], [9, 3, 1, "", "RECALL"], [9, 3, 1, "", "RECALL_MACRO"], [9, 3, 1, "", "RECALL_MICRO"], [9, 3, 1, "", "RECALL_WEIGHTED"], [9, 3, 1, "", "ROC_AUC"]], "optunaz.config.optconfig.KNeighborsClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.KNeighborsClassifier.Parameters": [[9, 2, 1, "", "KNeighborsClassifierParametersN_Neighbors"], [9, 3, 1, "", "metric"], [9, 3, 1, "", "n_neighbors"], [9, 3, 1, "", "weights"]], "optunaz.config.optconfig.KNeighborsClassifier.Parameters.KNeighborsClassifierParametersN_Neighbors": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.KNeighborsMetric": [[9, 3, 1, "", "EUCLIDEAN"], [9, 3, 1, "", "MANHATTAN"], [9, 3, 1, "", "MINKOWSKI"]], "optunaz.config.optconfig.KNeighborsRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.KNeighborsRegressor.Parameters": [[9, 2, 1, "", "KNeighborsRegressorParametersN_Neighbors"], [9, 3, 1, "", "metric"], [9, 3, 1, "", "n_neighbors"], [9, 3, 1, "", "weights"]], "optunaz.config.optconfig.KNeighborsRegressor.Parameters.KNeighborsRegressorParametersN_Neighbors": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.KNeighborsWeights": [[9, 3, 1, "", "DISTANCE"], [9, 3, 1, "", "UNIFORM"]], "optunaz.config.optconfig.Lasso": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.Lasso.Parameters": [[9, 2, 1, "", "LassoParametersAlpha"], [9, 3, 1, "", "alpha"]], "optunaz.config.optconfig.Lasso.Parameters.LassoParametersAlpha": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.LogisticRegression": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.LogisticRegression.Parameters": [[9, 3, 1, "", "C"], [9, 2, 1, "", "LogisticRegressionParametersParameterC"], [9, 3, 1, "", "solver"]], "optunaz.config.optconfig.LogisticRegression.Parameters.LogisticRegressionParametersParameterC": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.Mapie": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.Mapie.Parameters": [[9, 3, 1, "", "estimator"], [9, 3, 1, "", "mapie_alpha"]], "optunaz.config.optconfig.OptimizationConfig": [[9, 2, 1, "", "Settings"], [9, 3, 1, "", "algorithms"], [9, 3, 1, "", "data"], [9, 3, 1, "", "description"], [9, 3, 1, "", "descriptors"], [9, 3, 1, "", "mode"], [9, 3, 1, "", "name"], [9, 4, 1, "", "set_algo_hashes"], [9, 4, 1, "", "set_cache"], [9, 3, 1, "", "settings"], [9, 3, 1, "", "task"], [9, 3, 1, "", "visualization"]], "optunaz.config.optconfig.OptimizationConfig.Settings": [[9, 3, 1, "", "cross_validation"], [9, 3, 1, "", "cv_split_strategy"], [9, 3, 1, "", "direction"], [9, 3, 1, "", "minimise_std_dev"], [9, 3, 1, "", "mode"], [9, 3, 1, "", "n_chemprop_trials"], [9, 3, 1, "", "n_jobs"], [9, 3, 1, "", "n_startup_trials"], [9, 3, 1, "", "n_trials"], [9, 3, 1, "", "optuna_storage"], [9, 3, 1, "", "random_seed"], [9, 3, 1, "", "scoring"], [9, 3, 1, "", "shuffle"], [9, 3, 1, "", "split_chemprop"], [9, 3, 1, "", "track_to_mlflow"], [9, 3, 1, "", "tracking_rest_endpoint"], [9, 3, 1, "", "use_cache"]], "optunaz.config.optconfig.PLSRegression": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.PLSRegression.Parameters": [[9, 2, 1, "", "NComponents"], [9, 3, 1, "", "n_components"]], "optunaz.config.optconfig.PLSRegression.Parameters.NComponents": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.PRFClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.PRFClassifier.Parameters": [[9, 2, 1, "", "PRFClassifierParametersMaxDepth"], [9, 2, 1, "", "PRFClassifierParametersMinPySumLeaf"], [9, 2, 1, "", "PRFClassifierParametersNEstimators"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "min_py_sum_leaf"], [9, 3, 1, "", "n_estimators"], [9, 3, 1, "", "use_py_gini"], [9, 3, 1, "", "use_py_leafs"]], "optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersMaxDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersMinPySumLeaf": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.PRFClassifier.Parameters.PRFClassifierParametersNEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.PRFClassifierMaxFeatures": [[9, 3, 1, "", "AUTO"], [9, 3, 1, "", "LOG2"], [9, 3, 1, "", "SQRT"]], "optunaz.config.optconfig.RandomForestClassifier": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.RandomForestClassifier.Parameters": [[9, 2, 1, "", "RandomForestClassifierParametersMaxDepth"], [9, 2, 1, "", "RandomForestClassifierParametersNEstimators"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig.RandomForestClassifier.Parameters.RandomForestClassifierParametersMaxDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.RandomForestClassifier.Parameters.RandomForestClassifierParametersNEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.RandomForestMaxFeatures": [[9, 3, 1, "", "AUTO"], [9, 3, 1, "", "LOG2"], [9, 3, 1, "", "SQRT"]], "optunaz.config.optconfig.RandomForestRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.RandomForestRegressor.Parameters": [[9, 2, 1, "", "RandomForestRegressorParametersMaxDepth"], [9, 2, 1, "", "RandomForestRegressorParametersNEstimators"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "max_features"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig.RandomForestRegressor.Parameters.RandomForestRegressorParametersMaxDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.RandomForestRegressor.Parameters.RandomForestRegressorParametersNEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.RegressionScore": [[9, 3, 1, "", "EXPLAINED_VARIANCE"], [9, 3, 1, "", "MAX_ERROR"], [9, 3, 1, "", "NEG_MEAN_ABSOLUTE_ERROR"], [9, 3, 1, "", "NEG_MEAN_SQUARED_ERROR"], [9, 3, 1, "", "NEG_MEDIAN_ABSOLUTE_ERROR"], [9, 3, 1, "", "R2"]], "optunaz.config.optconfig.Ridge": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.Ridge.Parameters": [[9, 2, 1, "", "Alpha"], [9, 3, 1, "", "alpha"]], "optunaz.config.optconfig.Ridge.Parameters.Alpha": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.SVC": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.SVC.Parameters": [[9, 3, 1, "", "C"], [9, 2, 1, "", "Gamma"], [9, 2, 1, "", "SVCParametersParameterC"], [9, 3, 1, "", "gamma"]], "optunaz.config.optconfig.SVC.Parameters.Gamma": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.SVC.Parameters.SVCParametersParameterC": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.SVR": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.SVR.Parameters": [[9, 3, 1, "", "C"], [9, 2, 1, "", "SVRParametersGamma"], [9, 2, 1, "", "SVRParametersParameterC"], [9, 3, 1, "", "gamma"]], "optunaz.config.optconfig.SVR.Parameters.SVRParametersGamma": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.SVR.Parameters.SVRParametersParameterC": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.XGBRegressor": [[9, 2, 1, "", "Parameters"], [9, 3, 1, "", "name"], [9, 3, 1, "", "parameters"]], "optunaz.config.optconfig.XGBRegressor.Parameters": [[9, 2, 1, "", "LearningRate"], [9, 2, 1, "", "MaxDepth"], [9, 2, 1, "", "NEstimators"], [9, 3, 1, "", "learning_rate"], [9, 3, 1, "", "max_depth"], [9, 3, 1, "", "n_estimators"]], "optunaz.config.optconfig.XGBRegressor.Parameters.LearningRate": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.XGBRegressor.Parameters.MaxDepth": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.config.optconfig.XGBRegressor.Parameters.NEstimators": [[9, 3, 1, "", "high"], [9, 3, 1, "", "low"]], "optunaz.datareader": [[8, 2, 1, "", "Dataset"], [8, 1, 1, "", "deduplicate"], [8, 1, 1, "", "isvalid"], [8, 1, 1, "", "merge"], [8, 1, 1, "", "read_data"], [8, 1, 1, "", "split"], [8, 1, 1, "", "transform"]], "optunaz.datareader.Dataset": [[8, 3, 1, "", "aux_column"], [8, 3, 1, "", "aux_transform"], [8, 4, 1, "", "check_sets"], [8, 3, 1, "", "deduplication_strategy"], [8, 4, 1, "", "get_merged_sets"], [8, 4, 1, "", "get_sets"], [8, 3, 1, "", "input_column"], [8, 3, 1, "", "intermediate_test_dataset_file"], [8, 3, 1, "", "intermediate_training_dataset_file"], [8, 3, 1, "", "log_transform"], [8, 3, 1, "", "log_transform_base"], [8, 3, 1, "", "log_transform_negative"], [8, 3, 1, "", "log_transform_unit_conversion"], [8, 3, 1, "", "probabilistic_threshold_representation"], [8, 3, 1, "", "probabilistic_threshold_representation_std"], [8, 3, 1, "", "probabilistic_threshold_representation_threshold"], [8, 3, 1, "", "response_column"], [8, 3, 1, "", "response_type"], [8, 3, 1, "", "save_intermediate_files"], [8, 3, 1, "", "split_strategy"], [8, 3, 1, "", "test_dataset_file"], [8, 3, 1, "", "training_dataset_file"]], "optunaz.descriptors": [[8, 2, 1, "", "Avalon"], [8, 2, 1, "", "CanonicalSmiles"], [8, 2, 1, "", "CompositeDescriptor"], [8, 2, 1, "", "ECFP"], [8, 2, 1, "", "ECFP_counts"], [8, 2, 1, "", "FittedSklearnScaler"], [8, 2, 1, "", "GenericScaffold"], [8, 2, 1, "", "JazzyDescriptors"], [8, 2, 1, "", "MACCS_keys"], [8, 2, 1, "", "MolDescriptor"], [8, 5, 1, "", "NoValidSmiles"], [8, 2, 1, "", "PathFP"], [8, 2, 1, "", "PhyschemDescriptors"], [8, 2, 1, "", "PrecomputedDescriptorFromFile"], [8, 2, 1, "", "RdkitDescriptor"], [8, 2, 1, "", "Scaffold"], [8, 2, 1, "", "ScaledDescriptor"], [8, 5, 1, "", "ScalingFittingError"], [8, 2, 1, "", "SmilesAndSideInfoFromFile"], [8, 2, 1, "", "SmilesFromFile"], [8, 2, 1, "", "UnfittedSklearnScaler"], [8, 2, 1, "", "UnscaledJazzyDescriptors"], [8, 2, 1, "", "UnscaledPhyschemDescriptors"], [8, 2, 1, "", "UnscaledZScalesDescriptors"], [8, 2, 1, "", "ValidDescriptor"], [8, 2, 1, "", "ZScalesDescriptors"], [8, 1, 1, "", "descriptor_from_config"], [8, 1, 1, "", "mol_from_smi"], [8, 1, 1, "", "numpy_from_rdkit"]], "optunaz.descriptors.Avalon": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.Avalon.Parameters": [[8, 3, 1, "", "nBits"]], "optunaz.descriptors.CanonicalSmiles": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.CompositeDescriptor": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 4, 1, "", "fp_info"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.CompositeDescriptor.Parameters": [[8, 3, 1, "", "descriptors"]], "optunaz.descriptors.ECFP": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ECFP.Parameters": [[8, 3, 1, "", "nBits"], [8, 3, 1, "", "radius"], [8, 3, 1, "", "returnRdkit"]], "optunaz.descriptors.ECFP_counts": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ECFP_counts.Parameters": [[8, 3, 1, "", "nBits"], [8, 3, 1, "", "radius"], [8, 3, 1, "", "useFeatures"]], "optunaz.descriptors.FittedSklearnScaler": [[8, 4, 1, "", "get_fitted_scaler"], [8, 3, 1, "", "name"], [8, 3, 1, "", "saved_params"]], "optunaz.descriptors.GenericScaffold": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.JazzyDescriptors": [[8, 2, 1, "", "Parameters"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.JazzyDescriptors.Parameters": [[8, 3, 1, "", "descriptor"], [8, 3, 1, "", "jazzy_filters"], [8, 3, 1, "", "jazzy_names"], [8, 3, 1, "", "scaler"]], "optunaz.descriptors.MACCS_keys": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.MolDescriptor": [[8, 4, 1, "", "calculate_from_smi"], [8, 4, 1, "", "parallel_compute_descriptor"]], "optunaz.descriptors.PathFP": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.PathFP.Parameters": [[8, 3, 1, "", "fpSize"], [8, 3, 1, "", "maxPath"]], "optunaz.descriptors.PhyschemDescriptors": [[8, 2, 1, "", "Parameters"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.PhyschemDescriptors.Parameters": [[8, 3, 1, "", "descriptor"], [8, 3, 1, "", "rdkit_names"], [8, 3, 1, "", "scaler"]], "optunaz.descriptors.PrecomputedDescriptorFromFile": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.PrecomputedDescriptorFromFile.Parameters": [[8, 3, 1, "", "file"], [8, 3, 1, "", "input_column"], [8, 3, 1, "", "response_column"]], "optunaz.descriptors.RdkitDescriptor": [[8, 4, 1, "", "calculate_from_mol"], [8, 4, 1, "", "calculate_from_smi"]], "optunaz.descriptors.Scaffold": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ScaledDescriptor": [[8, 2, 1, "", "ScaledDescriptorParameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"], [8, 4, 1, "", "set_unfitted_scaler_data"]], "optunaz.descriptors.ScaledDescriptor.ScaledDescriptorParameters": [[8, 3, 1, "", "descriptor"], [8, 3, 1, "", "scaler"]], "optunaz.descriptors.SmilesAndSideInfoFromFile": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters": [[8, 2, 1, "", "Aux_Weight_Pc"], [8, 3, 1, "", "aux_weight_pc"], [8, 3, 1, "", "file"], [8, 3, 1, "", "input_column"]], "optunaz.descriptors.SmilesAndSideInfoFromFile.Parameters.Aux_Weight_Pc": [[8, 3, 1, "", "high"], [8, 3, 1, "", "low"], [8, 3, 1, "", "q"]], "optunaz.descriptors.SmilesFromFile": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.UnfittedSklearnScaler": [[8, 2, 1, "", "MolData"], [8, 4, 1, "", "get_fitted_scaler_for_fp"], [8, 3, 1, "", "mol_data"], [8, 3, 1, "", "name"]], "optunaz.descriptors.UnfittedSklearnScaler.MolData": [[8, 3, 1, "", "file_path"], [8, 3, 1, "", "smiles_column"]], "optunaz.descriptors.UnscaledJazzyDescriptors": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.UnscaledJazzyDescriptors.Parameters": [[8, 3, 1, "", "jazzy_filters"], [8, 3, 1, "", "jazzy_names"]], "optunaz.descriptors.UnscaledPhyschemDescriptors": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_mol"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.UnscaledPhyschemDescriptors.Parameters": [[8, 3, 1, "", "rdkit_names"]], "optunaz.descriptors.UnscaledZScalesDescriptors": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ValidDescriptor": [[8, 2, 1, "", "Parameters"], [8, 4, 1, "", "calculate_from_smi"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ZScalesDescriptors": [[8, 2, 1, "", "Parameters"], [8, 3, 1, "", "name"], [8, 3, 1, "", "parameters"]], "optunaz.descriptors.ZScalesDescriptors.Parameters": [[8, 3, 1, "", "descriptor"], [8, 3, 1, "", "scaler"]], "optunaz.evaluate": [[8, 1, 1, "", "get_merged_train_score"], [8, 1, 1, "", "get_scores"], [8, 1, 1, "", "get_train_test_scores"], [8, 1, 1, "", "score_all"], [8, 1, 1, "", "score_all_smiles"]], "optunaz.explainability": [[8, 1, 1, "", "ExplainPreds"], [8, 1, 1, "", "ShapExplainer"], [8, 1, 1, "", "explain_ECFP"], [8, 1, 1, "", "get_ecfp_fpinfo"], [8, 1, 1, "", "get_ecfpcount_fpinfo"], [8, 1, 1, "", "get_fp_info"], [8, 1, 1, "", "runShap"]], "optunaz.metircs": [[8, 1, 1, "", "auc_pr_cal"], [8, 1, 1, "", "bedroc_score"], [8, 1, 1, "", "concordance_index"], [8, 1, 1, "", "validate_cls_input"]], "optunaz.model_writer": [[8, 2, 1, "", "Predictor"], [8, 2, 1, "", "QSARtunaModel"], [8, 1, 1, "", "get_metadata"], [8, 1, 1, "", "get_transform"], [8, 1, 1, "", "perform_ptr"], [8, 1, 1, "", "save_model"], [8, 1, 1, "", "wrap_model"]], "optunaz.model_writer.Predictor": [[8, 4, 1, "", "explain"], [8, 4, 1, "", "predict"], [8, 4, 1, "", "predict_proba"], [8, 4, 1, "", "predict_uncert"]], "optunaz.model_writer.QSARtunaModel": [[8, 3, 1, "", "aux_transform"], [8, 3, 1, "", "descriptor"], [8, 3, 1, "", "metadata"], [8, 3, 1, "", "mode"], [8, 4, 1, "", "predict_from_smiles"], [8, 3, 1, "", "predictor"], [8, 3, 1, "", "transform"]], "optunaz.objective": [[8, 5, 1, "", "NoValidDescriptors"], [8, 2, 1, "", "Objective"], [8, 1, 1, "", "null_scores"]], "optunaz.objective.Objective": [[8, 3, 1, "", "cache"], [8, 3, 1, "", "optconfig"], [8, 3, 1, "", "train_aux"], [8, 3, 1, "", "train_smiles"], [8, 3, 1, "", "train_y"]], "optunaz.optbuild": [[8, 1, 1, "", "main"], [8, 1, 1, "", "predict_pls"]], "optunaz.predict": [[8, 5, 1, "", "ArgsError"], [8, 5, 1, "", "AuxCovariateMissing"], [8, 5, 1, "", "PrecomputedError"], [8, 5, 1, "", "UncertaintyError"], [8, 1, 1, "", "check_precomp_args"], [8, 1, 1, "", "main"], [8, 1, 1, "", "validate_args"], [8, 1, 1, "", "validate_aux"], [8, 1, 1, "", "validate_set_precomputed"], [8, 1, 1, "", "validate_uncertainty"]], "optunaz.schemagen": [[8, 1, 1, "", "doctitle"], [8, 1, 1, "", "main"], [8, 1, 1, "", "patch_schema_generic"], [8, 1, 1, "", "patch_schema_optunaz"], [8, 1, 1, "", "type_base_schema"]], "optunaz.three_step_opt_build_merge": [[8, 1, 1, "", "base_chemprop_params"], [8, 1, 1, "", "build_best"], [8, 1, 1, "", "build_merged"], [8, 1, 1, "", "buildconfig_best"], [8, 1, 1, "", "log_scores"], [8, 1, 1, "", "optimize"], [8, 1, 1, "", "run_study"], [8, 1, 1, "", "split_optimize"]], "optunaz.utils": [[11, 0, 0, "-", "enums"], [10, 0, 0, "-", "files_paths"], [10, 1, 1, "", "load_df_from_file"], [10, 0, 0, "-", "load_json"], [10, 1, 1, "", "md5_hash"], [10, 1, 1, "", "mkdict"], [10, 0, 0, "-", "mlflow"], [12, 0, 0, "-", "preprocessing"], [10, 1, 1, "", "remove_failed_idx"], [10, 0, 0, "-", "schema"], [10, 0, 0, "-", "tracking"]], "optunaz.utils.enums": [[11, 2, 1, "", "MlflowLogParams"], [11, 2, 1, "", "StudyUserAttrs"], [11, 2, 1, "", "TrialParams"], [11, 2, 1, "", "TrialUserAttrs"], [11, 0, 0, "-", "building_configuration_enum"], [11, 0, 0, "-", "configuration_enum"], [11, 0, 0, "-", "interface_enum"], [11, 0, 0, "-", "model_runner_enum"], [11, 0, 0, "-", "objective_enum"], [11, 0, 0, "-", "optimization_configuration_enum"], [11, 0, 0, "-", "prediction_configuration_enum"], [11, 0, 0, "-", "return_values_enum"], [11, 0, 0, "-", "visualization_enum"]], "optunaz.utils.enums.MlflowLogParams": [[11, 3, 1, "", "TRIAL_NUMBER"]], "optunaz.utils.enums.StudyUserAttrs": [[11, 3, 1, "", "OPTCONFIG"]], "optunaz.utils.enums.TrialParams": [[11, 3, 1, "", "ALGORITHM_HASH"], [11, 3, 1, "", "ALGORITHM_NAME"], [11, 3, 1, "", "DESCRIPTOR"]], "optunaz.utils.enums.TrialUserAttrs": [[11, 3, 1, "", "TEST_SCORES"], [11, 3, 1, "", "TRAIN_SCORES"]], "optunaz.utils.enums.building_configuration_enum": [[11, 2, 1, "", "BuildingConfigurationEnum"]], "optunaz.utils.enums.building_configuration_enum.BuildingConfigurationEnum": [[11, 3, 1, "", "GENERAL_CLASSIFIER"], [11, 3, 1, "", "GENERAL_HYPERPARAMETERS"], [11, 3, 1, "", "GENERAL_REGRESSOR"], [11, 3, 1, "", "METADATA"], [11, 3, 1, "", "METADATA_BESTTRIAL"], [11, 3, 1, "", "METADATA_BESTVALUE"]], "optunaz.utils.enums.configuration_enum": [[11, 2, 1, "", "ConfigurationEnum"]], "optunaz.utils.enums.configuration_enum.ConfigurationEnum": [[11, 3, 1, "", "ALGORITHMS"], [11, 3, 1, "", "ALGORITHMS_ADABOOSTCLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_ADABOOSTCLASSIFIER_LEARNING_RATE"], [11, 3, 1, "", "ALGORITHMS_ADABOOSTCLASSIFIER_N_ESTIMATORS"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_ENSEMBLE"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_ESTIMATOR"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_METHOD"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_N_FOLDS"], [11, 3, 1, "", "ALGORITHMS_CALIBRATEDCLASSIFIERCV_PARAMS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_ACTIVATION"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_AGGREGATION"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_AGGREGATION_NORM"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_BATCH_SIZE"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_CLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_DEPTH"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_DROPOUT"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_ENSEMBLE_SIZE"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_EPOCHS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FEATURES_GENERATOR"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FFN_HIDDEN_SIZE"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FFN_NUM_LAYERS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FINAL_LR_RATIO_EXP"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_FRZN"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_HIDDEN_SIZE"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_HYPEROPT_CLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_HYPEROPT_REGRESSOR"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_INIT_LR_RATIO_EXP"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_MAX_LR_EXP"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_NUM_ITERS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_PRETRAINED_MODEL"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_REGRESSOR"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_SEARCH_PARAMETER_LEVEL"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_STARTUP_RANDOM_ITERS"], [11, 3, 1, "", "ALGORITHMS_CHEMPROP_WARMUP_EPOCHS_RATIO"], [11, 3, 1, "", "ALGORITHMS_HIGH"], [11, 3, 1, "", "ALGORITHMS_INTERFACE_SKLEARN"], [11, 3, 1, "", "ALGORITHMS_INTERFACE_XGBOOST"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORSCLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORSREGRESSOR"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORS_METRIC"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORS_N_NEIGHBORS"], [11, 3, 1, "", "ALGORITHMS_KNEIGHBORS_WEIGHTS"], [11, 3, 1, "", "ALGORITHMS_LASSO"], [11, 3, 1, "", "ALGORITHMS_LASSO_ALPHA"], [11, 3, 1, "", "ALGORITHMS_LOGISTICREGRESSION"], [11, 3, 1, "", "ALGORITHMS_LOGISTICREGRESSION_C"], [11, 3, 1, "", "ALGORITHMS_LOGISTICREGRESSION_SOLVER"], [11, 3, 1, "", "ALGORITHMS_LOW"], [11, 3, 1, "", "ALGORITHMS_MAPIE"], [11, 3, 1, "", "ALGORITHMS_MAPIE_ALPHA"], [11, 3, 1, "", "ALGORITHMS_PLSREGRESSION"], [11, 3, 1, "", "ALGORITHMS_PLSREGRESSION_N_COMPONENTS"], [11, 3, 1, "", "ALGORITHMS_PRF"], [11, 3, 1, "", "ALGORITHMS_PRF_MAX_DEPTH"], [11, 3, 1, "", "ALGORITHMS_PRF_MAX_FEATURES"], [11, 3, 1, "", "ALGORITHMS_PRF_MINPYSUMLEAF"], [11, 3, 1, "", "ALGORITHMS_PRF_N_ESTIMATORS"], [11, 3, 1, "", "ALGORITHMS_PRF_USE_PY_GINI"], [11, 3, 1, "", "ALGORITHMS_PRF_USE_PY_LEAFS"], [11, 3, 1, "", "ALGORITHMS_Q"], [11, 3, 1, "", "ALGORITHMS_RFCLASSIFIER"], [11, 3, 1, "", "ALGORITHMS_RFREGRESSOR"], [11, 3, 1, "", "ALGORITHMS_RF_MAX_DEPTH"], [11, 3, 1, "", "ALGORITHMS_RF_MAX_FEATURES"], [11, 3, 1, "", "ALGORITHMS_RF_N_ESTIMATORS"], [11, 3, 1, "", "ALGORITHMS_RIDGE"], [11, 3, 1, "", "ALGORITHMS_RIDGE_ALPHA"], [11, 3, 1, "", "ALGORITHMS_SVC"], [11, 3, 1, "", "ALGORITHMS_SVC_C"], [11, 3, 1, "", "ALGORITHMS_SVC_GAMMA"], [11, 3, 1, "", "ALGORITHMS_SVR"], [11, 3, 1, "", "ALGORITHMS_SVR_C"], [11, 3, 1, "", "ALGORITHMS_SVR_GAMMA"], [11, 3, 1, "", "ALGORITHMS_XGBREGRESSOR"], [11, 3, 1, "", "ALGORITHMS_XGBREGRESSOR_LEARNING_RATE"], [11, 3, 1, "", "ALGORITHMS_XGBREGRESSOR_MAX_DEPTH"], [11, 3, 1, "", "ALGORITHMS_XGBREGRESSOR_N_ESTIMATORS"], [11, 3, 1, "", "DATA"], [11, 3, 1, "", "DATA_INPUTCOLUMN"], [11, 3, 1, "", "DATA_RESPONSECOLUMN"], [11, 3, 1, "", "DATA_TEST"], [11, 3, 1, "", "DATA_TRAINING"], [11, 3, 1, "", "DESCRIPTORS"], [11, 3, 1, "", "DESCRIPTORS_AVALON"], [11, 3, 1, "", "DESCRIPTORS_AVALON_NBITS"], [11, 3, 1, "", "DESCRIPTORS_COMPOSITE"], [11, 3, 1, "", "DESCRIPTORS_ECFP"], [11, 3, 1, "", "DESCRIPTORS_ECFPCOUNTS"], [11, 3, 1, "", "DESCRIPTORS_ECFPCOUNTS_RADIUS"], [11, 3, 1, "", "DESCRIPTORS_ECFPCOUNTS_USEFEATURES"], [11, 3, 1, "", "DESCRIPTORS_ECFP_NBITS"], [11, 3, 1, "", "DESCRIPTORS_ECFP_RADIUS"], [11, 3, 1, "", "DESCRIPTORS_JAZZY"], [11, 3, 1, "", "DESCRIPTORS_JAZZY_JAZZYNAMES"], [11, 3, 1, "", "DESCRIPTORS_MACCSKEYS"], [11, 3, 1, "", "DESCRIPTORS_PATHFP"], [11, 3, 1, "", "DESCRIPTORS_PATHFP_FPSIZE"], [11, 3, 1, "", "DESCRIPTORS_PATHFP_MAXPATH"], [11, 3, 1, "", "DESCRIPTORS_PHYSCHEM"], [11, 3, 1, "", "DESCRIPTORS_PHYSCHEM_RDKITNAMES"], [11, 3, 1, "", "DESCRIPTORS_PRECOMPUTED"], [11, 3, 1, "", "DESCRIPTORS_PRECOMPUTED_FILE"], [11, 3, 1, "", "DESCRIPTORS_PRECOMPUTED_INPUT_COLUMNN"], [11, 3, 1, "", "DESCRIPTORS_PRECOMPUTED_RESPONSE_COLUMN"], [11, 3, 1, "", "DESCRIPTORS_SCALED"], [11, 3, 1, "", "DESCRIPTORS_SCALED_DESCRIPTOR"], [11, 3, 1, "", "DESCRIPTORS_SCALED_DESCRIPTOR_PARAMETERS"], [11, 3, 1, "", "DESCRIPTORS_SMILES"], [11, 3, 1, "", "DESCRIPTORS_SMILES_AND_SI"], [11, 3, 1, "", "DESCRIPTORS_SMILES_AND_SI_AUX_WEIGHT_PC"], [11, 3, 1, "", "DESCRIPTORS_SMILES_AND_SI_FILE"], [11, 3, 1, "", "DESCRIPTORS_SMILES_AND_SI_INPUT_COLUMN"], [11, 3, 1, "", "DESCRIPTORS_UNSC_JAZZY"], [11, 3, 1, "", "DESCRIPTORS_UNSC_PHYSCHEM"], [11, 3, 1, "", "DESCRIPTORS_UNSC_ZSCALES"], [11, 3, 1, "", "DESCRIPTORS_ZSCALES"], [11, 3, 1, "", "GENERAL_DISABLED"], [11, 3, 1, "", "GENERAL_PARAMETERS"], [11, 3, 1, "", "SETTINGS"], [11, 3, 1, "", "SETTINGS_CROSS_VALIDATION"], [11, 3, 1, "", "SETTINGS_DIRECTION"], [11, 3, 1, "", "SETTINGS_MODE"], [11, 3, 1, "", "SETTINGS_MODE_CLASSIFICATION"], [11, 3, 1, "", "SETTINGS_MODE_REGRESSION"], [11, 3, 1, "", "SETTINGS_N_JOBS"], [11, 3, 1, "", "SETTINGS_N_TRIALS"], [11, 3, 1, "", "SETTINGS_SHUFFLE"], [11, 3, 1, "", "TASK"], [11, 3, 1, "", "TASK_BUILDING"], [11, 3, 1, "", "TASK_OPTIMIZATION"]], "optunaz.utils.enums.interface_enum": [[11, 2, 1, "", "InterfaceEnum"]], "optunaz.utils.enums.interface_enum.InterfaceEnum": [[11, 3, 1, "", "CALIBRATED_SET"], [11, 3, 1, "", "CHEMPROP_SET"], [11, 3, 1, "", "PRF_SET"], [11, 3, 1, "", "SKLEARN_SET"], [11, 3, 1, "", "XGBOOST_SET"]], "optunaz.utils.enums.model_runner_enum": [[11, 2, 1, "", "ModelRunnerDataframeEnum"]], "optunaz.utils.enums.model_runner_enum.ModelRunnerDataframeEnum": [[11, 3, 1, "", "SET"], [11, 3, 1, "", "SMILES"], [11, 3, 1, "", "TEST"], [11, 3, 1, "", "TRAIN"], [11, 3, 1, "", "Y_PRED"], [11, 3, 1, "", "Y_TRUE"]], "optunaz.utils.enums.objective_enum": [[11, 2, 1, "", "ObjectiveEnum"]], "optunaz.utils.enums.objective_enum.ObjectiveEnum": [[11, 3, 1, "", "ATTRIBUTE_TRIAL_TRAIN_SCORE"], [11, 3, 1, "", "EXTRA_COLUMN_BESTHIT"]], "optunaz.utils.enums.optimization_configuration_enum": [[11, 2, 1, "", "OptimizationConfigurationEnum"]], "optunaz.utils.enums.prediction_configuration_enum": [[11, 2, 1, "", "PredictionConfigurationEnum"]], "optunaz.utils.enums.prediction_configuration_enum.PredictionConfigurationEnum": [[11, 3, 1, "", "DATA_DATASET"]], "optunaz.utils.enums.return_values_enum": [[11, 2, 1, "", "SklearnReturnValueEnum"], [11, 2, 1, "", "XGBoostReturnValueEnum"]], "optunaz.utils.enums.return_values_enum.SklearnReturnValueEnum": [[11, 3, 1, "", "CROSS_VALIDATE_FIT_TIME"], [11, 3, 1, "", "CROSS_VALIDATE_SCORE_TIME"], [11, 3, 1, "", "CROSS_VALIDATE_TEST_SCORE"], [11, 3, 1, "", "CROSS_VALIDATE_TRAIN_SCORE"]], "optunaz.utils.enums.return_values_enum.XGBoostReturnValueEnum": [[11, 3, 1, "", "CROSS_VALIDATE_FIT_TIME"], [11, 3, 1, "", "CROSS_VALIDATE_SCORE_TIME"], [11, 3, 1, "", "CROSS_VALIDATE_TEST_SCORE"], [11, 3, 1, "", "CROSS_VALIDATE_TRAIN_SCORE"]], "optunaz.utils.enums.visualization_enum": [[11, 2, 1, "", "VisualizationEnum"]], "optunaz.utils.enums.visualization_enum.VisualizationEnum": [[11, 3, 1, "", "OPTUNA_SYSTEM_ATTRS_INTERMEDIATE_VALUES"], [11, 3, 1, "", "OPTUNA_SYSTEM_ATTRS_NUMBER"], [11, 3, 1, "", "OPTUNA_SYSTEM_ATTRS_TRIAL_ID"], [11, 3, 1, "", "VISUALIZATION"], [11, 3, 1, "", "VISUALIZATION_CLASSIFIER"], [11, 3, 1, "", "VISUALIZATION_FILE_FORMAT"], [11, 3, 1, "", "VISUALIZATION_OUTPUT_FOLDER"], [11, 3, 1, "", "VISUALIZATION_PLOTS"], [11, 3, 1, "", "VISUALIZATION_PLOTS_CONTOUR"], [11, 3, 1, "", "VISUALIZATION_PLOTS_HISTORY"], [11, 3, 1, "", "VISUALIZATION_PLOTS_PARALLEL_COORDINATE"], [11, 3, 1, "", "VISUALIZATION_PLOTS_SLICE"], [11, 3, 1, "", "VISUALIZATION_REGRESSOR"], [11, 3, 1, "", "VISUALIZATION_USE_XVFB"]], "optunaz.utils.files_paths": [[10, 1, 1, "", "attach_root_path"], [10, 1, 1, "", "move_up_directory"]], "optunaz.utils.load_json": [[10, 1, 1, "", "loadJSON"]], "optunaz.utils.mlflow": [[10, 2, 1, "", "MLflowCallback"], [10, 1, 1, "", "add_ellipsis"], [10, 1, 1, "", "shorten_names"]], "optunaz.utils.mlflow.MLflowCallback": [[10, 3, 1, "", "optconfig"], [10, 4, 1, "", "prepare_tags"], [10, 4, 1, "", "tmp_buildconfig"], [10, 3, 1, "", "tracking_uri"], [10, 3, 1, "", "trial_number_offset"]], "optunaz.utils.preprocessing": [[12, 0, 0, "-", "deduplicator"], [12, 0, 0, "-", "splitter"], [12, 0, 0, "-", "transform"]], "optunaz.utils.preprocessing.deduplicator": [[12, 2, 1, "", "Deduplicator"], [12, 2, 1, "", "KeepAllNoDeduplication"], [12, 2, 1, "", "KeepAvg"], [12, 2, 1, "", "KeepFirst"], [12, 2, 1, "", "KeepLast"], [12, 2, 1, "", "KeepMax"], [12, 2, 1, "", "KeepMedian"], [12, 2, 1, "", "KeepMin"], [12, 2, 1, "", "KeepRandom"]], "optunaz.utils.preprocessing.deduplicator.Deduplicator": [[12, 4, 1, "", "dedup"]], "optunaz.utils.preprocessing.deduplicator.KeepAllNoDeduplication": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepAvg": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepFirst": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepLast": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepMax": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepMedian": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepMin": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"]], "optunaz.utils.preprocessing.deduplicator.KeepRandom": [[12, 4, 1, "", "dedup"], [12, 3, 1, "", "name"], [12, 3, 1, "", "seed"]], "optunaz.utils.preprocessing.splitter": [[12, 2, 1, "", "GroupingSplitter"], [12, 2, 1, "", "HistogramStratifiedShuffleSplit"], [12, 2, 1, "", "KFold"], [12, 2, 1, "", "NoSplitting"], [13, 2, 1, "", "Predefined"], [13, 2, 1, "", "Random"], [13, 2, 1, "", "ScaffoldSplit"], [12, 2, 1, "", "SklearnSplitter"], [12, 2, 1, "", "Splitter"], [13, 2, 1, "", "Stratified"], [13, 2, 1, "", "Temporal"], [12, 1, 1, "", "butina_cluster"], [12, 1, 1, "", "fd_bin"], [12, 1, 1, "", "stratify"]], "optunaz.utils.preprocessing.splitter.GroupingSplitter": [[12, 4, 1, "", "groups"]], "optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit": [[12, 3, 1, "", "bins"], [12, 4, 1, "", "get_n_splits"], [12, 3, 1, "", "n_splits"], [12, 3, 1, "", "random_state"], [12, 4, 1, "", "split"], [12, 3, 1, "", "test_fraction"]], "optunaz.utils.preprocessing.splitter.KFold": [[12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [12, 3, 1, "", "random_state"], [12, 3, 1, "", "shuffle"], [12, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.NoSplitting": [[12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [12, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.Predefined": [[12, 3, 1, "", "column_name"], [12, 4, 1, "", "get_sklearn_splitter"], [12, 4, 1, "", "groups"], [12, 3, 1, "", "name"], [13, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.Random": [[12, 3, 1, "", "fraction"], [12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [12, 3, 1, "", "seed"]], "optunaz.utils.preprocessing.splitter.ScaffoldSplit": [[12, 3, 1, "", "bins"], [12, 3, 1, "", "butina_cluster"], [12, 4, 1, "", "get_n_splits"], [12, 4, 1, "", "get_sklearn_splitter"], [13, 4, 1, "", "groups"], [12, 3, 1, "", "make_scaffold_generic"], [12, 3, 1, "", "name"], [12, 3, 1, "", "random_state"], [13, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.SklearnSplitter": [[12, 4, 1, "", "get_n_splits"], [12, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.Splitter": [[12, 4, 1, "", "get_sklearn_splitter"], [12, 4, 1, "", "split"]], "optunaz.utils.preprocessing.splitter.Stratified": [[12, 3, 1, "", "bins"], [12, 3, 1, "", "fraction"], [12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [12, 3, 1, "", "seed"]], "optunaz.utils.preprocessing.splitter.Temporal": [[12, 3, 1, "", "fraction"], [12, 4, 1, "", "get_sklearn_splitter"], [12, 3, 1, "", "name"], [13, 4, 1, "", "split"]], "optunaz.utils.preprocessing.transform": [[12, 2, 1, "", "AuxTransformer"], [12, 2, 1, "", "DataTransform"], [12, 2, 1, "", "LogBase"], [12, 2, 1, "", "LogNegative"], [14, 2, 1, "", "ModelDataTransform"], [14, 2, 1, "", "PTRTransform"], [14, 2, 1, "", "VectorFromColumn"], [14, 2, 1, "", "ZScales"]], "optunaz.utils.preprocessing.transform.AuxTransformer": [[12, 4, 1, "", "transform"]], "optunaz.utils.preprocessing.transform.DataTransform": [[12, 4, 1, "", "transform"]], "optunaz.utils.preprocessing.transform.LogBase": [[12, 3, 1, "", "LOG"], [12, 3, 1, "", "LOG10"], [12, 3, 1, "", "LOG2"]], "optunaz.utils.preprocessing.transform.LogNegative": [[12, 3, 1, "", "FALSE"], [12, 3, 1, "", "TRUE"]], "optunaz.utils.preprocessing.transform.ModelDataTransform": [[14, 2, 1, "", "Parameters"], [12, 3, 1, "", "base_dict"], [12, 3, 1, "", "base_negation"], [12, 3, 1, "", "name"], [12, 3, 1, "", "parameters"], [12, 3, 1, "", "reverse_dict"], [12, 4, 1, "", "reverse_transform"], [12, 4, 1, "", "reverse_transform_df"], [12, 4, 1, "", "reverse_transform_one"], [12, 4, 1, "", "transform"], [12, 4, 1, "", "transform_df"], [12, 4, 1, "", "transform_one"]], "optunaz.utils.preprocessing.transform.ModelDataTransform.Parameters": [[12, 3, 1, "", "base"], [12, 3, 1, "", "conversion"], [12, 3, 1, "", "negation"]], "optunaz.utils.preprocessing.transform.PTRTransform": [[14, 2, 1, "", "Parameters"], [12, 3, 1, "", "name"], [12, 3, 1, "", "parameters"], [12, 4, 1, "", "reverse_transform"], [12, 4, 1, "", "transform"]], "optunaz.utils.preprocessing.transform.PTRTransform.Parameters": [[12, 3, 1, "", "std"], [12, 3, 1, "", "threshold"]], "optunaz.utils.preprocessing.transform.VectorFromColumn": [[14, 2, 1, "", "Parameters"], [12, 3, 1, "", "name"], [12, 3, 1, "", "parameters"], [12, 4, 1, "", "transform"]], "optunaz.utils.preprocessing.transform.VectorFromColumn.Parameters": [[12, 3, 1, "", "delimiter"]], "optunaz.utils.preprocessing.transform.ZScales": [[14, 2, 1, "", "Parameters"], [12, 3, 1, "", "name"], [12, 3, 1, "", "parameters"], [12, 4, 1, "", "transform"]], "optunaz.utils.schema": [[10, 1, 1, "", "add_boolean_guards_for_schema_properties"], [10, 1, 1, "", "addsibling"], [10, 1, 1, "", "addtitles"], [10, 1, 1, "", "copytitle"], [10, 1, 1, "", "create_dependency"], [10, 1, 1, "", "delsibling"], [10, 1, 1, "", "getref"], [10, 1, 1, "", "remove_schema_properties"], [10, 1, 1, "", "replaceenum"], [10, 1, 1, "", "replacekey"], [10, 1, 1, "", "replacevalue"]], "optunaz.utils.tracking": [[10, 2, 1, "", "BuildTrackingData"], [10, 2, 1, "", "Datapoint"], [10, 2, 1, "", "InternalTrackingCallback"], [10, 2, 1, "", "TrackingData"], [10, 1, 1, "", "get_authorization_header"], [10, 1, 1, "", "removeprefix"], [10, 1, 1, "", "round_scores"], [10, 1, 1, "", "track_build"]], "optunaz.utils.tracking.BuildTrackingData": [[10, 3, 1, "", "response_column_name"], [10, 3, 1, "", "test_points"], [10, 3, 1, "", "test_scores"]], "optunaz.utils.tracking.Datapoint": [[10, 3, 1, "", "expected"], [10, 3, 1, "", "predicted"], [10, 3, 1, "", "smiles"]], "optunaz.utils.tracking.InternalTrackingCallback": [[10, 3, 1, "", "optconfig"], [10, 3, 1, "", "trial_number_offset"]], "optunaz.utils.tracking.TrackingData": [[10, 3, 1, "", "all_cv_test_scores"], [10, 3, 1, "", "buildconfig"], [10, 3, 1, "", "scoring"], [10, 3, 1, "", "trial_number"], [10, 3, 1, "", "trial_state"], [10, 3, 1, "", "trial_value"]], "optunaz.visualizer": [[8, 2, 1, "", "Visualizer"]], "optunaz.visualizer.Visualizer": [[8, 4, 1, "", "plot_by_configuration"], [8, 4, 1, "", "plot_contour"], [8, 4, 1, "", "plot_history"], [8, 4, 1, "", "plot_parallel_coordinate"], [8, 4, 1, "", "plot_slice"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method", "5": "py:exception"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"], "5": ["py", "exception", "Python exception"]}, "titleterms": {"qsartuna": [0, 4, 6, 7], "\ud80c\udd9b": 0, "qsar": 0, "us": 0, "optim": [0, 6], "hyperparamet": 0, "tune": 0, "formerli": 0, "optuna": 0, "az": 0, "qptuna": 0, "background": [0, 6], "The": [0, 6], "three": [0, 6], "step": [0, 6], "process": [0, 6], "json": 0, "base": [0, 7], "command": 0, "line": 0, "interfac": 0, "configur": [0, 6], "file": [0, 6], "run": [0, 6], "via": 0, "singulart": 0, "submit": 0, "slurm": 0, "model": [0, 6], "option": [0, 6], "inspect": 0, "from": [0, 6, 7], "python": 0, "jupyt": 0, "notebook": 0, "avail": [1, 2, 3, 13, 14], "algorithm": [1, 6], "adaboostclassifi": 1, "lasso": 1, "kneighborsclassifi": 1, "kneighborsregressor": 1, "logisticregress": 1, "plsregress": 1, "randomforestclassifi": 1, "randomforestregressor": 1, "ridg": 1, "svc": 1, "svr": 1, "xgbregressor": 1, "prfclassifi": 1, "chempropregressor": 1, "chempropclassifi": 1, "chemprophyperoptclassifi": 1, "chemprophyperoptregressor": 1, "chempropregressorpretrain": 1, "calibratedclassifiercvwithva": 1, "mapi": [1, 6], "dedupl": [2, 7, 12], "keepfirst": 2, "keeplast": 2, "keeprandom": 2, "keepmin": 2, "keepmax": 2, "keepavg": 2, "keepmedian": 2, "keepkeepallnodedupl": 2, "descriptor": [3, 6, 8], "avalon": 3, "ecfp": 3, "ecfp_count": 3, "pathfp": 3, "maccs_kei": 3, "unscaledphyschemdescriptor": 3, "unscaledjazzydescriptor": 3, "unscaledzscalesdescriptor": 3, "physchemdescriptor": 3, "jazzydescriptor": 3, "precomputeddescriptorfromfil": 3, "zscale": [3, 14], "smilesfromfil": 3, "smilesandsideinfofromfil": 3, "scaleddescriptor": 3, "compositedescriptor": 3, "welcom": 4, "document": 4, "develop": 4, "optunaz": [5, 8, 9, 10, 11, 12], "cli": 6, "tutori": 6, "thi": 6, "prepar": 6, "regress": 6, "exampl": 6, "creat": 6, "visual": [6, 8], "progress": 6, "pick": 6, "best": [6, 7], "trial": 6, "build": 6, "merg": 6, "preprocess": [6, 7, 12], "split": [6, 7], "data": [6, 7], "train": 6, "test": 6, "set": 6, "remov": 6, "duplic": [6, 7], "dataset": 6, "choos": 6, "score": 6, "function": 6, "advanc": 6, "functoinail": 6, "probabilist": [6, 7], "random": [6, 7, 13], "forest": 6, "prf": 6, "interlud": [6, 7], "cautionari": 6, "advic": 6, "y": 6, "respons": 6, "column": 6, "valid": 6, "chemprop": 6, "simpl": 6, "separ": 6, "shallow": 6, "method": 6, "default": 6, "behavior": 6, "turn": 6, "hyperopt": 6, "within": [6, 7], "functionail": 6, "veri": 6, "larg": 6, "comput": 6, "cost": 6, "A": 6, "note": 6, "mpnn": 6, "search": 6, "space": 6, "side": 6, "inform": 6, "multi": 6, "task": 6, "learn": 6, "mtl": 6, "combin": 6, "onli": 6, "recommend": 6, "long": 6, "time": 6, "pre": 6, "adapt": 6, "transfer": 6, "fingerprint": 6, "encod": 6, "latent": 6, "represent": [6, 7], "probabl": 6, "calibr": 6, "classif": 6, "uncertainti": 6, "estim": 6, "vennab": 6, "ensembl": 6, "dropout": 6, "explain": [6, 8], "shap": 6, "interpret": 6, "log": [6, 7], "transform": [6, 7, 12, 14], "covari": 6, "one": 6, "e": 6, "g": 6, "dose": 6, "point": 6, "co": 6, "variat": 6, "proteochemometr": 6, "pcm": 6, "more": 6, "vectorfromsmil": 6, "z": 6, "scale": 6, "object": [6, 8], "priorit": 6, "perform": [6, 7], "standard": 6, "deviat": 6, "further": 6, "precomput": 6, "introduct": 7, "translat": 7, "sdf": 7, "csv": 7, "need": 7, "deal": 7, "compar": 7, "differ": 7, "unif": 7, "strategi": 7, "tempor": [7, 13], "stratifi": [7, 13], "scaffold": 7, "input": 7, "user": 7, "import": 7, "logarithm": 7, "dataread": [7, 8], "threshold": 7, "ptr": [7, 14], "experiment": 7, "error": 7, "definit": 7, "implement": 7, "conclus": 7, "calcul": 7, "evalu": [7, 8], "reproduc": 7, "practic": 7, "packag": [8, 9, 10, 11, 12], "subpackag": [8, 10], "submodul": [8, 9, 10, 11, 12], "builder": 8, "modul": [8, 9, 10, 11, 12], "metirc": 8, "model_writ": 8, "optbuild": 8, "predict": 8, "schemagen": 8, "three_step_opt_build_merg": 8, "content": [8, 9, 10, 11, 12], "config": 9, "build_from_opt": 9, "buildconfig": 9, "optconfig": 9, "util": [10, 11, 12], "files_path": 10, "load_json": 10, "mlflow": 10, "schema": 10, "track": 10, "enum": 11, "building_configuration_enum": 11, "configuration_enum": 11, "interface_enum": 11, "model_runner_enum": 11, "objective_enum": 11, "optimization_configuration_enum": 11, "prediction_configuration_enum": 11, "return_values_enum": 11, "visualization_enum": 11, "splitter": [12, 13], "predefin": 13, "scaffoldsplit": 13, "modeldatatransform": 14, "vectorfromcolumn": 14}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "nbsphinx": 4, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 56}})
\ No newline at end of file
diff --git a/docs/sphinx-source/algorithms.rst b/docs/sphinx-source/algorithms.rst
index 38f7060..4c7d25e 100644
--- a/docs/sphinx-source/algorithms.rst
+++ b/docs/sphinx-source/algorithms.rst
@@ -103,7 +103,7 @@ ChemPropHyperoptRegressor
     :members:
 
 
-ChemPropHyperoptRegressorPretrained
+ChemPropRegressorPretrained
 #########################
 ..  autoclass:: optunaz.config.optconfig.ChemPropRegressorPretrained
     :members: