arXiv subjects

Santiago Romero-Brufau

Publications and source records attributed to Santiago Romero-Brufau.

4 recordsLinked to original sources

arXiv2026

Morphology signal in whole slide image foundation models can automatically triage slides

Patient exams in the cancer diagnosis and staging process typically generate several whole slide images (WSIs). One of the initial steps in training models on WSI data is identifying one or a few slides containing tumor or other diagnostic biomarkers necessary for downstream prediction tasks such as estimating recurrence risk or progression-free survival. This step requires tedious manual curation by experienced pathologists. Many published datasets make the artificial assumption of 1 slide per patient. Alternatively, all slides per patient may be used for model training, which may dilute the signal from the few slides containing tumor or other relevant information. In this paper, we present a pipeline to overcome these challenges using publicly available WSI foundation models (FMs). Our evaluations show that ranking WSIs based on predictions from zero-shot classification using WSI FMs accurately identifies slides with the most tumor, indicating that WSI FMs contain sufficient morphology signal to automatically triage slides. We also present a formulation for ranked evaluation to benchmark FM performance in slide triage. We show, on multiple datasets, that tumor slides are identified in the top-2 ranked slides for patients with up to 43 slides.

cs.CV↗

arXiv2026

BRIDGE: Benchmarking Large Language Models for Understanding Real-world Clinical Practice Text

Large language models (LLMs) hold great promise for medical applications and are evolving rapidly, with new models being released at an accelerated pace. However, benchmarking on large-scale real-world data such as electronic health records (EHRs) is critical, as clinical decisions are directly informed by these sources, yet current evaluations remain limited. Most existing benchmarks rely on medical exam-style questions or PubMed-derived text, failing to capture the complexity of real-world clinical data. Others focus narrowly on specific application scenarios, limiting their generalizability across broader clinical use. To address this gap, we present BRIDGE, a comprehensive multilingual benchmark comprising 87 tasks sourced from real-world clinical data sources across nine languages. It covers eight major task types spanning the entire continuum of patient care across six clinical stages and 20 representative applications, including triage and referral, consultation, information extraction, diagnosis, prognosis, and billing coding, and involves 14 clinical specialties. We systematically evaluated 95 LLMs (including DeepSeek-R1, GPT-4o, Gemini series, and Qwen3 series) under various inference strategies. Our results reveal substantial performance variation across model sizes, languages, natural language processing tasks, and clinical specialties. Notably, we demonstrate that open-source LLMs can achieve performance comparable to proprietary models, while medically fine-tuned LLMs based on older architectures often underperform versus updated general-purpose models. The BRIDGE and its corresponding leaderboard serve as a foundational resource and a unique reference for the development and evaluation of new LLMs in real-world clinical text understanding. The BRIDGE leaderboard: https://huggingface.co/spaces/YLab-Open/BRIDGE-Medical-Leaderboard

cs.CL↗

arXiv2021

DeepABM: Scalable, efficient and differentiable agent-based simulations via graph neural networks

We introduce DeepABM, a framework for agent-based modeling that leverages geometric message passing of graph neural networks for simulating action and interactions over large agent populations. Using DeepABM allows scaling simulations to large agent populations in real-time and running them efficiently on GPU architectures. To demonstrate the effectiveness of DeepABM, we build DeepABM-COVID simulator to provide support for various non-pharmaceutical interventions (quarantine, exposure notification, vaccination, testing) for the COVID-19 pandemic, and can scale to populations of representative size in real-time on a GPU. Specifically, DeepABM-COVID can model 200 million interactions (over 100,000 agents across 180 time-steps) in 90 seconds, and is made available online to help researchers with modeling and analysis of various interventions. We explain various components of the framework and discuss results from one research study to evaluate the impact of delaying the second dose of the COVID-19 vaccine in collaboration with clinical and public health experts. While we simulate COVID-19 spread, the ideas introduced in the paper are generic and can be easily extend to other forms of agent-based simulations. Furthermore, while beyond scope of this document, DeepABM enables inverse agent-based simulations which can be used to learn physical parameters in the (micro) simulations using gradient-based optimization with large-scale real-world (macro) data. We are optimistic that the current work can have interesting implications for bringing ABM and AI communities closer.

cs.MA↗

arXiv2017

Prediction and Inference with Missing Data in Patient Alert Systems

We describe the Bedside Patient Rescue (BPR) project, the goal of which is risk prediction of adverse events for non-ICU patients using ~200 variables (vitals, lab results, assessments, ...). There are several missing predictor values for most patients, which in the health sciences is the norm, rather than the exception. A Bayesian approach is presented that addresses many of the shortcomings to standard approaches to missing predictors: (i) treatment of the uncertainty due to imputation is straight-forward in the Bayesian paradigm, (ii) the predictor distribution is flexibly modeled as an infinite normal mixture with latent variables to explicitly account for discrete predictors (i.e., as in multivariate probit regression models), and (iii) certain missing not at random situations can be handled effectively by allowing the indicator of missingness into the predictor distribution only to inform the distribution of the missing variables. The proposed approach also has the benefit of providing a distribution for the prediction, including the uncertainty inherent in the imputation. Therefore, we can ask questions such as: is it possible this individual is at high risk but we are missing too much information to know for sure? How much would we reduce the uncertainty in our risk prediction by obtaining a particular missing value? This approach is applied to the BPR problem resulting in excellent predictive capability to identify deteriorating patients.

stat.AP↗