MEDS Ecosystem
Tools, dataset ETLs, and models that work with MEDS. Search by name or description, or filter by topic below. Not sure where to start? Which tool do I use for what? walks through the MEDS workflow step by step. Dataset statistics compares the datasets that the public ETLs produce.
Know of a tool, model, or dataset ETL that works with MEDS but isn't listed here?
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static/data/ecosystem.yaml
are also welcome!
MEDS Visualizations
Plots data extracted from MEDS datasets, such as code frequencies, in Jupyter notebooks.
⭐ 1 stars
📦 0.0.5
ehrlint
Audits a prediction task on a MEDS or OMOP dataset for leakage, such as post-index features or patient overlap across splits.
⭐ 0 stars
MEDS to CEHR
Converts MEDS datasets into CEHR-GPT's visit-based patient sequences, without depending on the CEHR-GPT model itself.
⭐ 0 stars
MEDS2RDF
Converts MEDS datasets into RDF knowledge graphs based on the MEDS Ontology, streaming the triples to memory or to files.
⭐ 4 stars
📦 v2.0.0
ETL Template
A Copier template for creating a config-only MEDS-Extract ETL package that converts a new dataset into MEDS.
⭐ 7 stars
📦 0.1.0
MEDS-ETL
A collection of ETLs that convert MIMIC-IV 2.2 and OMOP CDM 5.3 and 5.4 data into MEDS 0.3.3.
_Use for the MIMIC dataset is deprecated_!
⭐ 44 stars
📦 0.3.11
EHR2MEDS
Formats raw EHR data dumps and converts them to MEDS, via an intermediate format called preMEDS.
⭐ 4 stars
MESSY Synth
Generates synthetic raw data matching a MEDS-Extract config, so an ETL can be demoed or smoke-tested without the real dataset.
⭐ 0 stars
📦 0.0.1
MIMIC-IV
Converts MIMIC-IV, a dataset of emergency department and ICU patients at Beth Israel Deaconess Medical Center in Boston, into MEDS.
🚀 Demo Available
⭐ 27 stars
📦 0.2.0
MIMIC-IV Demo
The MIMIC-IV Clinical Database Demo, with 100 critical care patients, already converted into MEDS and openly downloadable.
AUMCdb
Converts AmsterdamUMCdb, a de-identified ICU database from Amsterdam University Medical Centers, into MEDS.
⭐ 3 stars
📦 0.1.0
NWICU
Converts NWICU, the Northwestern ICU database from a network of hospitals in Chicago, into MEDS.
⭐ 4 stars
📦 0.0.13
SICdb
Converts SICdb, the Salzburg Intensive Care database of admissions to four ICUs at University Hospital Salzburg, into MEDS.
⭐ 6 stars
📦 0.1.0
INSPIRE
Converts INSPIRE, a perioperative dataset of about 130,000 surgical cases from an academic institution in South Korea, into MEDS.
⭐ 3 stars
📦 v0.1.0
eICU
Converts the eICU Collaborative Research Database, a multi-center database of ICU admissions across the United States, into MEDS.
🚀 Demo Available
⭐ 7 stars
📦 0.2.0
HiRID
Converts HiRID, a high time-resolution ICU dataset from Bern University Hospital in Switzerland, into MEDS.
⭐ 3 stars
📦 0.1.0
CDSL
Converts the tabular data of CDSL, on patients hospitalized with confirmed or suspected COVID-19 at Spain's HM Hospitales, into MEDS.
⭐ 0 stars
📦 0.0.1
ALOTT
Converts the EMR tables of ALOTT, a database pairing bedside telemetry with EMR data from two hospitals, into MEDS.
⭐ 0 stars
📦 0.0.1
PIC
Converts the Paediatric Intensive Care (PIC) database, from the Children's Hospital of Zhejiang University School of Medicine, into MEDS.
⭐ 0 stars
📦 0.0.3
Zigong
Converts a database of ICU patients with infection at Zigong Fourth People's Hospital in Sichuan, China, into MEDS.
⭐ 0 stars
📦 0.3.1
MC-MED
Converts MC-MED, clinical and monitoring data from adult emergency department visits at Stanford Health Care, into MEDS.
⭐ 0 stars
📦 0.1.0
K-MIMIC (synthetic)
Converts Synthetic K-MIMIC (SYN-ICU), synthetic ICU data generated from Seoul National University Hospital records, into MEDS.
⭐ 0 stars
EHRSHOT
A benchmark for few-shot evaluation of EHR foundation models, with the full records of 6,739 Stanford Medicine patients and 15 tasks.
_Distributed natively in MEDS (`EHRSHOT_MEDS.zip` on Redivis); no ETL needed._
⭐ 234 stars