├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── config.yml │ └── feature_request.md ├── dependabot.yml ├── pull_request_template.md └── workflows │ └── code_checks.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE.md ├── README.md ├── finetune.py ├── interpret.py ├── odyssey ├── __init__.py ├── data │ ├── DataProcessor.ipynb │ ├── __init__.py │ ├── constants.py │ ├── dataset.py │ ├── processor.py │ └── tokenizer.py ├── evals │ ├── __init__.py │ ├── evaluation.py │ └── prediction.py ├── interp │ ├── AttentionVisualization.ipynb │ ├── __init__.py │ ├── attribution.py │ ├── grad_attribution.ipynb │ └── utils.py ├── models │ ├── __init__.py │ ├── baseline │ │ ├── Bi-LSTM.ipynb │ │ ├── Bi-LSTM.py │ │ └── XGBoost.ipynb │ ├── cehr_bert │ │ ├── __init__.py │ │ └── model.py │ ├── cehr_big_bird │ │ ├── __init__.py │ │ └── model.py │ ├── configs │ │ ├── cehr_bert.yaml │ │ ├── cehr_bigbird.yaml │ │ ├── cehr_multibird.yaml │ │ ├── ehr_mamba.yaml │ │ └── ehr_mamba2.yaml │ ├── ehr_mamba │ │ ├── __init__.py │ │ ├── mamba_utils.py │ │ └── model.py │ ├── ehr_mamba2 │ │ ├── __init__.py │ │ └── model.py │ ├── embeddings.py │ └── model_utils.py └── utils │ ├── __init__.py │ ├── log.py │ └── utils.py ├── pretrain.py ├── pyproject.toml ├── results.md ├── slurm_scripts.md ├── tests ├── __init__.py └── odyssey │ ├── __init__.py │ ├── data │ └── test_dataset.py │ └── utils │ ├── __init__.py │ └── test_log.py └── uv.lock /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/config.yml: -------------------------------------------------------------------------------- 1 | blank_issues_enabled: false 2 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/.github/ISSUE_TEMPLATE/feature_request.md -------------------------------------------------------------------------------- /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/pull_request_template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/.github/pull_request_template.md -------------------------------------------------------------------------------- /.github/workflows/code_checks.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/.github/workflows/code_checks.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/README.md -------------------------------------------------------------------------------- /finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/finetune.py -------------------------------------------------------------------------------- /interpret.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/interpret.py -------------------------------------------------------------------------------- /odyssey/__init__.py: -------------------------------------------------------------------------------- 1 | """Odyssey package.""" 2 | -------------------------------------------------------------------------------- /odyssey/data/DataProcessor.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/data/DataProcessor.ipynb -------------------------------------------------------------------------------- /odyssey/data/__init__.py: -------------------------------------------------------------------------------- 1 | """Data sub-package.""" 2 | -------------------------------------------------------------------------------- /odyssey/data/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/data/constants.py -------------------------------------------------------------------------------- /odyssey/data/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/data/dataset.py -------------------------------------------------------------------------------- /odyssey/data/processor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/data/processor.py -------------------------------------------------------------------------------- /odyssey/data/tokenizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/data/tokenizer.py -------------------------------------------------------------------------------- /odyssey/evals/__init__.py: -------------------------------------------------------------------------------- 1 | """Prediction sub-package.""" 2 | -------------------------------------------------------------------------------- /odyssey/evals/evaluation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/evals/evaluation.py -------------------------------------------------------------------------------- /odyssey/evals/prediction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/evals/prediction.py -------------------------------------------------------------------------------- /odyssey/interp/AttentionVisualization.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/interp/AttentionVisualization.ipynb -------------------------------------------------------------------------------- /odyssey/interp/__init__.py: -------------------------------------------------------------------------------- 1 | """Interpretability sub-package.""" 2 | -------------------------------------------------------------------------------- /odyssey/interp/attribution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/interp/attribution.py -------------------------------------------------------------------------------- /odyssey/interp/grad_attribution.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/interp/grad_attribution.ipynb -------------------------------------------------------------------------------- /odyssey/interp/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/interp/utils.py -------------------------------------------------------------------------------- /odyssey/models/__init__.py: -------------------------------------------------------------------------------- 1 | """Models sub-package.""" 2 | -------------------------------------------------------------------------------- /odyssey/models/baseline/Bi-LSTM.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/baseline/Bi-LSTM.ipynb -------------------------------------------------------------------------------- /odyssey/models/baseline/Bi-LSTM.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/baseline/Bi-LSTM.py -------------------------------------------------------------------------------- /odyssey/models/baseline/XGBoost.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/baseline/XGBoost.ipynb -------------------------------------------------------------------------------- /odyssey/models/cehr_bert/__init__.py: -------------------------------------------------------------------------------- 1 | """CEHR-BERT model sub-package.""" 2 | -------------------------------------------------------------------------------- /odyssey/models/cehr_bert/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/cehr_bert/model.py -------------------------------------------------------------------------------- /odyssey/models/cehr_big_bird/__init__.py: -------------------------------------------------------------------------------- 1 | """CEHR-Big Bird model sub-package.""" 2 | -------------------------------------------------------------------------------- /odyssey/models/cehr_big_bird/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/cehr_big_bird/model.py -------------------------------------------------------------------------------- /odyssey/models/configs/cehr_bert.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/configs/cehr_bert.yaml -------------------------------------------------------------------------------- /odyssey/models/configs/cehr_bigbird.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/configs/cehr_bigbird.yaml -------------------------------------------------------------------------------- /odyssey/models/configs/cehr_multibird.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/configs/cehr_multibird.yaml -------------------------------------------------------------------------------- /odyssey/models/configs/ehr_mamba.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/configs/ehr_mamba.yaml -------------------------------------------------------------------------------- /odyssey/models/configs/ehr_mamba2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/configs/ehr_mamba2.yaml -------------------------------------------------------------------------------- /odyssey/models/ehr_mamba/__init__.py: -------------------------------------------------------------------------------- 1 | """EHR-Mamba model sub-package.""" 2 | -------------------------------------------------------------------------------- /odyssey/models/ehr_mamba/mamba_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/ehr_mamba/mamba_utils.py -------------------------------------------------------------------------------- /odyssey/models/ehr_mamba/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/ehr_mamba/model.py -------------------------------------------------------------------------------- /odyssey/models/ehr_mamba2/__init__.py: -------------------------------------------------------------------------------- 1 | """EHR-Mamba2 model sub-package.""" 2 | -------------------------------------------------------------------------------- /odyssey/models/ehr_mamba2/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/ehr_mamba2/model.py -------------------------------------------------------------------------------- /odyssey/models/embeddings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/embeddings.py -------------------------------------------------------------------------------- /odyssey/models/model_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/models/model_utils.py -------------------------------------------------------------------------------- /odyssey/utils/__init__.py: -------------------------------------------------------------------------------- 1 | """Utils sub-package.""" 2 | -------------------------------------------------------------------------------- /odyssey/utils/log.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/utils/log.py -------------------------------------------------------------------------------- /odyssey/utils/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/odyssey/utils/utils.py -------------------------------------------------------------------------------- /pretrain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/pretrain.py -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/pyproject.toml -------------------------------------------------------------------------------- /results.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/results.md -------------------------------------------------------------------------------- /slurm_scripts.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/slurm_scripts.md -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | """Test odyssey.""" 2 | -------------------------------------------------------------------------------- /tests/odyssey/__init__.py: -------------------------------------------------------------------------------- 1 | """Test odyssey.""" 2 | -------------------------------------------------------------------------------- /tests/odyssey/data/test_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/tests/odyssey/data/test_dataset.py -------------------------------------------------------------------------------- /tests/odyssey/utils/__init__.py: -------------------------------------------------------------------------------- 1 | """Test utils.""" 2 | -------------------------------------------------------------------------------- /tests/odyssey/utils/test_log.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/tests/odyssey/utils/test_log.py -------------------------------------------------------------------------------- /uv.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VectorInstitute/odyssey/HEAD/uv.lock --------------------------------------------------------------------------------