Medical-Event-Data-Standard / Medical-Event-Data-Standard/MEDS-DEV
Add MEDS-EIC-AR as a registered model
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- Dominant language
- Python
- Stars
- 43
- Forks
- 10
- PR merge metrics
- No merged PRs in 30d
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.yamldeclaringunsupervised: train(pretrain) andsupervised: {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.txtpinningMEDS-EIC-AR==<version>(latest stable).README.mdwith 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/largefrom day one (matching themeds_tab/tinypattern), 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.predictflow apply, or do we need a new lane?
Pinging @mmcdermott (model author) for guidance on the right structure.
Refs
- Upstream: https://github.com/mmcdermott/MEDS_EIC_AR
- Existing model.yaml patterns for reference:
cehrbert/model.yaml,meds_tab/tiny/model.yaml.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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