arXiv subjects

Gary E. Weissman

Publications and source records attributed to Gary E. Weissman.

3 recordsLinked to original sources

arXiv2026

Auditable CT Phenotyping Through Report-derived Radiological Observations

Medical image foundation models can predict clinical phenotypes from computed tomography (CT), but strong performance leaves open whether they read disease-specific findings or shortcuts that correlate with the diagnosis. We tested this in 221 electronic-health-record (EHR) phenotypes using Auditable CT phenotyping (ACT), built on report-derived radiological observations. We trained ACT on 38,317 patients, mined 376,194 observations and evaluated it in 25,183 held-out patients. ACT exceeded five vision-language baselines on zero-shot annotation, and CT-CLIP across 221 phenotypes from unseen CT pulmonary angiography, both under zero-shot scoring (0.651 versus 0.572) and under linear probing (0.709 versus 0.662). Reading each probe exposes what accuracy conceals: only 97 observations occupy the 221 rank-1 positions, and one phrase describing aortic and coronary calcification ranks first for 20 phenotypes, including osteoporosis, urinary tract infection and major depressive disorder. Restricting the bank to clinician-specified evidence redirects those probes onto phenotype-related observations in 86 phenotypes at no accuracy cost (0.751 versus 0.741). Accurate CT-based EHR phenotyping can therefore rest on observations that are not valid evidence for the coded phenotype and that ACT can identify and intervene on.

cs.CV↗

arXiv2026

T-FIX: Text-Based Explanations with Features Interpretable to eXperts

As LLMs are deployed in knowledge-intensive settings (e.g., surgery, astronomy, therapy), users are often domain experts who expect not just answers, but explanations that mirror professional reasoning. Yet evaluating whether an LLM "thinks like an expert" remains difficult: existing approaches rely on per-example expert annotation, making them costly, hard to scale, and tied to a single notion of correct reasoning within each domain. To address this gap, we introduce T-FIX, a unified evaluation framework that operationalizes expert alignment as a desired attribute of LLM-generated explanations. T-FIX spans seven scientific tasks across three domains, with each task evaluated against expert-defined criteria that capture domain-grounded reasoning rather than generic explanation quality. Our framework enables automatic, personalizable evaluation of expert alignment that generalizes to unseen explanations without ongoing expert involvement. Code is available at https://github.com/BrachioLab/FIX-2/.

cs.CL↗

arXiv2025

Enhancing Phenotype Discovery in Electronic Health Records through Prior Knowledge-Guided Unsupervised Learning

Objectives: Unsupervised learning with electronic health record (EHR) data has shown promise for phenotype discovery, but approaches typically disregard existing clinical information, limiting interpretability. We operationalize a Bayesian latent class framework for phenotyping that incorporates domain-specific knowledge to improve clinical meaningfulness of EHR-derived phenotypes and illustrate its utility by identifying an asthma sub-phenotype informed by features of Type 2 (T2) inflammation. Materials and methods: We illustrate a framework for incorporating clinical knowledge into a Bayesian latent class model via informative priors to guide unsupervised clustering toward clinically relevant subgroups. This approach models missingness, accounting for potential missing-not-at-random patterns, and provides patient-level probabilities for phenotype assignment with uncertainty. Using reusable and flexible code, we applied the model to a large asthma EHR cohort, specifying informative priors for T2 inflammation-related features and weakly informative priors for other clinical variables, allowing the data to inform posterior distributions. Results and Conclusion: Using encounter data from January 2017 to February 2024 for 44,642 adult asthma patients, we found a bimodal posterior distribution of phenotype assignment, indicating clear class separation. The T2 inflammation-informed class (38.7%) was characterized by elevated eosinophil levels and allergy markers, plus high healthcare utilization and medication use, despite weakly informative priors on the latter variables. These patterns suggest an "uncontrolled T2-high" sub-phenotype. This demonstrates how our Bayesian latent class modeling approach supports hypothesis generation and cohort identification in EHR-based studies of heterogeneous diseases without well-established phenotype definitions.

stat.AP↗