Jason Fries

Michael Wornow, Yizhe Xu, Rahul Thapa et al. · stanford

The successes of foundation models such as ChatGPT and AlphaFold have spurred significant interest in building similar models for electronic medical records (EMRs) to improve patient care and hospital operations. However, recent hype has obscured critical gaps in our understanding of these models' capabilities. We review over 80 foundation models trained on non-imaging EMR data (i.e. clinical text and/or structured data) and create a taxonomy delineating their architectures, training data, and potential use cases. We find that most models are trained on small, narrowly-scoped clinical datasets (e.g. MIMIC-III) or broad, public biomedical corpora (e.g. PubMed) and are evaluated on tasks that do not provide meaningful insights on their usefulness to health systems. In light of these findings, we propose an improved evaluation framework for measuring the benefits of clinical foundation models that is more closely grounded to metrics that matter in healthcare.

Ethan Steinberg, Jason Fries, Yizhe Xu et al.

We present a self-supervised, time-to-event (TTE) foundation model called MOTOR (Many Outcome Time Oriented Representations) which is pretrained on timestamped sequences of events in electronic health records (EHR) and health insurance claims. TTE models are used for estimating the probability distribution of the time until a specific event occurs, which is an important task in medical settings. TTE models provide many advantages over classification using fixed time horizons, including naturally handling censored observations, but are challenging to train with limited labeled data. MOTOR addresses this challenge by pretraining on up to 55M patient records (9B clinical events). We evaluate MOTOR's transfer learning performance on 19 tasks, across 3 patient databases (a private EHR system, MIMIC-IV, and Merative claims data). Task-specific models adapted from MOTOR improve time-dependent C statistics by 4.6% over state-of-the-art, improve label efficiency by up to 95% ,and are more robust to temporal distributional shifts. We further evaluate cross-site portability by adapting our MOTOR foundation model for six prediction tasks on the MIMIC-IV dataset, where it outperforms all baselines. MOTOR is the first foundation model for medical TTE predictions and we release a 143M parameter pretrained model for research use at [redacted URL].

Lin Lawrence Guo, Jason Fries, Ethan Steinberg et al.

Foundation models hold promise for transforming AI in healthcare by providing modular components that are easily adaptable to downstream healthcare tasks, making AI development more scalable and cost-effective. Structured EHR foundation models, trained on coded medical records from millions of patients, demonstrated benefits including increased performance with fewer training labels, and improved robustness to distribution shifts. However, questions remain on the feasibility of sharing these models across different hospitals and their performance for local task adaptation. This multi-center study examined the adaptability of a recently released structured EHR foundation model ($FM_{SM}$), trained on longitudinal medical record data from 2.57M Stanford Medicine patients. Experiments were conducted using EHR data at The Hospital for Sick Children and MIMIC-IV. We assessed both adaptability via continued pretraining on local data, and task adaptability compared to baselines of training models from scratch at each site, including a local foundation model. We evaluated the performance of these models on 8 clinical prediction tasks. In both datasets, adapting the off-the-shelf $FM_{SM}$ matched the performance of GBM models locally trained on all data while providing a 13% improvement in settings with few task-specific training labels. With continued pretraining on local data, label efficiency substantially improved, such that $FM_{SM}$ required fewer than 1% of training examples to match the fully trained GBM's performance. Continued pretraining was also 60 to 90% more sample-efficient than training local foundation models from scratch. Our findings show that adapting shared EHR foundation models across hospitals provides improved prediction performance at less cost, underscoring the utility of base foundation models as modular components to streamline the development of healthcare AI.

Lin Lawrence Guo, Santiago Eduardo Arciniegas, Joseph Jihyung Lee et al.

Foundation models for structured electronic health records (EHRs) are pretrained on longitudinal sequences of timestamped clinical events to learn adaptable patient representations. Tokenization -- how these timelines are converted into discrete model inputs -- determines what information is preserved, how efficiently it is encoded, and which relationships must be learned versus precomputed. Yet the impact of tokenization design choices on downstream performance and computational efficiency remains largely unexplored. Here, we pretrained a transformer on pediatric EHR data under a factorial design, varying tokenization along event encoding, time encoding, and workflow annotation. We evaluated area-under-the-receiver-operating-characteristic curve across 74 clinical prediction tasks. Joint event encoding and positional time encoding outperformed their alternatives (73/74 and 71/74 tasks) while requiring 39.5% and 9.6% fewer pretraining floating-point operations, respectively. Targeted ablations traced the joint encoding advantage to local binding efficiency, that is, code-attribute pairs are combined into single tokens, rather than split across tokens that the model must learn to associate during pretraining. External evaluation on an adult intensive care unit cohort demonstrated that this advantage generalizes despite substantial vocabulary mismatch, while temporal and workflow effects remain institution-specific. These results establish tokenization as a tractable lever for improving both the performance and efficiency of EHR foundation models.

Louis Blankemeier, Ashwin Kumar, Joseph Paul Cohen et al.

The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short reports. Here to overcome these shortcomings for abdominal CT interpretation, we introduce Merlin, a 3D VLM that learns from volumetric CT scans, electronic health record data and radiology reports. This approach is enabled by a multistage pretraining framework that does not require additional manual annotations. We trained Merlin using a high-quality clinical dataset of paired CT scans (>6 million images from 15,331 CT scans), diagnosis codes (>1.8 million codes) and radiology reports (>6 million tokens). We comprehensively evaluated Merlin on 6 task types and 752 individual tasks that covered diagnostic, prognostic and quality-related tasks. The non-adapted (off-the-shelf) tasks included zero-shot classification of findings (30 findings), phenotype classification (692 phenotypes) and zero-shot cross-modal retrieval (image-to-findings and image-to-impression). The model-adapted tasks included 5-year chronic disease prediction (6 diseases), radiology report generation and 3D semantic segmentation (20 organs). We validated Merlin at scale, with internal testing on 5,137 CT scans and external testing on 44,098 CT scans from 3 independent sites and 2 public datasets. The results demonstrated high generalization across institutions and anatomies. Merlin outperformed 2D VLMs, CT foundation models and off-the-shelf radiology models. We also release our trained models, code, and dataset, available at: https://github.com/StanfordMIMI/Merlin.

Alexander Ratner, Stephen H. Bach, Henry Ehrenberg et al.

Labeling training data is increasingly the largest bottleneck in deploying machine learning systems. We present Snorkel, a first-of-its-kind system that enables users to train state-of-the-art models without hand labeling any training data. Instead, users write labeling functions that express arbitrary heuristics, which can have unknown accuracies and correlations. Snorkel denoises their outputs without access to ground truth by incorporating the first end-to-end implementation of our recently proposed machine learning paradigm, data programming. We present a flexible interface layer for writing labeling functions based on our experience over the past year collaborating with companies, agencies, and research labs. In a user study, subject matter experts build models 2.8x faster and increase predictive performance an average 45.5% versus seven hours of hand labeling. We study the modeling tradeoffs in this new setting and propose an optimizer for automating tradeoff decisions that gives up to 1.8x speedup per pipeline execution. In two collaborations, with the U.S. Department of Veterans Affairs and the U.S. Food and Drug Administration, and on four open-source text and image data sets representative of other deployments, Snorkel provides 132% average improvements to predictive performance over prior heuristic approaches and comes within an average 3.60% of the predictive performance of large hand-curated training sets.

Hyewon Jeong, Sarah Jabbour, Yuzhe Yang et al. · uw

The third ML4H symposium was held in person on December 10, 2023, in New Orleans, Louisiana, USA. The symposium included research roundtable sessions to foster discussions between participants and senior researchers on timely and relevant topics for the \ac{ML4H} community. Encouraged by the successful virtual roundtables in the previous year, we organized eleven in-person roundtables and four virtual roundtables at ML4H 2022. The organization of the research roundtables at the conference involved 17 Senior Chairs and 19 Junior Chairs across 11 tables. Each roundtable session included invited senior chairs (with substantial experience in the field), junior chairs (responsible for facilitating the discussion), and attendees from diverse backgrounds with interest in the session's topic. Herein we detail the organization process and compile takeaways from these roundtable discussions, including recent advances, applications, and open challenges for each topic. We conclude with a summary and lessons learned across all roundtables. This document serves as a comprehensive review paper, summarizing the recent advancements in machine learning for healthcare as contributed by foremost researchers in the field.

Emily Alsentzer, Marie-Laure Charpignon, Bill Chen et al.

The 6th Annual Conference on Health, Inference, and Learning (CHIL 2025), hosted by the Association for Health Learning and Inference (AHLI), was held in person on June 25-27, 2025, at the University of California, Berkeley, in Berkeley, California, USA. As part of this year's program, we hosted Research Roundtables to catalyze collaborative, small-group dialogue around critical, timely topics at the intersection of machine learning and healthcare. Each roundtable was moderated by a team of senior and junior chairs who fostered open exchange, intellectual curiosity, and inclusive engagement. The sessions emphasized rigorous discussion of key challenges, exploration of emerging opportunities, and collective ideation toward actionable directions in the field. In total, eight roundtables were held by 19 roundtable chairs on topics of "Explainability, Interpretability, and Transparency," "Uncertainty, Bias, and Fairness," "Causality," "Domain Adaptation," "Foundation Models," "Learning from Small Medical Data," "Multimodal Methods," and "Scalable, Translational Healthcare Solutions."

Frederic Sala, Paroma Varma, Jason Fries et al.

Since manually labeling training data is slow and expensive, recent industrial and scientific research efforts have turned to weaker or noisier forms of supervision sources. However, existing weak supervision approaches fail to model multi-resolution sources for sequential data, like video, that can assign labels to individual elements or collections of elements in a sequence. A key challenge in weak supervision is estimating the unknown accuracies and correlations of these sources without using labeled data. Multi-resolution sources exacerbate this challenge due to complex correlations and sample complexity that scales in the length of the sequence. We propose Dugong, the first framework to model multi-resolution weak supervision sources with complex correlations to assign probabilistic labels to training data. Theoretically, we prove that Dugong, under mild conditions, can uniquely recover the unobserved accuracy and correlation parameters and use parameter sharing to improve sample complexity. Our method assigns clinician-validated labels to population-scale biomedical video repositories, helping outperform traditional supervision by 36.8 F1 points and addressing a key use case where machine learning has been severely limited by the lack of expert labeled data. On average, Dugong improves over traditional supervision by 16.0 F1 points and existing weak supervision approaches by 24.2 F1 points across several video and sensor classification tasks.

Madalina Fiterau, Suvrat Bhooshan, Jason Fries et al.

In healthcare applications, temporal variables that encode movement, health status and longitudinal patient evolution are often accompanied by rich structured information such as demographics, diagnostics and medical exam data. However, current methods do not jointly optimize over structured covariates and time series in the feature extraction process. We present ShortFuse, a method that boosts the accuracy of deep learning models for time series by explicitly modeling temporal interactions and dependencies with structured covariates. ShortFuse introduces hybrid convolutional and LSTM cells that incorporate the covariates via weights that are shared across the temporal domain. ShortFuse outperforms competing models by 3% on two biomedical applications, forecasting osteoarthritis-related cartilage degeneration and predicting surgical outcomes for cerebral palsy patients, matching or exceeding the accuracy of models that use features engineered by domain experts.

Jason Fries, Sen Wu, Alex Ratner et al.

We present SwellShark, a framework for building biomedical named entity recognition (NER) systems quickly and without hand-labeled data. Our approach views biomedical resources like lexicons as function primitives for autogenerating weak supervision. We then use a generative model to unify and denoise this supervision and construct large-scale, probabilistically labeled datasets for training high-accuracy NER taggers. In three biomedical NER tasks, SwellShark achieves competitive scores with state-of-the-art supervised benchmarks using no hand-labeled training data. In a drug name extraction task using patient medical records, one domain expert using SwellShark achieved within 5.1% of a crowdsourced annotation approach -- which originally utilized 20 teams over the course of several weeks -- in 24 hours.