From 4db6a79f9325ff21b3a827e8af31c813f63e3684 Mon Sep 17 00:00:00 2001 From: marakeby Date: Fri, 16 Apr 2021 07:22:31 -0400 Subject: [PATCH] run analysis, rename folders --- README.md | 20 +-- .../figure_3/figure3_b_gene_importance.py | 14 ++- analysis/figure_3/figure_3_sankey_all.py | 10 +- config_path.py | 3 - run/run_me_melanoma.py | 115 ------------------ {run => train}/__init__.py | 0 ...ossvalidation_ML_params_search_logistic.py | 0 .../crossvalidation_ML_params_search_svm.py | 0 .../onesplit_ML_params_search_adaboost.py | 0 .../onesplit_ML_params_search_randomforest.py | 0 .../onesplit_ML_params_search_svm.py | 0 .../onesplit_ML_params_search_svm_linear.py | 0 .../onesplit_ML_params_search_tree.py | 0 .../onsplit_ML_params_search_logistic.py | 0 .../P1000/compare/crossvalidation_ML_test.py | 0 .../params/P1000/compare/onsplit_ML_test.py | 0 ...esplit_number_samples_dense_sameweights.py | 0 .../params/P1000/dense/onsplit_dense.py | 0 .../external_validation/pnet_validation.py | 0 .../crossvalidation_average_reg_10.py | 0 .../crossvalidation_average_reg_10_tanh.py | 0 ...dation_number_samples_dense_sameweights.py | 0 .../crossvalidation_average_reg_10_tanh.py | 0 ...split_average_reg_10_tanh_large_testing.py | 0 ...average_reg_10_tanh_large_testing_inner.py | 0 .../review/10custom_arch/onsplit_kegg.py | 0 ...average_reg_10_tanh_large_testing_count.py | 0 ...erage_reg_10_tanh_large_testing_hotspot.py | 0 ...idation_average_reg_10_tanh_single_copy.py | 0 ...e_reg_10_tanh_large_testing_single_copy.py | 0 .../params/P1000/review/LOOCV_reg_10_tanh.py | 0 ...dation_average_reg_10_tanh_cancer_genes.py | 0 ...t_average_reg_10_tanh_large_testing_TMB.py | 0 ...verage_reg_10_tanh_large_testing_fusion.py | 0 ...e_reg_10_tanh_large_testing_fusion_zero.py | 0 ...0_tanh_large_testing_inner_fusion_genes.py | 0 ...rage_reg_10_tanh_large_testing_inner_LR.py | 0 ...it_average_reg_10_tanh_large_testing_ge.py | 0 {run => train}/run_me.py | 54 ++++---- 39 files changed, 54 insertions(+), 162 deletions(-) delete mode 100644 run/run_me_melanoma.py rename {run => train}/__init__.py (100%) rename {run => train}/params/P1000/ML_params_search/crossvalidation_ML_params_search_logistic.py (100%) rename {run => train}/params/P1000/ML_params_search/crossvalidation_ML_params_search_svm.py (100%) rename {run => train}/params/P1000/ML_params_search/onesplit_ML_params_search_adaboost.py (100%) rename {run => train}/params/P1000/ML_params_search/onesplit_ML_params_search_randomforest.py (100%) rename {run => train}/params/P1000/ML_params_search/onesplit_ML_params_search_svm.py (100%) rename {run => train}/params/P1000/ML_params_search/onesplit_ML_params_search_svm_linear.py (100%) rename {run => train}/params/P1000/ML_params_search/onesplit_ML_params_search_tree.py (100%) rename {run => train}/params/P1000/ML_params_search/onsplit_ML_params_search_logistic.py (100%) rename {run => train}/params/P1000/compare/crossvalidation_ML_test.py (100%) rename {run => train}/params/P1000/compare/onsplit_ML_test.py (100%) rename {run => train}/params/P1000/dense/onesplit_number_samples_dense_sameweights.py (100%) rename {run => train}/params/P1000/dense/onsplit_dense.py (100%) rename {run => train}/params/P1000/external_validation/pnet_validation.py (100%) rename {run => train}/params/P1000/number_samples/crossvalidation_average_reg_10.py (100%) rename {run => train}/params/P1000/number_samples/crossvalidation_average_reg_10_tanh.py (100%) rename {run => train}/params/P1000/number_samples/crossvalidation_number_samples_dense_sameweights.py (100%) rename {run => train}/params/P1000/pnet/crossvalidation_average_reg_10_tanh.py (100%) rename {run => train}/params/P1000/pnet/onsplit_average_reg_10_tanh_large_testing.py (100%) rename {run => train}/params/P1000/pnet/onsplit_average_reg_10_tanh_large_testing_inner.py (100%) rename {run => train}/params/P1000/review/10custom_arch/onsplit_kegg.py (100%) rename {run => train}/params/P1000/review/9hotspot/onsplit_average_reg_10_tanh_large_testing_count.py (100%) rename {run => train}/params/P1000/review/9hotspot/onsplit_average_reg_10_tanh_large_testing_hotspot.py (100%) rename {run => train}/params/P1000/review/9single_copy/crossvalidation_average_reg_10_tanh_single_copy.py (100%) rename {run => train}/params/P1000/review/9single_copy/onsplit_average_reg_10_tanh_large_testing_single_copy.py (100%) rename {run => train}/params/P1000/review/LOOCV_reg_10_tanh.py (100%) rename {run => train}/params/P1000/review/crossvalidation_average_reg_10_tanh_cancer_genes.py (100%) rename {run => train}/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_TMB.py (100%) rename {run => train}/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion.py (100%) rename {run => train}/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion_zero.py (100%) rename {run => train}/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_inner_fusion_genes.py (100%) rename {run => train}/params/P1000/review/learning_rate/onsplit_average_reg_10_tanh_large_testing_inner_LR.py (100%) rename {run => train}/params/P1000/review/onsplit_average_reg_10_tanh_large_testing_ge.py (100%) rename {run => train}/run_me.py (85%) diff --git a/README.md b/README.md index 6870371..fd38daa 100644 --- a/README.md +++ b/README.md @@ -153,19 +153,23 @@ To get a local copy up and running follow these simple steps. export PYTHONPATH=~/pnet_prostate_paper:$PYTHONPATH ``` -3. To train all models run (time consuming process) - ```sh - cd ./run - python run_me.py +3. To generate all paper figures, run + ```sh + cd ./analysis + python run_it_all.py ``` -4. To generate paper figures run the different files under the 'analysis' directory, e.g. + +4. To generate individual paper figure run the different files under the 'analysis' directory, e.g. ```sh cd ./analysis python figure_1_d_auc_prc.py ``` - - - + +5. To re-train all models from scratch run (time consuming process) + ```sh + cd ./train + python run_me.py + ``` diff --git a/analysis/figure_3/figure3_b_gene_importance.py b/analysis/figure_3/figure3_b_gene_importance.py index 44b8559..1355c54 100644 --- a/analysis/figure_3/figure3_b_gene_importance.py +++ b/analysis/figure_3/figure3_b_gene_importance.py @@ -8,6 +8,8 @@ from os.path import join, dirname, realpath, exists from os import makedirs +module_path = dirname(realpath(__file__)) + def plot_high_genes_sns(df, col='avg_score', name='', saving_directory='.'): df.index=df.index.map(shorten_names) x_pos = range(df.shape[0]) @@ -239,12 +241,12 @@ def plot_high_genes2(ax, layer=1, graph ='hist', direction='h'): else: column = 'coef' - node_importance = pd.read_csv('extracted/node_importance_graph_adjusted.csv', index_col=0) + node_importance = pd.read_csv(join(module_path,'./extracted/node_importance_graph_adjusted.csv'), index_col=0) high_nodes = node_importance[node_importance.layer == layer].abs().nlargest(10, columns=[column]) # high_nodes = node_importance[node_importance.layer == layer].abs().nlargest(10, columns=['coef']) features = list(high_nodes.index) - response = pd.read_csv('extracted/response.csv', index_col=0) - df_in = pd.read_csv('./extracted/gradient_importance_detailed_{}.csv'.format(layer), index_col=0) + response = pd.read_csv(join(module_path,'./extracted/response.csv'), index_col=0) + df_in = pd.read_csv(join(module_path, './extracted/gradient_importance_detailed_{}.csv').format(layer), index_col=0) df_in = df_in.copy() df_in = df_in.join(response) df_in['group'] = df_in.response @@ -365,11 +367,11 @@ def shorten_names(name): name= name[:60]+'...' return name -current_dir = dirname(realpath(__file__)) + def run(): - node_importance = pd.read_csv(join(current_dir,'extracted/node_importance_graph_adjusted.csv'), index_col=0) - response = pd.read_csv(join(current_dir, 'extracted/response.csv'), index_col=0) + node_importance = pd.read_csv(join(module_path,'extracted/node_importance_graph_adjusted.csv'), index_col=0) + response = pd.read_csv(join(module_path, 'extracted/response.csv'), index_col=0) print response.head() layers = list(node_importance.layer.unique()) print layers diff --git a/analysis/figure_3/figure_3_sankey_all.py b/analysis/figure_3/figure_3_sankey_all.py index a18448a..00d504e 100644 --- a/analysis/figure_3/figure_3_sankey_all.py +++ b/analysis/figure_3/figure_3_sankey_all.py @@ -88,11 +88,11 @@ def get_nodes_per_layer_filtered(nodes_per_layer_df, all_node_ids, all_node_labe nodes_per_layer_filtered_df.index = nodes_per_layer_filtered_df.index.map(lambda x: mapping_dict[x]) return nodes_per_layer_filtered_df -features_weights = pd.read_csv(join(module_path,'./extracted/gradient_importance_0.csv'), index_col =[0,1]) -features_weights = features_weights.reset_index() -features_weights.columns= ['target', 'source', 'value'] -features_weights['layer'] = 0 -features_weights.head() +# features_weights = pd.read_csv(join(module_path,'./extracted/gradient_importance_0.csv'), index_col =[0,1]) +# features_weights = features_weights.reset_index() +# features_weights.columns= ['target', 'source', 'value'] +# features_weights['layer'] = 0 +# features_weights.head() def get_links_with_first_layer(): ''' diff --git a/config_path.py b/config_path.py index bb705eb..ed031ac 100644 --- a/config_path.py +++ b/config_path.py @@ -6,13 +6,10 @@ PATHWAY_PATH = join(DATA_PATH, 'pathways') REACTOM_PATHWAY_PATH = join(PATHWAY_PATH, 'Reactome') PROSTATE_DATA_PATH = join(DATA_PATH, 'prostate') -MELANOMA_DATA_PATH = join(DATA_PATH, 'melanoma') RUN_PATH = join(BASE_PATH, 'run') LOG_PATH = join(BASE_PATH, '_logs') PROSTATE_LOG_PATH = join(LOG_PATH, 'p1000') -MELANOMA_LOG_PATH = join(LOG_PATH, 'melanoma') PARAMS_PATH = join(RUN_PATH, 'params') POSTATE_PARAMS_PATH = join(PARAMS_PATH, 'P1000') -MELANOMA_PARAMS_PATH = join(PARAMS_PATH, 'melanoma') PLOTS_PATH = join(BASE_PATH, '_plots') diff --git a/run/run_me_melanoma.py b/run/run_me_melanoma.py deleted file mode 100644 index d95b6cd..0000000 --- a/run/run_me_melanoma.py +++ /dev/null @@ -1,115 +0,0 @@ -import sys -from os.path import join, dirname, realpath - -from pipeline.LeaveOneOut_pipeline import LeaveOneOutPipeline - -current_dir = dirname(realpath(__file__)) -sys.path.insert(0, dirname(current_dir)) - -import datetime -from utils.logs import set_logging, DebugFolder -from config_path import MELANOMA_LOG_PATH, MELANOMA_PARAMS_PATH -from pipeline.train_validate import TrainValidatePipeline -from pipeline.one_split import OneSplitPipeline -from pipeline.crossvalidation_pipeline import CrossvalidationPipeline - -import sys -import os -import imp -import logging -import random -import timeit -import numpy as np -import tensorflow as tf - -os.environ['KMP_DUPLICATE_LIB_OK'] = 'True' - -random_seed = 234 -random.seed(random_seed) -np.random.seed(random_seed) -tf.random.set_random_seed(random_seed) - - -timeStamp = '_{0:%b}-{0:%d}_{0:%H}-{0:%M}'.format(datetime.datetime.now()) - -def elapsed_time(start_time, end_time): - elapsed_time = end_time - start_time - elapsed_mins = int(elapsed_time / 60) - elapsed_secs = int(elapsed_time - (elapsed_mins * 60)) - return elapsed_mins, elapsed_secs - -params_file_list = [] - -# pnet -# params_file_list.append('./pnet/onsplit_average_reg_10_tanh_large_testing') -# params_file_list.append('./pnet/onsplit_average_reg_10_tanh_large_testing_inner') -# params_file_list.append('./pnet/crossvalidation_average_reg_10_tanh') - -# other ML models -# params_file_list.append('./compare/onsplit_ML_test') -# params_file_list.append('./compare/crossvalidation_ML_test') - -# dense -# params_file_list.append('./dense/onesplit_number_samples_dense_sameweights') -# params_file_list.append('./dense/onsplit_dense') - -# number_samples -# params_file_list.append('./number_samples/crossvalidation_average_reg_10') -# ## params_file_list.append('./number_samples/crossvalidation_average_reg_10_tanh') -# params_file_list.append('./number_samples/crossvalidation_number_samples_dense_sameweights') - -# external_validation -# params_file_list.append('./external_validation/pnet_validation') - -#reviews -#LOOCV -# params_file_list.append('./review/LOOCV_reg_10_tanh') -# params_file_list.append('./review/onsplit_average_reg_10_tanh_large_testing_ge') -# params_file_list.append('./review/fusion/onsplit_average_reg_10_tanh_large_testing_TMB') -# params_file_list.append('./review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion') - -#cancer genes - -# params_file_list.append('./review/onsplit_average_reg_10_tanh_large_testing') - -# params_file_list.append('./review/onsplit_average_reg_10_cancer_genes_testing') -# params_file_list.append('./review/crossvalidation_average_reg_10_tanh_cancer_genes') - -# melanoma -params_file_list.append('./pnet/onsplit_average_reg_10_tanh_large_testing_inner') - - - -for params_file in params_file_list: - log_dir = join(MELANOMA_LOG_PATH, params_file) - log_dir = log_dir - set_logging(log_dir) - params_file = join(MELANOMA_PARAMS_PATH, params_file) - logging.info('random seed %d' % random_seed) - params_file_full = params_file + '.py' - print params_file_full - params = imp.load_source(params_file, params_file_full) - - DebugFolder(log_dir) - if params.pipeline['type'] == 'one_split': - pipeline = OneSplitPipeline(task=params.task, data_params=params.data, model_params=params.models, - pre_params=params.pre, feature_params=params.features, pipeline_params=params.pipeline, - exp_name=log_dir) - - elif params.pipeline['type'] == 'crossvalidation': - pipeline = CrossvalidationPipeline(task=params.task, data_params=params.data, feature_params=params.features, - model_params=params.models, pre_params=params.pre, - pipeline_params=params.pipeline, exp_name=log_dir) - elif params.pipeline['type'] == 'Train_Validate': - pipeline = TrainValidatePipeline(data_params=params.data, model_params=params.models, pre_params=params.pre, - feature_params=params.features, pipeline_params=params.pipeline, exp_name=log_dir) - - elif params.pipeline['type'] == 'LOOCV': - pipeline = LeaveOneOutPipeline(task=params.task, data_params=params.data, feature_params=params.features, - model_params=params.models, pre_params=params.pre, - pipeline_params=params.pipeline, exp_name=log_dir) - start = timeit.default_timer() - pipeline.run() - stop = timeit.default_timer() - mins, secs = elapsed_time(start, stop) - logging.info('Elapsed Time: {}m {}s'.format(mins,secs)) diff --git a/run/__init__.py b/train/__init__.py similarity index 100% rename from run/__init__.py rename to train/__init__.py diff --git a/run/params/P1000/ML_params_search/crossvalidation_ML_params_search_logistic.py b/train/params/P1000/ML_params_search/crossvalidation_ML_params_search_logistic.py similarity index 100% rename from run/params/P1000/ML_params_search/crossvalidation_ML_params_search_logistic.py rename to train/params/P1000/ML_params_search/crossvalidation_ML_params_search_logistic.py diff --git a/run/params/P1000/ML_params_search/crossvalidation_ML_params_search_svm.py b/train/params/P1000/ML_params_search/crossvalidation_ML_params_search_svm.py similarity index 100% rename from run/params/P1000/ML_params_search/crossvalidation_ML_params_search_svm.py rename to train/params/P1000/ML_params_search/crossvalidation_ML_params_search_svm.py diff --git a/run/params/P1000/ML_params_search/onesplit_ML_params_search_adaboost.py b/train/params/P1000/ML_params_search/onesplit_ML_params_search_adaboost.py similarity index 100% rename from run/params/P1000/ML_params_search/onesplit_ML_params_search_adaboost.py rename to train/params/P1000/ML_params_search/onesplit_ML_params_search_adaboost.py diff --git a/run/params/P1000/ML_params_search/onesplit_ML_params_search_randomforest.py b/train/params/P1000/ML_params_search/onesplit_ML_params_search_randomforest.py similarity index 100% rename from run/params/P1000/ML_params_search/onesplit_ML_params_search_randomforest.py rename to train/params/P1000/ML_params_search/onesplit_ML_params_search_randomforest.py diff --git a/run/params/P1000/ML_params_search/onesplit_ML_params_search_svm.py b/train/params/P1000/ML_params_search/onesplit_ML_params_search_svm.py similarity index 100% rename from run/params/P1000/ML_params_search/onesplit_ML_params_search_svm.py rename to train/params/P1000/ML_params_search/onesplit_ML_params_search_svm.py diff --git a/run/params/P1000/ML_params_search/onesplit_ML_params_search_svm_linear.py b/train/params/P1000/ML_params_search/onesplit_ML_params_search_svm_linear.py similarity index 100% rename from run/params/P1000/ML_params_search/onesplit_ML_params_search_svm_linear.py rename to train/params/P1000/ML_params_search/onesplit_ML_params_search_svm_linear.py diff --git a/run/params/P1000/ML_params_search/onesplit_ML_params_search_tree.py b/train/params/P1000/ML_params_search/onesplit_ML_params_search_tree.py similarity index 100% rename from run/params/P1000/ML_params_search/onesplit_ML_params_search_tree.py rename to train/params/P1000/ML_params_search/onesplit_ML_params_search_tree.py diff --git a/run/params/P1000/ML_params_search/onsplit_ML_params_search_logistic.py b/train/params/P1000/ML_params_search/onsplit_ML_params_search_logistic.py similarity index 100% rename from run/params/P1000/ML_params_search/onsplit_ML_params_search_logistic.py rename to train/params/P1000/ML_params_search/onsplit_ML_params_search_logistic.py diff --git a/run/params/P1000/compare/crossvalidation_ML_test.py b/train/params/P1000/compare/crossvalidation_ML_test.py similarity index 100% rename from run/params/P1000/compare/crossvalidation_ML_test.py rename to train/params/P1000/compare/crossvalidation_ML_test.py diff --git a/run/params/P1000/compare/onsplit_ML_test.py b/train/params/P1000/compare/onsplit_ML_test.py similarity index 100% rename from run/params/P1000/compare/onsplit_ML_test.py rename to train/params/P1000/compare/onsplit_ML_test.py diff --git a/run/params/P1000/dense/onesplit_number_samples_dense_sameweights.py b/train/params/P1000/dense/onesplit_number_samples_dense_sameweights.py similarity index 100% rename from run/params/P1000/dense/onesplit_number_samples_dense_sameweights.py rename to train/params/P1000/dense/onesplit_number_samples_dense_sameweights.py diff --git a/run/params/P1000/dense/onsplit_dense.py b/train/params/P1000/dense/onsplit_dense.py similarity index 100% rename from run/params/P1000/dense/onsplit_dense.py rename to train/params/P1000/dense/onsplit_dense.py diff --git a/run/params/P1000/external_validation/pnet_validation.py b/train/params/P1000/external_validation/pnet_validation.py similarity index 100% rename from run/params/P1000/external_validation/pnet_validation.py rename to train/params/P1000/external_validation/pnet_validation.py diff --git a/run/params/P1000/number_samples/crossvalidation_average_reg_10.py b/train/params/P1000/number_samples/crossvalidation_average_reg_10.py similarity index 100% rename from run/params/P1000/number_samples/crossvalidation_average_reg_10.py rename to train/params/P1000/number_samples/crossvalidation_average_reg_10.py diff --git a/run/params/P1000/number_samples/crossvalidation_average_reg_10_tanh.py b/train/params/P1000/number_samples/crossvalidation_average_reg_10_tanh.py similarity index 100% rename from run/params/P1000/number_samples/crossvalidation_average_reg_10_tanh.py rename to train/params/P1000/number_samples/crossvalidation_average_reg_10_tanh.py diff --git a/run/params/P1000/number_samples/crossvalidation_number_samples_dense_sameweights.py b/train/params/P1000/number_samples/crossvalidation_number_samples_dense_sameweights.py similarity index 100% rename from run/params/P1000/number_samples/crossvalidation_number_samples_dense_sameweights.py rename to train/params/P1000/number_samples/crossvalidation_number_samples_dense_sameweights.py diff --git a/run/params/P1000/pnet/crossvalidation_average_reg_10_tanh.py b/train/params/P1000/pnet/crossvalidation_average_reg_10_tanh.py similarity index 100% rename from run/params/P1000/pnet/crossvalidation_average_reg_10_tanh.py rename to train/params/P1000/pnet/crossvalidation_average_reg_10_tanh.py diff --git a/run/params/P1000/pnet/onsplit_average_reg_10_tanh_large_testing.py b/train/params/P1000/pnet/onsplit_average_reg_10_tanh_large_testing.py similarity index 100% rename from run/params/P1000/pnet/onsplit_average_reg_10_tanh_large_testing.py rename to train/params/P1000/pnet/onsplit_average_reg_10_tanh_large_testing.py diff --git a/run/params/P1000/pnet/onsplit_average_reg_10_tanh_large_testing_inner.py b/train/params/P1000/pnet/onsplit_average_reg_10_tanh_large_testing_inner.py similarity index 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b/train/params/P1000/review/9hotspot/onsplit_average_reg_10_tanh_large_testing_hotspot.py similarity index 100% rename from run/params/P1000/review/9hotspot/onsplit_average_reg_10_tanh_large_testing_hotspot.py rename to train/params/P1000/review/9hotspot/onsplit_average_reg_10_tanh_large_testing_hotspot.py diff --git a/run/params/P1000/review/9single_copy/crossvalidation_average_reg_10_tanh_single_copy.py b/train/params/P1000/review/9single_copy/crossvalidation_average_reg_10_tanh_single_copy.py similarity index 100% rename from run/params/P1000/review/9single_copy/crossvalidation_average_reg_10_tanh_single_copy.py rename to train/params/P1000/review/9single_copy/crossvalidation_average_reg_10_tanh_single_copy.py diff --git a/run/params/P1000/review/9single_copy/onsplit_average_reg_10_tanh_large_testing_single_copy.py b/train/params/P1000/review/9single_copy/onsplit_average_reg_10_tanh_large_testing_single_copy.py similarity index 100% rename from run/params/P1000/review/9single_copy/onsplit_average_reg_10_tanh_large_testing_single_copy.py rename to train/params/P1000/review/9single_copy/onsplit_average_reg_10_tanh_large_testing_single_copy.py diff --git a/run/params/P1000/review/LOOCV_reg_10_tanh.py b/train/params/P1000/review/LOOCV_reg_10_tanh.py similarity index 100% rename from run/params/P1000/review/LOOCV_reg_10_tanh.py rename to train/params/P1000/review/LOOCV_reg_10_tanh.py diff --git a/run/params/P1000/review/crossvalidation_average_reg_10_tanh_cancer_genes.py b/train/params/P1000/review/crossvalidation_average_reg_10_tanh_cancer_genes.py similarity index 100% rename from run/params/P1000/review/crossvalidation_average_reg_10_tanh_cancer_genes.py rename to train/params/P1000/review/crossvalidation_average_reg_10_tanh_cancer_genes.py diff --git a/run/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_TMB.py b/train/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_TMB.py similarity index 100% rename from run/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_TMB.py rename to train/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_TMB.py diff --git a/run/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion.py b/train/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion.py similarity index 100% rename from run/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion.py rename to train/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion.py diff --git a/run/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion_zero.py b/train/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion_zero.py similarity index 100% rename from run/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion_zero.py rename to train/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion_zero.py diff --git a/run/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_inner_fusion_genes.py b/train/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_inner_fusion_genes.py similarity index 100% rename from run/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_inner_fusion_genes.py rename to train/params/P1000/review/fusion/onsplit_average_reg_10_tanh_large_testing_inner_fusion_genes.py diff --git a/run/params/P1000/review/learning_rate/onsplit_average_reg_10_tanh_large_testing_inner_LR.py b/train/params/P1000/review/learning_rate/onsplit_average_reg_10_tanh_large_testing_inner_LR.py similarity index 100% rename from run/params/P1000/review/learning_rate/onsplit_average_reg_10_tanh_large_testing_inner_LR.py rename to train/params/P1000/review/learning_rate/onsplit_average_reg_10_tanh_large_testing_inner_LR.py diff --git a/run/params/P1000/review/onsplit_average_reg_10_tanh_large_testing_ge.py b/train/params/P1000/review/onsplit_average_reg_10_tanh_large_testing_ge.py similarity index 100% rename from run/params/P1000/review/onsplit_average_reg_10_tanh_large_testing_ge.py rename to train/params/P1000/review/onsplit_average_reg_10_tanh_large_testing_ge.py diff --git a/run/run_me.py b/train/run_me.py similarity index 85% rename from run/run_me.py rename to train/run_me.py index 6ad8759..b0d124e 100644 --- a/run/run_me.py +++ b/train/run_me.py @@ -44,51 +44,55 @@ def elapsed_time(start_time, end_time): params_file_list.append('./pnet/onsplit_average_reg_10_tanh_large_testing') params_file_list.append('./pnet/onsplit_average_reg_10_tanh_large_testing_inner') params_file_list.append('./pnet/crossvalidation_average_reg_10_tanh') - -# other ML models +# +# # other ML models params_file_list.append('./compare/onsplit_ML_test') params_file_list.append('./compare/crossvalidation_ML_test') - -# dense +# +# # dense params_file_list.append('./dense/onesplit_number_samples_dense_sameweights') params_file_list.append('./dense/onsplit_dense') - -# number_samples +# +# # number_samples params_file_list.append('./number_samples/crossvalidation_average_reg_10') ## params_file_list.append('./number_samples/crossvalidation_average_reg_10_tanh') params_file_list.append('./number_samples/crossvalidation_number_samples_dense_sameweights') - -# external_validation +# +# # external_validation params_file_list.append('./external_validation/pnet_validation') - -#reviews------------------------------------ -#LOOCV -params_file_list.append('./review/LOOCV_reg_10_tanh') -#ge +# +# #reviews------------------------------------ +# #LOOCV +# params_file_list.append('./review/LOOCV_reg_10_tanh') +# #ge params_file_list.append('./review/onsplit_average_reg_10_tanh_large_testing_ge') -#fusion -params_file_list.append('./review/fusion/onsplit_average_reg_10_tanh_large_testing_TMB') +# #fusion +# params_file_list.append('./review/fusion/onsplit_average_reg_10_tanh_large_testing_TMB') params_file_list.append('./review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion') params_file_list.append('./review/fusion/onsplit_average_reg_10_tanh_large_testing_fusion_zero') params_file_list.append('./review/fusion/onsplit_average_reg_10_tanh_large_testing_inner_fusion_genes') - -#single copy +# +# #single copy params_file_list.append('./review/9single_copy/onsplit_average_reg_10_tanh_large_testing_single_copy') params_file_list.append('./review/9single_copy/crossvalidation_average_reg_10_tanh_single_copy') - -#custom arch +# +# #custom arch params_file_list.append('./review/10custom_arch/onsplit_kegg') - -#learning rate +# +# #learning rate params_file_list.append('./review/learning_rate/onsplit_average_reg_10_tanh_large_testing_inner_LR') +#hotspot +params_file_list.append('./review/9hotspot/onsplit_average_reg_10_tanh_large_testing_hotspot') +params_file_list.append('./review/9hotspot/onsplit_average_reg_10_tanh_large_testing_count') + #cancer genes -# params_file_list.append('./review/onsplit_average_reg_10_tanh_large_testing') -# params_file_list.append('./review/onsplit_average_reg_10_cancer_genes_testing') -# params_file_list.append('./review/crossvalidation_average_reg_10_tanh_cancer_genes') +params_file_list.append('./review/onsplit_average_reg_10_tanh_large_testing') +params_file_list.append('./review/onsplit_average_reg_10_cancer_genes_testing') +params_file_list.append('./review/crossvalidation_average_reg_10_tanh_cancer_genes') + -# melanoma