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project.yml
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title: "scispaCy pipeline"
description: "All the steps needed in the scispaCy pipeline"
vars:
version_string: "0.5.4"
gpu_id: 0
freqs_loc_s3: "s3://ai2-s2-scispacy/data/gorc_subset.freqs"
freqs_loc_local: "assets/gorc_subset.freqs"
vectors_loc_s3: "s3://ai2-s2-scispacy/data/pubmed_with_header.txt.gz"
vectors_loc_local: "assets/pubmed_with_header.txt.gz"
genia_loc_s3: "s3://ai2-s2-scispacy/data/genia"
genia_train_loc_local: "assets/genia_train.json"
genia_dev_loc_local: "assets/genia_dev.json"
genia_test_loc_local: "assets/genia_test.json"
genia_train_spacy_loc: "project_data/genia_train.spacy"
genia_dev_spacy_loc: "project_data/genia_dev.spacy"
genia_test_spacy_loc: "project_data/genia_test.spacy"
ontonotes_loc_s3: "s3://ai2-s2-scispacy/data/ud_ontonotes.tar.gz"
ontonotes_train_spacy_loc: "project_data/train"
ontonotes_dev_spacy_loc: "project_data/dev"
ontonotes_test_spacy_loc: "project_data/test"
ontonotes_loc_local: "assets/ud_ontonotes"
med_mentions_loc_s3: "s3://ai2-s2-scispacy/data/med_mentions.tar.gz"
corpus_pubtator_loc_local: "assets/corpus_pubtator.txt"
ner_loc_s3: "s3://ai2-s2-scispacy/data/ner/"
bc5cdr_loc_local: "assets/BC5CDR-IOB"
jnlpba_loc_local: "assets/JNLPBA-IOB"
craft_loc_local: "assets/CRAFT-IOB"
bionlp13cg_loc_local: "assets/BioNLP13CG-IOB"
vocab_sm_loc: "project_data/vocab_sm.jsonl"
vocab_md_loc: "project_data/vocab_md.jsonl"
vocab_lg_loc: "project_data/vocab_lg.jsonl"
vectors_md_loc: "output/en_core_sci_md_vectors"
vectors_lg_loc: "output/en_core_sci_lg_vectors"
parser_tagger_sm_loc: "output/en_core_sci_sm_parser_tagger"
parser_tagger_md_loc: "output/en_core_sci_md_parser_tagger"
parser_tagger_lg_loc: "output/en_core_sci_lg_parser_tagger"
parser_tagger_scibert_loc: "output/en_core_sci_scibert_parser_tagger"
ner_sm_loc: "output/en_core_sci_sm_ner"
ner_md_loc: "output/en_core_sci_md_ner"
ner_lg_loc: "output/en_core_sci_lg_ner"
ner_scibert_loc: "output/en_core_sci_scibert_ner"
bc5cdr_md_loc: "output/en_ner_bc5cdr_md"
jnlpba_md_loc: "output/en_ner_jnlpba_md"
craft_md_loc: "output/en_ner_craft_md"
bionlp13cg_md_loc: "output/en_ner_bionlp13cg_md"
parser_tagger_config_loc: "configs/base_parser_tagger.cfg"
parser_tagger_scibert_config_loc: "configs/base_parser_tagger_scibert.cfg"
ner_config_loc: "configs/base_ner.cfg"
ner_scibert_config_loc: "configs/base_ner_scibert.cfg"
specialized_ner_config_loc: "configs/base_specialized_ner.cfg"
code_loc: "scispacy/base_project_code.py"
meta_sm_loc: "data/meta_small.json"
meta_md_loc: "data/meta_medium.json"
meta_lg_loc: "data/meta_large.json"
meta_scibert_loc: "data/meta_scibert.json"
meta_bc5cdr_loc: "data/bc5cdr_ner.json"
meta_bionlp13cg_loc: "data/bionlp13cg_ner.json"
meta_craft_loc: "data/craft_ner.json"
meta_jnlpba_loc: "data/jnlpba_ner.json"
package_sm_loc: "packages/en_core_sci_sm-${vars.version_string}/en_core_sci_sm/en_core_sci_sm-${vars.version_string}"
package_md_loc: "packages/en_core_sci_md-${vars.version_string}/en_core_sci_md/en_core_sci_md-${vars.version_string}"
package_lg_loc: "packages/en_core_sci_lg-${vars.version_string}/en_core_sci_lg/en_core_sci_lg-${vars.version_string}"
package_scibert_loc: "packages/en_core_sci_scibert-${vars.version_string}/en_core_sci_scibert/en_core_sci_scibert-${vars.version_string}"
package_bc5cdr_loc: "packages/en_ner_bc5cdr_md-${vars.version_string}/en_ner_bc5cdr_md/en_ner_bc5cdr_md-${vars.version_string}"
package_bionlp13cg_loc: "packages/en_ner_bionlp13cg_md-${vars.version_string}/en_ner_bionlp13cg_md/en_ner_bionlp13cg_md-${vars.version_string}"
package_craft_loc: "packages/en_ner_craft_md-${vars.version_string}/en_ner_craft_md/en_ner_craft_md-${vars.version_string}"
package_jnlpba_loc: "packages/en_ner_jnlpba_md-${vars.version_string}/en_ner_jnlpba_md/en_ner_jnlpba_md-${vars.version_string}"
# These are the directories that the project needs. The project CLI will make
# sure that they always exist.
directories: ["assets", "project_data", "output", "packages"]
workflows:
justdownload:
- download
small:
- download
- convert-shared
- convert-sm
- parser-tagger-train-sm
- evaluate-parser-tagger-sm
- ner-train-sm
- evaluate-ner-sm
- package-sm
- evaluate-package-sm
medium:
- download
- convert-shared
- convert-md
- vectors-init-md
- parser-tagger-train-md
- evaluate-parser-tagger-md
- ner-train-md
- evaluate-ner-md
- package-md
- evaluate-package-md
large:
- download
- convert-shared
- convert-lg
- vectors-init-lg
- parser-tagger-train-lg
- evaluate-parser-tagger-lg
- ner-train-lg
- evaluate-ner-lg
- package-lg
- evaluate-package-lg
scibert:
- download
- convert-shared
- convert-lg # use the large vocab, but not the vectors
- parser-tagger-train-scibert
- evaluate-parser-tagger-scibert
- ner-train-scibert
- evaluate-ner-scibert
- package-scibert
- evaluate-package-scibert
specialized-ner:
- ner-train-specialized
- evaluate-specialized-ner
- package-ner
- evaluate-package-ner
all:
- download
- convert-shared
- convert-sm
- convert-md
- convert-lg
- vectors-init-md
- vectors-init-lg
- parser-tagger-train-sm
- parser-tagger-train-md
- parser-tagger-train-lg
- parser-tagger-train-scibert
- ner-train-sm
- ner-train-md
- ner-train-lg
- ner-train-specialized
- ner-train-scibert
- evaluate-parser-tagger-sm
- evaluate-parser-tagger-md
- evaluate-parser-tagger-lg
- evaluate-parser-tagger-scibert
- evaluate-ner-sm
- evaluate-ner-md
- evaluate-ner-lg
- evaluate-specialized-ner
- evaluate-ner-scibert
- package-sm
- package-md
- package-lg
- package-ner
- package-scibert
- evaluate-package-sm
- evaluate-package-md
- evaluate-package-lg
- evaluate-package-ner
- evaluate-package-scibert
commands:
- name: download
help: "Download the necessary files"
script:
- "aws s3 cp ${vars.freqs_loc_s3} ${vars.freqs_loc_local} --no-sign-request"
- "aws s3 cp ${vars.vectors_loc_s3} ${vars.vectors_loc_local} --no-sign-request"
- "aws s3 cp ${vars.genia_loc_s3}/train.json ${vars.genia_train_loc_local} --no-sign-request"
- "aws s3 cp ${vars.genia_loc_s3}/dev.json ${vars.genia_dev_loc_local} --no-sign-request"
- "aws s3 cp ${vars.genia_loc_s3}/test.json ${vars.genia_test_loc_local} --no-sign-request"
- "aws s3 cp ${vars.ontonotes_loc_s3} ${vars.ontonotes_loc_local}.tar.gz"
- "tar -xzvf ${vars.ontonotes_loc_local}.tar.gz -C assets/"
- "rm ${vars.ontonotes_loc_local}.tar.gz"
- "aws s3 cp ${vars.med_mentions_loc_s3} assets/med_mentions.tar.gz --no-sign-request"
- "tar -xzvf assets/med_mentions.tar.gz -C assets/"
- "rm assets/med_mentions.tar.gz"
- "aws s3 cp ${vars.ner_loc_s3} assets --recursive --exclude '*' --include '*.tsv' --no-sign-request"
outputs:
- "${vars.freqs_loc_local}"
- "${vars.vectors_loc_local}"
- "${vars.genia_train_loc_local}"
- "${vars.genia_dev_loc_local}"
- "${vars.genia_test_loc_local}"
- "${vars.ontonotes_loc_local}/train"
- "${vars.ontonotes_loc_local}/dev"
- "${vars.ontonotes_loc_local}/test"
- "${vars.corpus_pubtator_loc_local}"
- "${vars.bc5cdr_loc_local}/train.tsv"
- "${vars.bc5cdr_loc_local}/devel.tsv"
- "${vars.bc5cdr_loc_local}/test.tsv"
- "${vars.jnlpba_loc_local}/train.tsv"
- "${vars.jnlpba_loc_local}/devel.tsv"
- "${vars.jnlpba_loc_local}/test.tsv"
- "${vars.craft_loc_local}/train.tsv"
- "${vars.craft_loc_local}/devel.tsv"
- "${vars.craft_loc_local}/test.tsv"
- "${vars.bionlp13cg_loc_local}/train.tsv"
- "${vars.bionlp13cg_loc_local}/devel.tsv"
- "${vars.bionlp13cg_loc_local}/test.tsv"
- name: convert-shared
help: "Convert the data to spaCy's format"
script:
- "spacy convert ${vars.genia_train_loc_local} project_data --converter json --file-type spacy"
- "spacy convert ${vars.genia_dev_loc_local} project_data --converter json --file-type spacy"
- "spacy convert ${vars.genia_test_loc_local} project_data --converter json --file-type spacy"
- "spacy convert ${vars.ontonotes_loc_local} project_data --converter json --file-type spacy"
deps:
- "${vars.genia_train_loc_local}"
- "${vars.genia_dev_loc_local}"
- "${vars.genia_test_loc_local}"
- "${vars.ontonotes_loc_local}"
outputs:
- "${vars.genia_train_spacy_loc}"
- "${vars.genia_dev_spacy_loc}"
- "${vars.genia_test_spacy_loc}"
- "${vars.ontonotes_train_spacy_loc}"
- "${vars.ontonotes_dev_spacy_loc}"
- "${vars.ontonotes_test_spacy_loc}"
- name: convert-sm
help: "Convert a file of word/document frequency statistics to spacy's vocabulary format"
script:
- "python scripts/convert_freqs.py --input_path ${vars.freqs_loc_local} --output_path ${vars.vocab_sm_loc} --min_word_frequency 1000"
deps:
- "${vars.freqs_loc_local}"
outputs:
- "${vars.vocab_sm_loc}"
- name: convert-md
help: "Convert a file of word/document frequency statistics to spacy's vocabulary format"
script:
- "python scripts/convert_freqs.py --input_path ${vars.freqs_loc_local} --output_path ${vars.vocab_md_loc} --min_word_frequency 150"
deps:
- "${vars.freqs_loc_local}"
outputs:
- "${vars.vocab_md_loc}"
- name: convert-lg
help: "Convert a file of word/document frequency statistics to spacy's vocabulary format"
script:
- "python scripts/convert_freqs.py --input_path ${vars.freqs_loc_local} --output_path ${vars.vocab_lg_loc} --min_word_frequency 50"
deps:
- "${vars.freqs_loc_local}"
outputs:
- "${vars.vocab_lg_loc}"
- name: vectors-init-md
help: "Initialize the vectors"
script:
- "spacy init vectors en ${vars.vectors_loc_local} ${vars.vectors_md_loc} --prune 50000 --name en_core_sci_md.vectors --lexemes-jsonl ${vars.vocab_md_loc}"
deps:
- "${vars.vocab_md_loc}"
- "${vars.vectors_loc_local}"
outputs:
- "${vars.vectors_md_loc}"
- name: vectors-init-lg
help: "Initialize the vectors"
script:
- "spacy init vectors en ${vars.vectors_loc_local} ${vars.vectors_lg_loc} --prune 600000 --name en_core_sci_lg.vectors --lexemes-jsonl ${vars.vocab_lg_loc}"
deps:
- "${vars.vocab_lg_loc}"
- "${vars.vectors_loc_local}"
outputs:
- "${vars.vectors_lg_loc}"
- name: parser-tagger-train-sm
help: "Train the base models"
script:
- "spacy train ${vars.parser_tagger_config_loc} --output ${vars.parser_tagger_sm_loc} --code ${vars.code_loc} --paths.vocab_path ${vars.vocab_sm_loc} --vars.include_static_vectors False --gpu-id ${vars.gpu_id}"
deps:
- "${vars.parser_tagger_config_loc}"
- "${vars.genia_train_spacy_loc}"
- "${vars.genia_dev_spacy_loc}"
- "${vars.genia_test_spacy_loc}"
- "${vars.ontonotes_train_spacy_loc}"
outputs:
- "${vars.parser_tagger_sm_loc}/model-best"
- name: parser-tagger-train-md
help: "Train the base models"
script:
- "spacy train ${vars.parser_tagger_config_loc} --output ${vars.parser_tagger_md_loc} --code ${vars.code_loc} --paths.vectors ${vars.vectors_md_loc} --paths.vocab_path ${vars.vocab_md_loc} --vars.include_static_vectors True --gpu-id ${vars.gpu_id}"
deps:
- "${vars.parser_tagger_config_loc}"
- "${vars.genia_train_spacy_loc}"
- "${vars.genia_dev_spacy_loc}"
- "${vars.genia_test_spacy_loc}"
- "${vars.ontonotes_train_spacy_loc}"
- "${vars.vectors_md_loc}"
outputs:
- "${vars.parser_tagger_md_loc}/model-best"
- name: parser-tagger-train-lg
help: "Train the base models"
script:
- "spacy train ${vars.parser_tagger_config_loc} --output ${vars.parser_tagger_lg_loc} --code ${vars.code_loc} --paths.vectors ${vars.vectors_lg_loc} --paths.vocab_path ${vars.vocab_lg_loc} --vars.include_static_vectors True --gpu-id ${vars.gpu_id}"
deps:
- "${vars.parser_tagger_config_loc}"
- "${vars.genia_train_spacy_loc}"
- "${vars.genia_dev_spacy_loc}"
- "${vars.genia_test_spacy_loc}"
- "${vars.ontonotes_train_spacy_loc}"
- "${vars.vectors_lg_loc}"
outputs:
- "${vars.parser_tagger_lg_loc}/model-best"
- name: parser-tagger-train-scibert
help: "Train the scibert transformer model"
script:
- "spacy train ${vars.parser_tagger_scibert_config_loc} --output ${vars.parser_tagger_scibert_loc} --code ${vars.code_loc} --paths.vocab_path ${vars.vocab_lg_loc} --gpu-id ${vars.gpu_id}"
deps:
- "${vars.parser_tagger_scibert_config_loc}"
- "${vars.genia_train_spacy_loc}"
- "${vars.genia_dev_spacy_loc}"
- "${vars.genia_test_spacy_loc}"
- "${vars.ontonotes_train_spacy_loc}"
outputs:
- "${vars.parser_tagger_scibert_loc}/model-best"
- name: ner-train-sm
help: "Train the main ner"
script:
- "spacy train ${vars.ner_config_loc} --output ${vars.ner_sm_loc} --code ${vars.code_loc} --paths.parser_tagger_path ${vars.parser_tagger_sm_loc}/model-best --paths.vocab_path ${vars.vocab_sm_loc} --vars.include_static_vectors False --gpu-id ${vars.gpu_id}"
deps:
- "${vars.ner_config_loc}"
- "${vars.parser_tagger_sm_loc}/model-best"
- "${vars.corpus_pubtator_loc_local}"
outputs:
- "${vars.ner_sm_loc}/model-best"
- name: ner-train-md
help: "Train the main ner"
script:
- "spacy train ${vars.ner_config_loc} --output ${vars.ner_md_loc} --code ${vars.code_loc} --paths.vectors ${vars.vectors_md_loc} --paths.parser_tagger_path ${vars.parser_tagger_md_loc}/model-best --paths.vocab_path ${vars.vocab_md_loc} --vars.include_static_vectors True --gpu-id ${vars.gpu_id}"
deps:
- "${vars.ner_config_loc}"
- "${vars.parser_tagger_md_loc}/model-best"
- "${vars.corpus_pubtator_loc_local}"
- "${vars.vectors_md_loc}"
outputs:
- "${vars.ner_md_loc}/model-best"
- name: ner-train-lg
help: "Train the main ner"
script:
- "spacy train ${vars.ner_config_loc} --output ${vars.ner_lg_loc} --code ${vars.code_loc} --paths.vectors ${vars.vectors_lg_loc} --paths.parser_tagger_path ${vars.parser_tagger_lg_loc}/model-best --paths.vocab_path ${vars.vocab_lg_loc} --vars.include_static_vectors True --gpu-id ${vars.gpu_id}"
deps:
- "${vars.ner_config_loc}"
- "${vars.parser_tagger_lg_loc}/model-best"
- "${vars.corpus_pubtator_loc_local}"
- "${vars.vectors_lg_loc}"
outputs:
- "${vars.ner_lg_loc}/model-best"
- name: ner-train-scibert
help: "Train the scibert ner model."
script:
- "spacy train ${vars.ner_scibert_config_loc} --output ${vars.ner_scibert_loc} --code ${vars.code_loc} --paths.parser_tagger_path ${vars.parser_tagger_scibert_loc}/model-best --gpu-id ${vars.gpu_id}"
deps:
- "${vars.ner_scibert_config_loc}"
- "${vars.parser_tagger_scibert_loc}/model-best"
- "${vars.corpus_pubtator_loc_local}"
outputs:
- "${vars.ner_scibert_loc}/model-best"
- name: ner-train-specialized
help: "Train the specialized NER models"
script:
- "spacy train ${vars.specialized_ner_config_loc} --output ${vars.bc5cdr_md_loc} --code ${vars.code_loc} --paths.vectors ${vars.vectors_md_loc} --paths.parser_tagger_path ${vars.parser_tagger_md_loc}/model-best --paths.train_path ${vars.bc5cdr_loc_local}/train.tsv --paths.dev_path ${vars.bc5cdr_loc_local}/devel.tsv --paths.vocab_path ${vars.vocab_md_loc} --vars.include_static_vectors True --gpu-id ${vars.gpu_id}"
- "spacy train ${vars.specialized_ner_config_loc} --output ${vars.bionlp13cg_md_loc} --code ${vars.code_loc} --paths.vectors ${vars.vectors_md_loc} --paths.parser_tagger_path ${vars.parser_tagger_md_loc}/model-best --paths.train_path ${vars.bionlp13cg_loc_local}/train.tsv --paths.dev_path ${vars.bionlp13cg_loc_local}/devel.tsv --paths.vocab_path ${vars.vocab_md_loc} --vars.include_static_vectors True --gpu-id ${vars.gpu_id}"
- "spacy train ${vars.specialized_ner_config_loc} --output ${vars.craft_md_loc} --code ${vars.code_loc} --paths.vectors ${vars.vectors_md_loc} --paths.parser_tagger_path ${vars.parser_tagger_md_loc}/model-best --paths.train_path ${vars.craft_loc_local}/train.tsv --paths.dev_path ${vars.craft_loc_local}/devel.tsv --paths.vocab_path ${vars.vocab_md_loc} --vars.include_static_vectors True --gpu-id ${vars.gpu_id}"
- "spacy train ${vars.specialized_ner_config_loc} --output ${vars.jnlpba_md_loc} --code ${vars.code_loc} --paths.vectors ${vars.vectors_md_loc} --paths.parser_tagger_path ${vars.parser_tagger_md_loc}/model-best --paths.train_path ${vars.jnlpba_loc_local}/train.tsv --paths.dev_path ${vars.jnlpba_loc_local}/devel.tsv --paths.vocab_path ${vars.vocab_md_loc} --vars.include_static_vectors True --gpu-id ${vars.gpu_id}"
deps:
- "${vars.corpus_pubtator_loc_local}"
- "${vars.bc5cdr_loc_local}/train.tsv"
- "${vars.bc5cdr_loc_local}/devel.tsv"
- "${vars.bc5cdr_loc_local}/test.tsv"
- "${vars.jnlpba_loc_local}/train.tsv"
- "${vars.jnlpba_loc_local}/devel.tsv"
- "${vars.jnlpba_loc_local}/test.tsv"
- "${vars.craft_loc_local}/train.tsv"
- "${vars.craft_loc_local}/devel.tsv"
- "${vars.craft_loc_local}/test.tsv"
- "${vars.bionlp13cg_loc_local}/train.tsv"
- "${vars.bionlp13cg_loc_local}/devel.tsv"
- "${vars.bionlp13cg_loc_local}/test.tsv"
- "${vars.parser_tagger_md_loc}/model-best"
- "${vars.specialized_ner_config_loc}"
outputs:
- "${vars.bc5cdr_md_loc}/model-best"
- "${vars.bionlp13cg_md_loc}/model-best"
- "${vars.craft_md_loc}/model-best"
- "${vars.jnlpba_md_loc}/model-best"
- name: evaluate-parser-tagger-sm
help: "Evaluate the parser and tagger"
script:
- "spacy evaluate ${vars.parser_tagger_sm_loc}/model-best ${vars.genia_test_spacy_loc} --output ${vars.parser_tagger_sm_loc}/model_best_results.json --gpu-id ${vars.gpu_id}"
- "spacy evaluate ${vars.parser_tagger_sm_loc}/model-best ${vars.ontonotes_test_spacy_loc} --output ${vars.parser_tagger_sm_loc}/model_best_results_onto.json --gpu-id ${vars.gpu_id}"
deps:
- "${vars.parser_tagger_sm_loc}/model-best"
- "${vars.genia_test_spacy_loc}"
- "${vars.ontonotes_test_spacy_loc}"
outputs:
- "${vars.parser_tagger_sm_loc}/model_best_results.json"
- "${vars.parser_tagger_sm_loc}/model_best_results_onto.json"
- name: evaluate-parser-tagger-md
help: "Evaluate the parser and tagger"
script:
- "spacy evaluate ${vars.parser_tagger_md_loc}/model-best ${vars.genia_test_spacy_loc} --output ${vars.parser_tagger_md_loc}/model_best_results.json --gpu-id ${vars.gpu_id}"
- "spacy evaluate ${vars.parser_tagger_md_loc}/model-best ${vars.ontonotes_test_spacy_loc} --output ${vars.parser_tagger_md_loc}/model_best_results_onto.json --gpu-id ${vars.gpu_id}"
deps:
- "${vars.parser_tagger_md_loc}/model-best"
- "${vars.genia_test_spacy_loc}"
- "${vars.ontonotes_test_spacy_loc}"
outputs:
- "${vars.parser_tagger_md_loc}/model_best_results.json"
- "${vars.parser_tagger_md_loc}/model_best_results_onto.json"
- name: evaluate-parser-tagger-lg
help: "Evaluate the parser and tagger"
script:
- "spacy evaluate ${vars.parser_tagger_lg_loc}/model-best ${vars.genia_test_spacy_loc} --output ${vars.parser_tagger_lg_loc}/model_best_results.json --gpu-id ${vars.gpu_id}"
- "spacy evaluate ${vars.parser_tagger_lg_loc}/model-best ${vars.ontonotes_test_spacy_loc} --output ${vars.parser_tagger_lg_loc}/model_best_results_onto.json --gpu-id ${vars.gpu_id}"
deps:
- "${vars.parser_tagger_lg_loc}/model-best"
- "${vars.genia_test_spacy_loc}"
- "${vars.ontonotes_test_spacy_loc}"
outputs:
- "${vars.parser_tagger_lg_loc}/model_best_results.json"
- "${vars.parser_tagger_lg_loc}/model_best_results_onto.json"
- name: evaluate-parser-tagger-scibert
help: "Evaluate the parser and tagger scibert model"
script:
- "spacy evaluate ${vars.parser_tagger_scibert_loc}/model-best ${vars.genia_test_spacy_loc} --output ${vars.parser_tagger_scibert_loc}/model_best_results.json --gpu-id ${vars.gpu_id} --gpu-id ${vars.gpu_id}"
- "spacy evaluate ${vars.parser_tagger_scibert_loc}/model-best ${vars.ontonotes_test_spacy_loc} --output ${vars.parser_tagger_scibert_loc}/model_best_results_onto.json --gpu-id ${vars.gpu_id} --gpu-id ${vars.gpu_id}"
deps:
- "${vars.parser_tagger_scibert_loc}/model-best"
- "${vars.genia_test_spacy_loc}"
- "${vars.ontonotes_test_spacy_loc}"
outputs:
- "${vars.parser_tagger_scibert_loc}/model_best_results.json"
- "${vars.parser_tagger_scibert_loc}/model_best_results_onto.json"
- name: evaluate-ner-sm
help: "Evaluate NER"
script:
- "python scripts/evaluate_ner.py --model_path ${vars.ner_sm_loc}/model-best --dataset medmentions-test --output ${vars.ner_sm_loc}/model_best_results.json --med_mentions_folder_path assets/ --gpu_id ${vars.gpu_id}"
deps:
- "${vars.ner_sm_loc}"
- "${vars.corpus_pubtator_loc_local}"
outputs:
- "${vars.ner_sm_loc}/model_best_results.json"
- name: evaluate-ner-md
help: "Evaluate NER"
script:
- "python scripts/evaluate_ner.py --model_path ${vars.ner_md_loc}/model-best --dataset medmentions-test --output ${vars.ner_md_loc}/model_best_results.json --med_mentions_folder_path assets/ --gpu_id ${vars.gpu_id}"
deps:
- "${vars.ner_md_loc}"
- "${vars.corpus_pubtator_loc_local}"
outputs:
- "${vars.ner_md_loc}/model_best_results.json"
- name: evaluate-ner-lg
help: "Evaluate NER"
script:
- "python scripts/evaluate_ner.py --model_path ${vars.ner_lg_loc}/model-best --dataset medmentions-test --output ${vars.ner_lg_loc}/model_best_results.json --med_mentions_folder_path assets/ --gpu_id ${vars.gpu_id}"
deps:
- "${vars.ner_lg_loc}"
- "${vars.corpus_pubtator_loc_local}"
outputs:
- "${vars.ner_lg_loc}/model_best_results.json"
- name: evaluate-ner-scibert
help: "Evaluate NER scibert"
script:
- "python scripts/evaluate_ner.py --model_path ${vars.ner_scibert_loc}/model-best --dataset medmentions-test --output ${vars.ner_scibert_loc}/model_best_results.json --med_mentions_folder_path assets/ --gpu_id ${vars.gpu_id}"
deps:
- "${vars.ner_scibert_loc}"
- "${vars.corpus_pubtator_loc_local}"
outputs:
- "${vars.ner_scibert_loc}/model_best_results.json"
- name: evaluate-specialized-ner
help: "Evaluate specialize NER"
script:
- "python scripts/evaluate_ner.py --model_path ${vars.bc5cdr_md_loc}/model-best --dataset ${vars.bc5cdr_loc_local}/test.tsv --output ${vars.bc5cdr_md_loc}/model_best_results.json --gpu_id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.bionlp13cg_md_loc}/model-best --dataset ${vars.bionlp13cg_loc_local}/test.tsv --output ${vars.bionlp13cg_md_loc}/model_best_results.json --gpu_id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.craft_md_loc}/model-best --dataset ${vars.craft_loc_local}/test.tsv --output ${vars.craft_md_loc}/model_best_results.json --gpu_id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.jnlpba_md_loc}/model-best --dataset ${vars.jnlpba_loc_local}/test.tsv --output ${vars.jnlpba_md_loc}/model_best_results.json --gpu_id ${vars.gpu_id}"
deps:
- "${vars.bc5cdr_md_loc}/model-best"
- "${vars.bionlp13cg_md_loc}/model-best"
- "${vars.craft_md_loc}/model-best"
- "${vars.jnlpba_md_loc}/model-best"
- "${vars.bc5cdr_loc_local}/test.tsv"
- "${vars.jnlpba_loc_local}/test.tsv"
- "${vars.craft_loc_local}/test.tsv"
- "${vars.bionlp13cg_loc_local}/test.tsv"
outputs:
- "${vars.bc5cdr_md_loc}/model_best_results.json"
- "${vars.bionlp13cg_md_loc}/model_best_results.json"
- "${vars.craft_md_loc}/model_best_results.json"
- "${vars.jnlpba_md_loc}/model_best_results.json"
- name: package-sm
help: "Package the models"
script:
- "spacy package ${vars.ner_sm_loc}/model-best packages/ --meta-path ${vars.meta_sm_loc} --version ${vars.version_string}"
deps:
- "${vars.ner_sm_loc}/model-best"
outputs:
- "${vars.package_sm_loc}"
- name: evaluate-package-sm
help: "Evaluate the packaged models"
script:
- "spacy evaluate ${vars.package_sm_loc} ${vars.genia_test_spacy_loc} --output packages/sm_genia_results.json --gpu-id ${vars.gpu_id}"
- "spacy evaluate ${vars.package_sm_loc} ${vars.ontonotes_test_spacy_loc} --output packages/sm_onto_results.json --gpu-id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.package_sm_loc} --dataset medmentions-test --output packages/sm_mm_results.json --med_mentions_folder_path assets/ --gpu_id ${vars.gpu_id}"
deps:
- "${vars.package_sm_loc}"
outputs:
- "packages/sm_genia_results.json"
- "packages/sm_onto_results.json"
- "packages/sm_mm_results.json"
- name: package-md
help: "Package the models"
script:
- "spacy package ${vars.ner_md_loc}/model-best packages/ --meta-path ${vars.meta_md_loc} --version ${vars.version_string}"
deps:
- "${vars.ner_md_loc}/model-best"
outputs:
- "${vars.package_md_loc}"
- name: package-lg
help: "Package the models"
script:
- "spacy package ${vars.ner_lg_loc}/model-best packages/ --meta-path ${vars.meta_lg_loc} --version ${vars.version_string}"
deps:
- "${vars.ner_lg_loc}/model-best"
outputs:
- "${vars.package_lg_loc}"
- name: package-scibert
help: "Package the scibert model"
script:
- "spacy package ${vars.ner_scibert_loc}/model-best packages/ --meta-path ${vars.meta_scibert_loc} --version ${vars.version_string}"
deps:
- "${vars.meta_scibert_loc}"
- "${vars.ner_scibert_loc}/model-best"
outputs:
- "${vars.package_scibert_loc}"
- name: evaluate-package-md
help: "Evaluate the packaged models"
script:
- "spacy evaluate ${vars.package_md_loc} ${vars.genia_test_spacy_loc} --output packages/md_genia_results.json --gpu-id ${vars.gpu_id}"
- "spacy evaluate ${vars.package_md_loc} ${vars.ontonotes_test_spacy_loc} --output packages/md_onto_results.json --gpu-id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.package_md_loc} --dataset medmentions-test --output packages/md_mm_results.json --med_mentions_folder_path assets/ --gpu_id ${vars.gpu_id}"
deps:
- "${vars.package_md_loc}"
outputs:
- "packages/md_genia_results.json"
- "packages/md_onto_results.json"
- "packages/md_mm_results.json"
- name: evaluate-package-lg
help: "Evaluate the packaged models"
script:
- "spacy evaluate ${vars.package_lg_loc} ${vars.genia_test_spacy_loc} --output packages/lg_genia_results.json --gpu-id ${vars.gpu_id}"
- "spacy evaluate ${vars.package_lg_loc} ${vars.ontonotes_test_spacy_loc} --output packages/lg_onto_results.json --gpu-id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.package_lg_loc} --dataset medmentions-test --output packages/lg_mm_results.json --med_mentions_folder_path assets/ --gpu_id ${vars.gpu_id}"
deps:
- "${vars.package_lg_loc}"
outputs:
- "packages/lg_genia_results.json"
- "packages/lg_onto_results.json"
- "packages/lg_mm_results.json"
- name: evaluate-package-scibert
help: "Evaluate the packaged scibert model"
script:
- "spacy evaluate ${vars.package_scibert_loc} ${vars.genia_test_spacy_loc} --output packages/scibert_genia_results.json --gpu-id ${vars.gpu_id}"
- "spacy evaluate ${vars.package_scibert_loc} ${vars.ontonotes_test_spacy_loc} --output packages/scibert_onto_results.json --gpu-id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.package_scibert_loc} --dataset medmentions-test --output packages/scibert_mm_results.json --med_mentions_folder_path assets/ --gpu_id ${vars.gpu_id}"
deps:
- "${vars.package_scibert_loc}"
outputs:
- "packages/scibert_genia_results.json"
- "packages/scibert_onto_results.json"
- "packages/scibert_mm_results.json"
- name: package-ner
help: "Package the models"
script:
- "spacy package ${vars.bc5cdr_md_loc}/model-best packages/ --meta-path ${vars.meta_bc5cdr_loc} --version ${vars.version_string}"
- "spacy package ${vars.bionlp13cg_md_loc}/model-best packages/ --meta-path ${vars.meta_bionlp13cg_loc} --version ${vars.version_string}"
- "spacy package ${vars.craft_md_loc}/model-best packages/ --meta-path ${vars.meta_craft_loc} --version ${vars.version_string}"
- "spacy package ${vars.jnlpba_md_loc}/model-best packages/ --meta-path ${vars.meta_jnlpba_loc} --version ${vars.version_string}"
deps:
- "${vars.bc5cdr_md_loc}/model-best"
- "${vars.bionlp13cg_md_loc}/model-best"
- "${vars.craft_md_loc}/model-best"
- "${vars.jnlpba_md_loc}/model-best"
outputs:
- "${vars.package_bc5cdr_loc}"
- "${vars.package_bionlp13cg_loc}"
- "${vars.package_craft_loc}"
- "${vars.package_jnlpba_loc}"
- name: evaluate-package-ner
help: "Evaluate the packaged models"
script:
- "python scripts/evaluate_ner.py --model_path ${vars.package_bc5cdr_loc} --dataset ${vars.bc5cdr_loc_local}/test.tsv --output packages/bc5cdr_results.json --gpu_id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.package_bionlp13cg_loc} --dataset ${vars.bionlp13cg_loc_local}/test.tsv --output packages/bionlp13cg_results.json --gpu_id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.package_craft_loc} --dataset ${vars.craft_loc_local}/test.tsv --output packages/craft_results.json --gpu_id ${vars.gpu_id}"
- "python scripts/evaluate_ner.py --model_path ${vars.package_jnlpba_loc} --dataset ${vars.jnlpba_loc_local}/test.tsv --output packages/jnlpba_results.json --gpu_id ${vars.gpu_id}"
deps:
- "${vars.package_bc5cdr_loc}"
- "${vars.package_bionlp13cg_loc}"
- "${vars.package_craft_loc}"
- "${vars.package_jnlpba_loc}"
outputs:
- "packages/bc5cdr_results.json"
- "packages/bionlp13cg_results.json"
- "packages/craft_results.json"
- "packages/jnlpba_results.json"