CLAUDE.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
otk_api/README.md
otk_api/__init__.py
otk_api/model_analyzer.py
otk_api/update_gene_level_metrics.py
otk_api/api/__init__.py
otk_api/api/cleanup.py
otk_api/api/config.py
otk_api/api/data_validator.py
otk_api/api/i18n.py
otk_api/api/main.py
otk_api/api/models.py
otk_api/api/predictor_wrapper.py
otk_api/api/resource_manager.py
otk_api/api/schemas.py
otk_api/api/tasks.py
otk_api/download/__init__.py
otk_api/download/model_downloader.py
otk_api/models/gene_level_performance.png
otk_api/models/gene_level_tradeoff.png
otk_api/models/model_analysis_report.md
otk_api/models/model_ranking_heatmap.png
otk_api/models/performance_radar.png
otk_api/models/sample_level_heatmap.png
otk_api/models/sample_level_performance.png
otk_api/models/sample_level_tradeoff.png
otk_api/models/baseline_mlp/best_model.pkl
otk_api/models/baseline_mlp/config.yml
otk_api/models/baseline_mlp/training_summary.yml
otk_api/models/deep_residual/best_model.pkl
otk_api/models/deep_residual/config.yml
otk_api/models/deep_residual/training_summary.yml
otk_api/models/dgit_super/best_model.pkl
otk_api/models/dgit_super/config.yml
otk_api/models/dgit_super/training_summary.yml
otk_api/models/optimized_residual/best_model.pkl
otk_api/models/optimized_residual/config.yml
otk_api/models/optimized_residual/training_summary.yml
otk_api/models/source_data/dataset_statistics.csv
otk_api/models/source_data/gene_level_performance.csv
otk_api/models/source_data/sample_level_performance.csv
otk_api/models/tabpfn/config.yml
otk_api/models/tabpfn/training_summary.yml
otk_api/models/transformer/best_model.pkl
otk_api/models/transformer/config.yml
otk_api/models/transformer/training_summary.yml
otk_api/models/xgb_new/best_model.pkl
otk_api/models/xgb_new/config.yml
otk_api/models/xgb_new/feature_importance.csv
otk_api/models/xgb_new/training_summary.yml
otk_api/models/xgb_paper/best_model.pkl
otk_api/models/xgb_paper/config.yml
otk_api/models/xgb_paper/feature_importance.csv
otk_api/models/xgb_paper/training_summary.yml
otk_api/models/xgb_tuned/all_trials.csv
otk_api/models/xgb_tuned/best_model.pkl
otk_api/models/xgb_tuned/config.yml
otk_api/models/xgb_tuned/feature_importance.csv
otk_api/models/xgb_tuned/training_summary.yml
otk_api/static/gene_level_performance.png
otk_api/static/gene_level_tradeoff.png
otk_api/static/model_analysis_report.md
otk_api/static/model_ranking_heatmap.png
otk_api/static/performance_radar.png
otk_api/static/sample_level_heatmap.png
otk_api/static/sample_level_performance.png
otk_api/static/sample_level_tradeoff.png
otk_api/tests/test_predict_api.py
src/otk/__init__.py
src/otk/cli.py
src/otk/data/__init__.py
src/otk/data/data_processor.py
src/otk/data/data_split.py
src/otk/data/extract_gene_frequencies.py
src/otk/data/gene_frequencies.csv
src/otk/data/sample_y_sum.csv
src/otk/data/sorted_modeling_data.csv.gz
src/otk/data/split_2026.json
src/otk/models/__init__.py
src/otk/models/base_model.py
src/otk/models/config_generator.py
src/otk/models/custom_losses.py
src/otk/models/ecdna_losses.py
src/otk/models/neural_models.py
src/otk/models/tabpfn_model.py
src/otk/models/xgb11_model.py
src/otk/predict/__init__.py
src/otk/predict/predictor.py
src/otk/utils/__init__.py
src/otk_ecdna.egg-info/PKG-INFO
src/otk_ecdna.egg-info/SOURCES.txt
src/otk_ecdna.egg-info/dependency_links.txt
src/otk_ecdna.egg-info/entry_points.txt
src/otk_ecdna.egg-info/requires.txt
src/otk_ecdna.egg-info/top_level.txt