Tom J. Pollard

Thomas Sounack, Joshua Davis, Brigitte Durieux et al.

Encoder-based transformer models are central to biomedical and clinical Natural Language Processing (NLP), as their bidirectional self-attention makes them well-suited for efficiently extracting structured information from unstructured text through discriminative tasks. However, encoders have seen slower development compared to decoder models, leading to limited domain adaptation in biomedical and clinical settings. We introduce BioClinical ModernBERT, a domain-adapted encoder that builds on the recent ModernBERT release, incorporating long-context processing and substantial improvements in speed and performance for biomedical and clinical NLP. BioClinical ModernBERT is developed through continued pretraining on the largest biomedical and clinical corpus to date, with over 53.5 billion tokens, and addresses a key limitation of prior clinical encoders by leveraging 20 datasets from diverse institutions, domains, and geographic regions, rather than relying on data from a single source. It outperforms existing biomedical and clinical encoders on four downstream tasks spanning a broad range of use cases. We release both base (150M parameters) and large (396M parameters) versions of BioClinical ModernBERT, along with training checkpoints to support further research.

Alistair E. W. Johnson, Tom J. Pollard, Nathaniel R. Greenbaum et al.

Chest radiography is an extremely powerful imaging modality, allowing for a detailed inspection of a patient's thorax, but requiring specialized training for proper interpretation. With the advent of high performance general purpose computer vision algorithms, the accurate automated analysis of chest radiographs is becoming increasingly of interest to researchers. However, a key challenge in the development of these techniques is the lack of sufficient data. Here we describe MIMIC-CXR-JPG v2.0.0, a large dataset of 377,110 chest x-rays associated with 227,827 imaging studies sourced from the Beth Israel Deaconess Medical Center between 2011 - 2016. Images are provided with 14 labels derived from two natural language processing tools applied to the corresponding free-text radiology reports. MIMIC-CXR-JPG is derived entirely from the MIMIC-CXR database, and aims to provide a convenient processed version of MIMIC-CXR, as well as to provide a standard reference for data splits and image labels. All images have been de-identified to protect patient privacy. The dataset is made freely available to facilitate and encourage a wide range of research in medical computer vision.

Alistair E. W. Johnson, Tom J. Pollard, Tristan Naumann

A large volume of research has considered the creation of predictive models for clinical data; however, much existing literature reports results using only a single source of data. In this work, we evaluate the performance of models trained on the publicly-available eICU Collaborative Research Database. We show that cross-validation using many distinct centers provides a reasonable estimate of model performance in new centers. We further show that a single model trained across centers transfers well to distinct hospitals, even compared to a model retrained using hospital-specific data. Our results motivate the use of multi-center datasets for model development and highlight the need for data sharing among hospitals to maximize model performance.