Papers › ACES: Automatic Cohort Extraction System for Event-Stream Datasets

ACES: Automatic Cohort Extraction System for Event-Stream Datasets

28 Jun 2024arXiv:2406.19653archive 2025-07-28

Justin Xu, Jack Gallifant, Alistair E. W. Johnson, Matthew B. A. McDermott

Reproducibility remains a significant challenge in machine learning (ML) for healthcare. Datasets, model pipelines, and even task/cohort definitions are often private in this field, leading to a significant barrier in sharing, iterating, and understanding ML results on electronic health record (EHR) datasets. This paper addresses a significant part of this problem by introducing the Automatic Cohort Extraction System (ACES) for event-stream data. This library is designed to simultaneously simplify the development of task/cohorts for ML in healthcare and also enable the reproduction of these cohorts, both at an exact level for single datasets and at a conceptual level across datasets. To accomplish this, ACES provides (1) a highly intuitive and expressive configuration language for defining both dataset-specific concepts and dataset-agnostic inclusion/exclusion criteria, and (2) a pipeline to automatically extract patient records that meet these defined criteria from real-world data. ACES can be automatically applied to any dataset in either the Medical Event Data Standard (MEDS) or EventStreamGPT (ESGPT) formats, or to any dataset in which the necessary task-specific predicates can be extracted in an event-stream form. ACES has the potential to significantly lower the barrier to entry for defining ML tasks that learn representations, redefine the way researchers interact with EHR datasets, and significantly improve the state of reproducibility for ML studies in this modality. ACES is available at https://github.com/justin13601/aces. A short video demonstration of ACES is available at https://youtu.be/i_hCaHDydqA.

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