BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset. Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally. On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

Confidence intervals for the Cox model test error from cross-validation

Cross-validation (CV) is one of the most widely used techniques in statistical learning for estimating the test error of a model, but its behavior is not yet fully understood. It has been shown that standard confidence intervals for test error using estimates from CV may have coverage below nominal levels. This phenomenon occurs because each sample is used in both the training and testing procedures during CV and as a result, the CV estimates of the errors become correlated. Without accounting for this correlation, the estimate of the variance is smaller than it should be. One way to mitigate this issue is by estimating the mean squared error of the prediction error instead using nested CV. This approach has been shown to achieve superior coverage compared to intervals derived from standard CV. In this work, we generalize the nested CV idea to the Cox proportional hazards model and explore various choices of test error for this setting.

Training an Emotion Detection Classifier using Frames from a Mobile Therapeutic Game for Children with Developmental Disorders

Automated emotion classification could aid those who struggle to recognize emotion, including children with developmental behavioral conditions such as autism. However, most computer vision emotion models are trained on adult affect and therefore underperform on child faces. In this study, we designed a strategy to gamify the collection and the labeling of child affect data in an effort to boost the performance of automatic child emotion detection to a level closer to what will be needed for translational digital healthcare. We leveraged our therapeutic smartphone game, GuessWhat, which was designed in large part for children with developmental and behavioral conditions, to gamify the secure collection of video data of children expressing a variety of emotions prompted by the game. Through a secure web interface gamifying the human labeling effort, we gathered and labeled 2,155 videos, 39,968 emotion frames, and 106,001 labels on all images. With this drastically expanded pediatric emotion centric database (>30x larger than existing public pediatric affect datasets), we trained a pediatric emotion classification convolutional neural network (CNN) classifier of happy, sad, surprised, fearful, angry, disgust, and neutral expressions in children. The classifier achieved 66.9% balanced accuracy and 67.4% F1-score on the entirety of CAFE as well as 79.1% balanced accuracy and 78.0% F1-score on CAFE Subset A, a subset containing at least 60% human agreement on emotions labels. This performance is at least 10% higher than all previously published classifiers, the best of which reached 56.% balanced accuracy even when combining "anger" and "disgust" into a single class. This work validates that mobile games designed for pediatric therapies can generate high volumes of domain-relevant datasets to train state of the art classifiers to perform tasks highly relevant to precision health efforts.