Medical-Event-Data-Standard / Medical-Event-Data-Standard/MEDS-DEV
Add larger MEDS-Tab variants alongside meds_tab/tiny
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- Dominant language
- Python
- Stars
- 43
- Forks
- 10
- PR merge metrics
- No merged PRs in 30d
Description
The only MEDS-Tab variant currently registered is meds_tab/tiny — explicitly described as "a tiny, low-cost XGBoost baseline." Add at least one (ideally two) larger variants so MEDS-Tab can be evaluated as a competitive baseline rather than just a smoke-test.
What this needs
New sibling dirs under src/MEDS_DEV/models/meds_tab/, e.g.:
meds_tab/standard/— moderate-capacity sweep (more codes, more window sizes, more trials).meds_tab/large/— wider sweep / more aggregation types, intended as the "best-effort" tabular baseline.
Naming is up to @Oufattole / @teyaberg — the point is capacity variants, not new framework features.
Knobs to scale up
Pulling from meds_tab/tiny/model.yaml, the obvious dimensions are:
tabularization.aggs— currently[code/count, value/sum]. Addvalue/min,value/max,value/mean,value/std, etc.tabularization.window_sizes— currently[7d, 30d]. Add shorter (1h,6h,24h) and longer (90d,365d) windows.tabularization.max_included_codes— currently100. Bump to1000/10000/ unbounded.tabularization.min_code_inclusion_count— currentlynull. Could constrain for the larger sweep.hydra.sweeper.n_trials— currently20. Bump for the larger variants.hydra.sweeper.n_jobs— currently1. Parallelize where appropriate.
Open questions
- Capacity nomenclature:
tiny/small/base/largevstiny/standard/largevs something else? - Where does the gradient from "tiny" to "large" sit on real benchmark wall-clock — worth pinning at least one variant's hyperparams to what was used in the MEDS-Tab paper?
Pinging @Oufattole, @teyaberg — best to take the lead on what hyperparams make sense.
Refs
- Paper: https://arxiv.org/abs/2411.00200
- Existing variant:
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 with src/MEDS_DEV/models/meds_tab/tiny/model.yaml and inspect how sibling model directories are registered. Compare the tiny settings with the MEDS-Tab paper and resolve the capacity naming and hyperparameters with the mentioned maintainers. Done means at least one larger sibling variant is configured and available for benchmark evaluation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, yaml
- Domain
- machine-learning
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100