├── .gitignore ├── README.md ├── data ├── annotation │ ├── brat_export.csv │ ├── doccano_export.csv │ └── ngramviewer_export.csv ├── brat │ ├── collection_01 │ │ ├── PMC2193209.ann │ │ ├── PMC2193209.txt │ │ ├── PMC2634967.ann │ │ ├── PMC2634967.txt │ │ ├── PMC2646571.ann │ │ ├── PMC2646571.txt │ │ ├── PMC2938478.ann │ │ ├── PMC2938478.txt │ │ ├── PMC3046151.ann │ │ ├── PMC3046151.txt │ │ ├── PMC3095633.ann │ │ ├── PMC3095633.txt │ │ ├── PMC3173465.ann │ │ ├── PMC3173465.txt │ │ ├── PMC3189223.ann │ │ ├── PMC3189223.txt │ │ ├── PMC3235500.ann │ │ ├── PMC3235500.txt │ │ ├── PMC3304099.ann │ │ ├── PMC3304099.txt │ │ ├── annotation.conf │ │ └── visual.conf │ └── collection_02 │ │ ├── PMC200936.ann │ │ ├── PMC200936.txt │ │ ├── PMC2193209.ann │ │ ├── PMC2193209.txt │ │ ├── PMC2196041.ann │ │ ├── PMC2196041.txt │ │ ├── PMC2587175.ann │ │ ├── PMC2587175.txt │ │ ├── PMC2634967.ann │ │ ├── PMC2634967.txt │ │ ├── PMC2646571.ann │ │ ├── PMC2646571.txt │ │ ├── PMC2772737.ann │ │ ├── PMC2772737.txt │ │ ├── PMC2783637.ann │ │ ├── PMC2783637.txt │ │ ├── PMC2805085.ann │ │ ├── PMC2805085.txt │ │ ├── PMC2938478.ann │ │ ├── PMC2938478.txt │ │ ├── PMC2983473.ann │ │ ├── PMC2983473.txt │ │ ├── PMC2989239.ann │ │ ├── PMC2989239.txt │ │ ├── PMC2996551.ann │ │ ├── PMC2996551.txt │ │ ├── PMC3046151.ann │ │ ├── PMC3046151.txt │ │ ├── PMC3064981.ann │ │ ├── PMC3064981.txt │ │ ├── PMC3067507.ann │ │ ├── PMC3067507.txt │ │ ├── PMC3092345.ann │ │ ├── PMC3092345.txt │ │ ├── PMC3095633.ann │ │ ├── PMC3095633.txt │ │ ├── PMC3173465.ann │ │ ├── PMC3173465.txt │ │ ├── PMC3189223.ann │ │ ├── PMC3189223.txt │ │ ├── PMC3204990.ann │ │ ├── PMC3204990.txt │ │ ├── PMC3228524.ann │ │ ├── PMC3228524.txt │ │ ├── PMC3235500.ann │ │ ├── PMC3235500.txt │ │ ├── PMC3246047.ann │ │ ├── PMC3246047.txt │ │ ├── PMC3249647.ann │ │ ├── PMC3249647.txt │ │ ├── PMC3304099.ann │ │ ├── PMC3304099.txt │ │ ├── PMC3317433.ann │ │ ├── PMC3317433.txt │ │ ├── PMC3321800.ann │ │ ├── PMC3321800.txt │ │ ├── PMC3323935.ann │ │ ├── PMC3323935.txt │ │ ├── PMC3639604.ann │ │ ├── PMC3639604.txt │ │ ├── PMC3650071.ann │ │ ├── PMC3650071.txt │ │ ├── PMC3711858.ann │ │ ├── PMC3711858.txt │ │ ├── PMC3750006.ann │ │ ├── PMC3750006.txt │ │ ├── PMC3787487.ann │ │ ├── PMC3787487.txt │ │ ├── PMC3791721.ann │ │ ├── PMC3791721.txt │ │ ├── PMC3842119.ann │ │ ├── PMC3842119.txt │ │ ├── PMC3850168.ann │ │ ├── PMC3850168.txt │ │ ├── PMC3854702.ann │ │ ├── PMC3854702.txt │ │ ├── PMC3855395.ann │ │ ├── PMC3855395.txt │ │ ├── PMC3926063.ann │ │ ├── PMC3926063.txt │ │ ├── PMC3927957.ann │ │ ├── PMC3927957.txt │ │ ├── PMC4007342.ann │ │ ├── PMC4007342.txt │ │ ├── PMC4023883.ann │ │ ├── PMC4023883.txt │ │ ├── PMC4056277.ann │ │ ├── PMC4056277.txt │ │ ├── PMC4084624.ann │ │ ├── PMC4084624.txt │ │ ├── PMC4100769.ann │ │ ├── PMC4100769.txt │ │ ├── PMC4151505.ann │ │ ├── PMC4151505.txt │ │ ├── PMC4159719.ann │ │ ├── PMC4159719.txt │ │ ├── PMC4168117.ann │ │ ├── PMC4168117.txt │ │ ├── PMC4214202.ann │ │ ├── PMC4214202.txt │ │ ├── PMC4224975.ann │ │ ├── PMC4224975.txt │ │ ├── PMC4233385.ann │ │ ├── PMC4233385.txt │ │ ├── PMC4241840.ann │ │ ├── PMC4241840.txt │ │ ├── PMC4291544.ann │ │ ├── PMC4291544.txt │ │ ├── PMC4337382.ann │ │ ├── PMC4337382.txt │ │ ├── PMC4385920.ann │ │ ├── PMC4385920.txt │ │ ├── PMC4418961.ann │ │ ├── PMC4418961.txt │ │ ├── PMC4423225.ann │ │ ├── PMC4423225.txt │ │ ├── PMC4426480.ann │ │ ├── PMC4426480.txt │ │ ├── PMC4451961.ann │ │ ├── PMC4451961.txt │ │ ├── PMC4474185.ann │ │ ├── PMC4474185.txt │ │ ├── PMC4552951.ann │ │ ├── PMC4552951.txt │ │ ├── PMC4592272.ann │ │ ├── PMC4592272.txt │ │ ├── PMC4628936.ann │ │ ├── PMC4628936.txt │ │ ├── PMC4649113.ann │ │ ├── PMC4649113.txt │ │ ├── PMC4710466.ann │ │ ├── PMC4710466.txt │ │ ├── PMC4720349.ann │ │ ├── PMC4720349.txt │ │ ├── PMC4851424.ann │ │ ├── PMC4851424.txt │ │ ├── PMC4856445.ann │ │ ├── PMC4856445.txt │ │ ├── PMC4905708.ann │ │ ├── PMC4905708.txt │ │ ├── PMC4959015.ann │ │ ├── PMC4959015.txt │ │ ├── PMC5020626.ann │ │ ├── PMC5020626.txt │ │ ├── PMC5052263.ann │ │ ├── PMC5052263.txt │ │ ├── PMC5112176.ann │ │ ├── PMC5112176.txt │ │ ├── PMC5118948.ann │ │ ├── PMC5118948.txt │ │ ├── PMC5191835.ann │ │ ├── PMC5191835.txt │ │ ├── PMC5206501.ann │ │ ├── PMC5206501.txt │ │ ├── PMC5257256.ann │ │ ├── PMC5257256.txt │ │ ├── PMC5290235.ann │ │ ├── PMC5290235.txt │ │ ├── PMC5293011.ann │ │ ├── PMC5293011.txt │ │ ├── PMC5342705.ann │ │ ├── PMC5342705.txt │ │ ├── PMC5343661.ann │ │ ├── PMC5343661.txt │ │ ├── PMC5417820.ann │ │ ├── PMC5417820.txt │ │ ├── PMC5429091.ann │ │ ├── PMC5429091.txt │ │ ├── PMC5464295.ann │ │ ├── PMC5464295.txt │ │ ├── PMC5519767.ann │ │ ├── PMC5519767.txt │ │ ├── PMC5520220.ann │ │ ├── PMC5520220.txt │ │ ├── PMC5578684.ann │ │ ├── PMC5578684.txt │ │ ├── PMC5591438.ann │ │ ├── PMC5591438.txt │ │ ├── annotation.conf │ │ ├── unannotated │ │ ├── PMC5611819.ann │ │ ├── PMC5611819.txt │ │ ├── PMC5611846.ann │ │ ├── PMC5611846.txt │ │ ├── PMC5648021.ann │ │ ├── PMC5648021.txt │ │ ├── PMC5727967.ann │ │ ├── PMC5727967.txt │ │ ├── PMC5749247.ann │ │ ├── PMC5749247.txt │ │ ├── PMC5833121.ann │ │ ├── PMC5833121.txt │ │ ├── PMC5876181.ann │ │ ├── PMC5876181.txt │ │ ├── PMC5923349.ann │ │ ├── PMC5923349.txt │ │ ├── PMC5983667.ann │ │ ├── PMC5983667.txt │ │ ├── PMC6092975.ann │ │ ├── PMC6092975.txt │ │ ├── PMC6122729.ann │ │ ├── PMC6122729.txt │ │ ├── PMC6130380.ann │ │ ├── PMC6130380.txt │ │ ├── PMC6141714.ann │ │ ├── PMC6141714.txt │ │ ├── PMC6157333.ann │ │ ├── PMC6157333.txt │ │ ├── PMC6197911.ann │ │ ├── PMC6197911.txt │ │ ├── PMC6274670.ann │ │ ├── PMC6274670.txt │ │ ├── PMC6282816.ann │ │ ├── PMC6282816.txt │ │ ├── PMC6290922.ann │ │ ├── PMC6290922.txt │ │ ├── PMC6372559.ann │ │ ├── PMC6372559.txt │ │ ├── PMC6373736.ann │ │ └── PMC6373736.txt │ │ └── visual.conf ├── doccano │ ├── annotations_export_01.jsonl │ ├── annotations_export_02.jsonl │ ├── annotations_import_01.jsonl │ └── annotations_import_02.jsonl ├── meta │ ├── cell_types.csv │ ├── cytokines.csv │ ├── raw │ │ ├── cell_types.manual.csv │ │ ├── cl.raw.csv │ │ ├── cytokines.cameron.csv │ │ ├── cytokines.ckr.xls │ │ ├── cytokines.manual.csv │ │ ├── filters.csv │ │ ├── pro.raw.csv.gz │ │ ├── transcription_factors.lambert.csv │ │ └── transcription_factors.manual.csv │ ├── surface_proteins.csv │ └── transcription_factors.csv ├── results │ ├── labels.csv │ ├── predictions.csv.gz │ └── tags.csv.gz └── supervision │ └── immunexpresso │ ├── data.csv │ ├── import.csv │ └── verbs.csv ├── docker ├── Dockerfile ├── README.md └── requirements.txt ├── docs ├── annotations │ └── guideline.md └── images │ ├── annotation-examples.pdf │ ├── relation_examples.png │ └── training_outline.png ├── env.sh ├── pipeline ├── 01-entrez-import.ipynb ├── 01-pmcoa-import.ipynb ├── 02-meta-import-cl.ipynb ├── 02-meta-import-pro.ipynb ├── 03-meta-cell-types.ipynb ├── 03-meta-cytokines.ipynb ├── 03-meta-surface-proteins.ipynb ├── 03-meta-transcription-factors.ipynb ├── 04-immunexpresso.ipynb ├── 05-document-loader.ipynb ├── 06-candidate-generator.ipynb ├── 07-candidate-splits.ipynb ├── 08-candidate-lfs.ipynb ├── 09-modeling-lfs.ipynb ├── 10-modeling-sgm.ipynb ├── 11-modeling-bert.ipynb ├── 11-modeling-rnn-strong.ipynb ├── 11-modeling-rnn-weak.ipynb ├── 12-analysis-scores.ipynb ├── 13-analysis-relations.ipynb ├── misc │ ├── bert │ │ ├── v01 │ │ │ ├── run_tcre_dataset_utils.py │ │ │ └── training.py │ │ └── v02 │ │ │ ├── README.md │ │ │ ├── run_dataset.py │ │ │ ├── run_example.ipynb │ │ │ └── utils_dataset.py │ ├── eda │ │ ├── eda-cl.ipynb │ │ ├── eda-meta.ipynb │ │ ├── eda-parse-tree.ipynb │ │ ├── eda-phenotype.ipynb │ │ ├── eda-pmcoa.ipynb │ │ ├── eda-pro.ipynb │ │ ├── eda-scibert.ipynb │ │ ├── eda-snorkel-schema.ipynb │ │ └── eda-word2vec.ipynb │ ├── modeling │ │ ├── label-model-training-v1.ipynb │ │ ├── label-model-training-v2.ipynb │ │ ├── label-model-training-v3-r1-analysis.ipynb │ │ ├── label-model-training-v3-r2-analysis.ipynb │ │ └── label-model-training-v3.ipynb │ ├── scripts │ │ ├── click-test.py │ │ └── missing-cand-debug.py │ ├── simulation │ │ ├── sim-f1-scores.ipynb │ │ └── sim-rnn-scenarios.ipynb │ ├── snorkel │ │ ├── crosslink-cand-doc.ipynb │ │ ├── crosslink-cand-type.ipynb │ │ └── id-set-generator.ipynb │ ├── spacy │ │ └── spacy-examples.ipynb │ └── tokenization │ │ ├── protein-tokenization-analysis.ipynb │ │ ├── protein-tokenization-dataset.ipynb │ │ └── protein-tokenization-example.ipynb └── scripts │ ├── brat-label-export.ipynb │ ├── brat-label-import.ipynb │ ├── candidate-relocation.ipynb │ ├── docanno-annotator.ipynb │ ├── move-annotation-files.ipynb │ ├── snorkel-annotator.ipynb │ └── tagging-frequency.ipynb ├── results ├── summary.ipynb └── summary.render.ipynb └── src ├── ptkn ├── __init__.py ├── protein_tokenization.py └── protein_tokenization_test.py └── tcre ├── __init__.py ├── brat.py ├── entrez ├── __init__.py └── integration.py ├── env.py ├── exec ├── __init__.py └── v1 │ ├── __init__.py │ ├── bert │ ├── README.md │ ├── 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