alterlab-pyhealth

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Develops, tests, and deploys clinical machine learning models with the PyHealth healthcare AI toolkit. Use when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare (RETAIN, SafeDrug, Transformer, GNN). Part of the AlterLab Academic Skills suite.

AI & Automation 27 stars 4 forks Updated today MIT

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Skill Content

# PyHealth: Healthcare AI Toolkit ## Overview PyHealth is a comprehensive Python library for healthcare AI that provides specialized tools, models, and datasets for clinical machine learning. Use this skill when developing healthcare prediction models, processing clinical data, working with medical coding systems, or deploying AI solutions in healthcare settings. > **Version gotcha (read first).** This skill targets **PyHealth 2.x** (pin `pyhealth==2.0.1`). The 2.0 rewrite changed the API in ways the wider web (and pre-2024 tutorials) get wrong: > - **Tasks are classes you instantiate**, e.g. `MortalityPredictionMIMIC4()`, `DrugRecommendationMIMIC3()` — *not* the old snake-case `mortality_prediction_mimic4_fn` functions. Pass the instance to `dataset.set_task(task)`. > - **Datasets take an explicit `tables=[...]`** list (e.g. `tables=["diagnoses_icd", "procedures_icd", "prescriptions"]`). > - **Models require `label_key=`** in addition to `feature_keys=` and `mode=`. Common feature keys for EHR tasks are `"conditions"`, `"procedures"`, `"drugs"`. > - **Metric names have no `_score` suffix**: `pr_auc`, `roc_auc`, `f1`; multilabel/drug-rec use the `*_samples` family (`jaccard_samples`, `f1_samples`, `pr_auc_samples`, `ddi`). Pass `metrics=[...]` to the **`Trainer` constructor**, and `monitor=` one of those names. > - 2.0.1 requires **Python 3.12 or 3.13** (`>=3.12,<3.14`). > When unsure of a class/arg name, check the current source rather than trusting older snippets. ## Wh...

Details

Author
AlterLab-IEU
Repository
AlterLab-IEU/AlterLab-Academic-Skills
Created
2 months ago
Last Updated
today
Language
Python
License
MIT

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Anthropic · AI

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