The Patient is not a Moving Document: A World Model Training Paradigm for Longitudinal EHR

Large language models (LLMs) trained with next-word-prediction have achieved success as clinical foundation models. Representations from these language backbones yield strong linear probe performance across biomedical tasks, suggesting that patient semantics emerge from next-token prediction at scale. However, this paradigm treats patients as a document to be summarized rather than a dynamical system to be simulated; a patient's trajectory emerges from their state evolving under interventions and time, requiring models that simulate dynamics rather than predict tokens. To address this, we introduce SMB-Structure, a world model for structured EHR that grounds a joint-embedding prediction architecture (JEPA) with next-token prediction (SFT). SFT grounds our model to reconstruct future patient states in token space, while JEPA predicts those futures in latent space from the initial patient representation alone, forcing trajectory dynamics to be encoded before the next state is observed. We validate across two large-scale cohorts: Memorial Sloan Kettering (23,319 oncology patients; 323,000+ patient-years) and INSPECT (19,402 pulmonary embolism patients). Using a linear probe evaluated at multiple points along the disease trajectory, we demonstrate that our training paradigm learns embeddings that capture disease dynamics not recoverable by autoregressive baselines, enabling SMB-Structure to achieve competitive performance on complex tasks characterized by high patient heterogeneity. Model weights are available at https://huggingface.co/standardmodelbio/SMB-v1-1.7B-Structure.

Advancing High Resolution Vision-Language Models in Biomedicine

Multi-modal learning has significantly advanced generative AI, especially in vision-language modeling. Innovations like GPT-4V and open-source projects such as LLaVA have enabled robust conversational agents capable of zero-shot task completions. However, applying these technologies in the biomedical field presents unique challenges. Recent initiatives like LLaVA-Med have started to adapt instruction-tuning for biomedical contexts using large datasets such as PMC-15M. Our research offers three key contributions: (i) we present a new instruct dataset enriched with medical image-text pairs from Claude3-Opus and LLaMA3 70B, (ii) we propose a novel image encoding strategy using hierarchical representations to improve fine-grained biomedical visual comprehension, and (iii) we develop the Llama3-Med model, which achieves state-of-the-art zero-shot performance on biomedical visual question answering benchmarks, with an average performance improvement of over 10% compared to previous methods. These advancements provide more accurate and reliable tools for medical professionals, bridging gaps in current multi-modal conversational assistants and promoting further innovations in medical AI.

Seeing Beyond Cancer: Multi-Institutional Validation of Object Localization and 3D Semantic Segmentation using Deep Learning for Breast MRI

The clinical management of breast cancer depends on an accurate understanding of the tumor and its anatomical context to adjacent tissues and landmark structures. This context may be provided by semantic segmentation methods; however, previous works have been largely limited to a singular focus on the tumor alone and rarely other tissue types. In contrast, we present a method that exploits tissue-tissue interactions to accurately segment every major tissue type in the breast including: chest wall, skin, adipose tissue, fibroglandular tissue, vasculature and tumor via standard-of-care Dynamic Contrast Enhanced MRI. Comparing our method to prior state-of-the-art, we achieved a superior Dice score on tumor segmentation while maintaining competitive performance on other studied tissues across multiple institutions. Briefly, our method proceeds by localizing the tumor using 2D object detectors, then segmenting the tumor and surrounding tissues independently using two 3D U-nets, and finally integrating these results while mitigating false positives by checking for anatomically plausible tissue-tissue contacts. The object detection models were pre-trained on ImageNet and COCO, and operated on MIP (maximum intensity projection) images in the axial and sagittal planes, establishing a 3D tumor bounding box. By integrating multiple relevant peri-tumoral tissues, our work enables clinical applications in breast cancer staging, prognosis and surgical planning.