Papers › MIMIC-Extract: A Data Extraction, Preprocessing, and Representation Pipeline for MIMIC-III
MIMIC-Extract: A Data Extraction, Preprocessing, and Representation Pipeline for MIMIC-III
Shirly Wang, Matthew B. A. McDermott, Geeticka Chauhan, Michael C. Hughes, Tristan Naumann, Marzyeh Ghassemi
Robust machine learning relies on access to data that can be used with standardized frameworks in important tasks and the ability to develop models whose performance can be reasonably reproduced. In machine learning for healthcare, the community faces reproducibility challenges due to a lack of publicly accessible data and a lack of standardized data processing frameworks. We present MIMIC-Extract, an open-source pipeline for transforming raw electronic health record (EHR) data for critical care patients contained in the publicly-available MIMIC-III database into dataframes that are directly usable in common machine learning pipelines. MIMIC-Extract addresses three primary challenges in making complex health records data accessible to the broader machine learning community. First, it provides standardized data processing functions, including unit conversion, outlier detection, and aggregating semantically equivalent features, thus accounting for duplication and reducing missingness. Second, it preserves the time series nature of clinical data and can be easily integrated into clinically actionable prediction tasks in machine learning for health. Finally, it is highly extensible so that other researchers with related questions can easily use the same pipeline. We demonstrate the utility of this pipeline by showcasing several benchmark tasks and baseline results.
In Syntology Open this paper in Syntology's Atlas, the map of the papers in Syntology's graph and their citations.
For agents, Syntology's MCP tool lists every function and class Syntology harvested from this paper and whether it ran (how to connect): get_harvested_code_for_paper(arxiv_id="1907.08322")
Code
Syntology Ran 1 of 1 code samples harvested from 1 repository linked to this paper; 0 have no recorded run. Of those that ran: 1 ran · our draft was wrong.
By repository: official repository: 1 sample from 1 repository, 1 ran. The run record, sample by sample. “Ran” means executed on a synthesized input, not that the code is correct or reproduces the paper.
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
1 sample harvested; 1 ran; 0 honoured the contract we drafted; 0 have no recorded run. Read from Syntology's graph 2026-09-24; that is when this build read the record, not when the samples ran.
Licence: 0 of the 1 sample are pointer only, meaning Syntology does not serve that copy's text. This page shows no code text for any sample; each one links to its file in the repository.
Harvested from MLforHealth/MIMIC_Extract. “Ran” means the sample executed on a synthesized input. It does not mean the output is correct, and nothing here reproduces the paper's results. “Honoured” and “violated” refer to a contract Syntology drafted from the code itself; “our draft was wrong” and “fixture could not drive it” are failures of Syntology's instrument, not of the code.
Each sample ends with its code_sha256, Syntology's identity for that exact code. An agent fetches the stored sample with Syntology's MCP tool get_code(code_sha256="…") (how to connect); click an identity to copy that call.
Repository labels, per sample. official repository: The archive marks this repository official for the paper. named in the paper: The archive records that the paper mentions this repository; it is not marked official. community (archive-listed): In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper. found in paper text by Syntology: Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted. community: Not in the archive's code links for this paper; a community repository Syntology harvested. Samples from a repository marked official are listed first. Licence labels name the repository's licence as recorded at harvest. “Pointer only” means Syntology does not serve that copy's text, for one of four reasons: no licence file was found; the licence was not identified; the licence is recorded as permissive but that copy's record is not marked cleared; or the licence is outside the permissive list Syntology serves text under (MIT, Apache-2.0, BSD and similar). Some licences outside that list permit redistribution, such as WTFPL, and GPL-3.0 under its conditions; they are simply not on the list. Hover a licence label for the reason. File links open the file on GitHub at the default branch, which may have changed since the harvest.
16c701adbbcf1824 · report
Tasks
Results from the paper archive 2025-07-28
| Task | Dataset | Model | Metric | Value | Rank at snapshot | Leaderboard | Report |
|---|---|---|---|---|---|---|---|
| Length-of-Stay prediction | MIMIC-III | Random Forests (RF) | Accuracy (LOS>3 Days) | 69.5% | #3 of 5 | Archive leaderboard | report |
| Length-of-Stay prediction | MIMIC-III | Random Forests (RF) | Accuracy (LOS>7 Days) | 92.3 | #3 of 5 | Archive leaderboard | report |
| Length-of-Stay prediction | MIMIC-III | Logistic Regression (LR) | Accuracy (LOS>3 Days) | 68.6% | #4 of 5 | Archive leaderboard | report |
| Length-of-Stay prediction | MIMIC-III | Logistic Regression (LR) | Accuracy (LOS>7 Days) | 91.9 | #4 of 5 | Archive leaderboard | report |
| Length-of-Stay prediction | MIMIC-III | GRU-D | Accuracy (LOS>3 Days) | 68.3% | #5 of 5 | Archive leaderboard | report |
| Length-of-Stay prediction | MIMIC-III | GRU-D | Accuracy (LOS>7 Days) | 91.2 | #5 of 5 | Archive leaderboard | report |
Ranks are positions in the archive's leaderboards as they stood at the 2025-07-28 snapshot. Results published since then are not among these rows, so a rank here is not a current standing.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections