ACES: Automatic Cohort Extraction System for Event-Stream Datasets

Justin Xu, Jack Gallifant, ALISTAIR JOHNSON, Matthew B.A. McDermott

Keywords: Automatic Task Specification, Cohort Extraction, Electronic Health Records, Open Source Software, Benchmarks, Datasets

TL;DR: A software library to standardize reproducible task and cohort extraction in machine learning for healthcare

Abstract: Reproducibility remains a significant challenge in machine learning (ML) for healthcare. Datasets, model pipelines, and even task or 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. We address 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 tasks and cohorts for ML in healthcare and also enable their reproduction, 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 domain-specific configuration language for defining both dataset-specific concepts and dataset-agnostic inclusion or 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 Event Stream GPT (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 in representation learning, redefine the way researchers interact with EHR datasets, and significantly improve the state of reproducibility for ML studies using this modality. ACES is available at: https://github.com/justin13601/aces.

Primary Area: infrastructure, software libraries, hardware, systems, etc.

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Submission Number: 8187