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Add MIMIC-III readmission Transformer example and tests
Add MIMIC-III Readmission Prediction Example Using Transformer + Tests
Summary
This PR adds a new example demonstrating 30-day readmission prediction on MIMIC-III using the Transformer model. While PyHealth includes Transformer examples and readmission examples, this is the first to combine Transformer + readmission + MIMIC-III, filling a clear gap in the existing examples.
What's Included
New Example
examples/mimic3_readmission_transformer.py
- Full 5-stage PyHealth pipeline
- Supports Synthetic MIMIC-III and local MIMIC-III
- Well-documented module-level docstring
- CLI arguments for reproducible runs
New Tests
tests/test_mimic3_readmission_transformer.py
- Lightweight integration tests
- Validates the example pipeline end-to-end
- Skips automatically unless local or approved remote data is available
Why This Is Useful
- Introduces a missing model–task combination to the example library
- Demonstrates how to run Transformer on clinical prediction tasks
- Improves reproducibility of PyHealth examples
- Adds test coverage to ensure long-term stability
Testing
Synthetic MIMIC-III (online):
export PYHEALTH_RUN_ONLINE_EXAMPLES=1
pytest -q