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EHRMamba: Towards Generalizable and Scalable Foundation Models for Electronic Health Records
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EHRMamba: Towards Generalizable and Scalable Foundation Models for Electronic Health Records
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Transformers have significantly advanced the modeling of Electronic Health Records (EHR), yet their deployment in real-world healthcare is limited by several key challenges. Firstly, the quadratic computational cost and insufficient context length of these models hinder hospitals' ability in processing the extensive medical histories typical in EHR data. Additionally, existing models employ separate finetuning for each clinical task, complicating maintenance in healthcare environments. Moreover, these models focus exclusively on either clinical prediction or EHR forecasting, lacking proficiency in both tasks. To overcome these limitations, we introduce EHRMamba, a robust foundation model built on the Mamba architecture. EHRMamba can process sequences up to 300% longer than previous models due to its linear computational cost. We also introduce a novel approach to Multitask Prompted Finetuning (MPF) for EHR data, which enables EHRMamba to simultaneously learn multiple clinical tasks in a single finetuning phase, significantly enhancing deployment and cross-task generalization. Furthermore, our model leverages the HL7 FHIR data standard to simplify integration into existing hospital systems. Alongside EHRMamba, we open-source Odyssey, a toolkit designed to support the development and deployment of EHR foundation models, with an emphasis on data standardization and interpretability. Our evaluations on the MIMIC-IV dataset demonstrate that EHRMamba advances state-of-the-art performance across 6 major clinical tasks and excels in EHR forecasting, marking a significant leap forward in the field.
Forward citations
Cited by 14 Pith papers
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Clin-JEPA: A Multi-Phase Co-Training Framework for Joint-Embedding Predictive Pretraining on EHR Patient Trajectories
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Clin-JEPA: A Multi-Phase Co-Training Framework for Joint-Embedding Predictive Pretraining on EHR Patient Trajectories
A five-phase JEPA co-training curriculum on EHR trajectories is claimed to yield stable latent rollouts and a single multi-task clinical backbone on MIMIC-IV.
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Clin-JEPA: A Multi-Phase Co-Training Framework for Joint-Embedding Predictive Pretraining on EHR Patient Trajectories
A five-phase co-training framework enables stable JEPA pretraining on EHR trajectories, producing converging latent rollouts and higher multi-task AUROC than baselines on MIMIC-IV ICU data.
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WISTERIA learns robust clinical representations from noisy EHR labels by enforcing consistency across multiple weak supervision views plus ontology regularization.
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A hybrid Mamba-Transformer architecture with attention pooling reports higher AUROC and AUPRC than several EHR baselines on five clinical prediction tasks, though gains are small relative to reported variance.
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