LICENSE
README.md
pyproject.toml
ptm_bdl_framework.egg-info/PKG-INFO
ptm_bdl_framework.egg-info/SOURCES.txt
ptm_bdl_framework.egg-info/dependency_links.txt
ptm_bdl_framework.egg-info/requires.txt
ptm_bdl_framework.egg-info/top_level.txt
src/__init__.py
src/case_studies/__init__.py
src/case_studies/common/__init__.py
src/case_studies/common/download_ctrp.py
src/case_studies/common/reviewer_analyses.py
src/case_studies/common/step01_download_gdsc.py
src/case_studies/common/step03_download_structures.py
src/case_studies/common/step04_download_ptm_data.py
src/case_studies/egfr_erbb2_tki/__init__.py
src/case_studies/egfr_erbb2_tki/biology.py
src/case_studies/egfr_erbb2_tki/config.yaml
src/case_studies/egfr_erbb2_tki/data_pipeline/__init__.py
src/case_studies/egfr_erbb2_tki/data_pipeline/step01_download_gdsc.py
src/case_studies/egfr_erbb2_tki/data_pipeline/step02_download_mutations.py
src/case_studies/egfr_erbb2_tki/data_pipeline/step02_download_sequences.py
src/case_studies/egfr_erbb2_tki/data_pipeline/step03_download_structures.py
src/case_studies/egfr_erbb2_tki/data_pipeline/step04_download_ptm_data.py
src/case_studies/egfr_erbb2_tki/data_pipeline/step05_download_drugptm.py
src/case_studies/egfr_erbb2_tki/data_pipeline/step06_harmonize_dataset.py
src/case_studies/egfr_erbb2_tki/features/__init__.py
src/case_studies/egfr_erbb2_tki/features/step07_extract_esm2.py
src/case_studies/egfr_erbb2_tki/features/step08_extract_gearnet.py
src/case_studies/egfr_erbb2_tki/features/step09_extract_chemberta.py
src/case_studies/egfr_erbb2_tki/scripts/__init__.py
src/case_studies/egfr_erbb2_tki/scripts/ablation.py
src/case_studies/egfr_erbb2_tki/scripts/build_model.py
src/case_studies/egfr_erbb2_tki/scripts/crossval.py
src/case_studies/egfr_erbb2_tki/scripts/evaluate.py
src/case_studies/egfr_erbb2_tki/scripts/explain.py
src/case_studies/egfr_erbb2_tki/scripts/external_baselines.py
src/case_studies/egfr_erbb2_tki/scripts/loclo.py
src/case_studies/egfr_erbb2_tki/scripts/ml_baselines.py
src/case_studies/egfr_erbb2_tki/scripts/paper_figures.py
src/case_studies/egfr_erbb2_tki/scripts/paper_tables.py
src/case_studies/egfr_erbb2_tki/scripts/statistical_tests.py
src/case_studies/egfr_erbb2_tki/scripts/train.py
src/case_studies/hela_hdac/__init__.py
src/case_studies/hela_hdac/biology.py
src/case_studies/hela_hdac/config.yaml
src/case_studies/hela_hdac/data_pipeline/__init__.py
src/case_studies/hela_hdac/data_pipeline/step01_download_gdsc.py
src/case_studies/hela_hdac/data_pipeline/step02_download_sequences.py
src/case_studies/hela_hdac/data_pipeline/step03_download_structures.py
src/case_studies/hela_hdac/data_pipeline/step04_download_ptm_data.py
src/case_studies/hela_hdac/data_pipeline/step05_download_drugptm.py
src/case_studies/hela_hdac/data_pipeline/step06_harmonize_dataset.py
src/case_studies/hela_hdac/features/__init__.py
src/case_studies/hela_hdac/features/step07_extract_esm2.py
src/case_studies/hela_hdac/features/step08_extract_gearnet.py
src/case_studies/hela_hdac/features/step09_extract_chemberta.py
src/case_studies/hela_hdac/scripts/__init__.py
src/case_studies/hela_hdac/scripts/ablation.py
src/case_studies/hela_hdac/scripts/crossval.py
src/case_studies/hela_hdac/scripts/evaluate.py
src/case_studies/hela_hdac/scripts/explain.py
src/case_studies/hela_hdac/scripts/external_baselines.py
src/case_studies/hela_hdac/scripts/loclo.py
src/case_studies/hela_hdac/scripts/ml_baselines.py
src/case_studies/hela_hdac/scripts/paper_figures.py
src/case_studies/hela_hdac/scripts/paper_tables.py
src/case_studies/hela_hdac/scripts/statistical_tests.py
src/case_studies/hela_hdac/scripts/train.py
src/case_studies/k562_cml/__init__.py
src/case_studies/k562_cml/biology.py
src/case_studies/k562_cml/config.yaml
src/case_studies/k562_cml/data_pipeline/__init__.py
src/case_studies/k562_cml/data_pipeline/step01_download_gdsc.py
src/case_studies/k562_cml/data_pipeline/step02_download_sequences.py
src/case_studies/k562_cml/data_pipeline/step03_download_structures.py
src/case_studies/k562_cml/data_pipeline/step04_download_ptm_data.py
src/case_studies/k562_cml/data_pipeline/step05_download_drugptm.py
src/case_studies/k562_cml/data_pipeline/step06_harmonize_dataset.py
src/case_studies/k562_cml/features/__init__.py
src/case_studies/k562_cml/features/step07_extract_esm2.py
src/case_studies/k562_cml/features/step08_extract_gearnet.py
src/case_studies/k562_cml/features/step09_extract_chemberta.py
src/case_studies/k562_cml/scripts/__init__.py
src/case_studies/k562_cml/scripts/ablation.py
src/case_studies/k562_cml/scripts/crossval.py
src/case_studies/k562_cml/scripts/evaluate.py
src/case_studies/k562_cml/scripts/explain.py
src/case_studies/k562_cml/scripts/external_baselines.py
src/case_studies/k562_cml/scripts/loclo.py
src/case_studies/k562_cml/scripts/ml_baselines.py
src/case_studies/k562_cml/scripts/paper_figures.py
src/case_studies/k562_cml/scripts/paper_tables.py
src/case_studies/k562_cml/scripts/statistical_tests.py
src/case_studies/k562_cml/scripts/train.py
src/ptm_bdl/__init__.py
src/ptm_bdl/config.py
src/ptm_bdl/default_config.yaml
src/ptm_bdl/registry.py
src/ptm_bdl/data/__init__.py
src/ptm_bdl/data/collate.py
src/ptm_bdl/data/dataset.py
src/ptm_bdl/data/splits.py
src/ptm_bdl/evaluation/__init__.py
src/ptm_bdl/evaluation/baselines.py
src/ptm_bdl/evaluation/cold_split.py
src/ptm_bdl/evaluation/cross_dataset.py
src/ptm_bdl/evaluation/evaluator.py
src/ptm_bdl/evaluation/loclo.py
src/ptm_bdl/evaluation/statistical.py
src/ptm_bdl/model/__init__.py
src/ptm_bdl/model/ablation.py
src/ptm_bdl/model/encoder.py
src/ptm_bdl/model/fusion.py
src/ptm_bdl/model/predictor.py
src/ptm_bdl/model/static.py
src/ptm_bdl/training/__init__.py
src/ptm_bdl/training/factory.py
src/ptm_bdl/training/loss.py
src/ptm_bdl/training/metrics.py
src/ptm_bdl/training/trainer.py
src/ptm_bdl/xai/__init__.py
src/ptm_bdl/xai/attention.py
src/ptm_bdl/xai/homology.py
src/ptm_bdl/xai/integrated_gradients.py
src/ptm_bdl/xai/reporter.py
tests/test_model.py
tests/test_ptm_bdl.py
tests/test_training.py