HALO Implementation into PyHealth + Colab Notebook#812
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jalengg wants to merge 60 commits intosunlabuiuc:masterfrom
Draft
HALO Implementation into PyHealth + Colab Notebook#812jalengg wants to merge 60 commits intosunlabuiuc:masterfrom
jalengg wants to merge 60 commits intosunlabuiuc:masterfrom
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- Add HALO (Healthcare generative model using transformers) implementation - Include example training script with configurable parameters - Include example generation script for synthetic patient data - Add canonical SLURM scripts with optimal parameters (80 epochs, batch_size 48, lr 0.0001) - Register HALO in generators module - Update HALO_MIMIC3Dataset with latest preprocessing - Update README with HALO documentation
Remove README.rst changes that only documented CorGAN, not HALO. This PR should focus solely on HALO implementation.
…ls to HALO notebook Complete Tasks 3-7: - Configuration panel with demo defaults - Data upload with validation - Training logic with checkpoint management - Generation with CSV conversion - Results display with quality checks and download Notebook now has 24 cells with complete end-to-end workflow.
- Replace `!pip install` with subprocess.run() for error checking - Show clear error message if installation fails - Raise RuntimeError to stop notebook execution on failure Fixes #1
jalengg
commented
Feb 16, 2026
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| sys.path.insert(0, '/u/jalenj4/PyHealth') |
- Remove PATIENTS.csv and patient_ids.txt (not used by HALO_MIMIC3Dataset) - Handle Colab file renaming (ADMISSIONS (1).csv -> ADMISSIONS.csv) - Allow uploading files one at a time with progress tracking - Check Google Drive for existing files before requesting upload - Add FORK variable to installation cell for easier testing Fixes #4, #5, #6
7 tasks
Ensures Colab users always get the latest version from GitHub without using cached packages. Critical for picking up recent fixes like the halo_resources __init__.py. Fixes #18
Use os.path.join() instead of string concatenation to properly handle directory paths with or without trailing slashes. Fixes #19
Fixes #21 The YAML config files in pyhealth/datasets/configs/ were not being included when the package was installed via pip. This caused FileNotFoundError for multiple datasets including HALO, MIMIC3, MIMIC4, EHRShot, COVID-19 CXR, and Medical Transcriptions. Added MANIFEST.in to specify which non-Python files should be included in the package distribution.
Fixes #21 MANIFEST.in only affects sdist source distributions. When installing via `pip install git+https://...` (as in Colab), pip relies on package_data in setup.py to include non-Python files. Added explicit package_data to ensure YAML configs in pyhealth/datasets/configs/ are included in all install paths. Removed MANIFEST.in as it provided no benefit for pip-from-git installs.
jalengg
changed the title
…rom test_halo_model
…rd unique_patients in cell 22
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