Medical-Event-Data-Standard / Medical-Event-Data-Standard/MEDS-DEV

Add MEDS-EIC-AR as a registered model

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enhancement Models
Dominant language
Python
Stars
43
Forks
10
PR merge metrics
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Description

Register MEDS-EIC-AR (MEDS-EIC-AR on PyPI) as a model in src/MEDS_DEV/models/. It's a MEDS-native autoregressive generative model with zero-shot inference capability — fits the benchmark's dataset-agnostic invariant since it takes MEDS data directly without per-dataset conversion rules (unlike #248 / cehrgpt, where the conversion-type flag was blocking).

What this needs

  • src/MEDS_DEV/models/meds_eic_ar/ (probably the canonical name; PyPI dashes → underscores) with:
    • model.yaml declaring unsupervised: train (pretrain) and supervised: {train, predict} if the API supports fine-tuning + prediction. From the README, zero-shot inference is the headline use case — worth confirming whether MEDS-DEV's supervised lane fits or whether this is an unsupervised-only registration with a separate prediction path.
    • requirements.txt pinning MEDS-EIC-AR==<version> (latest stable).
    • README.md with a brief description + link to upstream.
    • refs.bib (Zenodo DOI is available: 10.5281/zenodo.17535558).

Open questions for the contributor

  • Capacity variants — should we expose tiny / standard / large from day one (matching the meds_tab/tiny pattern), or land a single default and add sizes later?
  • Optional dependencies (wandb, mlflow, flash-attn) — keep base install lean, mention extras in the README.
  • Zero-shot use: does the MEDS-DEV supervised.predict flow apply, or do we need a new lane?

Pinging @mmcdermott (model author) for guidance on the right structure.

Refs

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading the existing model.yaml patterns in cehrbert and meds_tab/tiny, then inspect the MEDS-EIC-AR README and PyPI release to confirm its API, latest stable version, and supervised or zero-shot support. Add the model directory with model.yaml, requirements.txt, README.md, and refs.bib, resolving capacity and optional-dependency choices; done means the registration matches a supported MEDS-DEV lane and references the upstream model.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

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