Ryan Stidham

Cristian Minoccheri, Emily Wittrup, Kayvan Najarian et al.

Computed tomography (CT) enterography is a primary imaging modality for assessing inflammatory bowel disease (IBD), yet the representational choices that best support automated analysis of this modality are unknown. We present the first study of vision-language transfer learning on abdominal CT enterography and identify two main findings. First, mean pooling of slice embeddings gives better categorical disease assessment (59.2\% three-class accuracy), whereas attention pooling gives better cross-modal retrieval (0.235 text-to-image MRR). This pattern holds across all LoRA configurations tested and suggests that the two aggregators emphasize different properties of the learned representation. Second, per-slice tissue contrast matters more than broader spatial coverage: multi-window RGB encoding, which maps complementary Hounsfield Unit windows to RGB channels, outperforms all strategies that increase spatial coverage through multiplanar sampling, and in this setting adding coronal and sagittal views reduces classification performance. For report generation, fine-tuning without retrieval context yields within-1 severity accuracy at the prevalence-matched chance level (70.4\% vs.\ 71\% random), suggesting little learned ordering beyond the class distribution. Retrieval-augmented generation (RAG) improves this across all configurations, scoring 7--14 percentage points above the chance baseline and improving ordinal MAE from 0.98 to 0.80--0.89. A three-teacher pseudolabel framework enables all comparisons without expert annotations. Together, these findings provide the first baselines for this underexplored modality and offer practical guidance for building vision-language systems for volumetric medical imaging.

Cristian Minoccheri, Sophia Tesic, Kayvan Najarian et al.

Randomized controlled trials estimate average treatment effects, but treatment response heterogeneity motivates personalized approaches. A critical question is whether statistically detectable heterogeneity translates into improved treatment decisions -- these are distinct questions that can yield contradictory answers. We present a modular causal machine learning framework that evaluates each question separately: permutation importance identifies which features predict heterogeneity, best linear predictor (BLP) testing assesses statistical significance, and doubly robust policy evaluation measures whether acting on the heterogeneity improves patient outcomes. We apply this framework to patient-level data from the UNIFI maintenance trial of ustekinumab in ulcerative colitis, comparing placebo, standard-dose ustekinumab every 12 weeks, and dose-intensified ustekinumab every 8 weeks, using cross-fitted X-learner models with baseline demographics, medication history, week-8 clinical scores, laboratory biomarkers, and video-derived endoscopic features. BLP testing identified strong associations between endoscopic features and treatment effect heterogeneity for ustekinumab versus placebo, yet doubly robust policy evaluation showed no improvement in expected remission from incorporating endoscopic features, and out-of-fold multi-arm evaluation showed worse performance. Diagnostic comparison of prognostic contribution against policy value revealed that endoscopic scores behaved as disease severity markers -- improving outcome prediction in untreated patients but adding noise to treatment selection -- while clinical variables (fecal calprotectin, age, CRP) captured the decision-relevant variation. These results demonstrate that causal machine learning applications to clinical trials should include policy-level evaluation alongside heterogeneity testing.

Cristian Minoccheri, Sophia Tesic, Kayvan Najarian et al.

Phenotyping is the process of distinguishing groups of patients to identify different types of disease progression. A recent trend employs low-rank matrix and tensor factorization methods for their capability of dealing with multi-modal, heterogeneous, and missing data. Symptom quantification is crucial for understanding patient experiences in inflammatory bowel disease, especially in conditions such as ulcerative colitis (UC). However, patient-reported symptoms are typically noisy, subjective, and significantly more sparse than other data types. For this reason, they are usually not included in phenotyping and other machine learning methods. This paper explores the application of computational phenotyping to leverage Patient-Reported Outcomes (PROs) using a novel supervised coupled matrix-tensor factorization (SCMTF) method, which integrates temporal PROs and temporal labs with static features to predict medication persistence in ulcerative colitis. This is the first tensor-based method that is both supervised and coupled, it is the first application to the UC domain, and the first application to PROs. We use a deep learning framework that makes the model flexible and easy to train. The proposed method allows us to handle the large amount of missing data in the PROs. The best model predicts changes in medication 8 and 20 months in the future with AUCs of 0.853 and 0.803 on the test set respectively. We derive interpretable phenotypes consisting of static features and temporal features (including their temporal patterns). We show that low-rank matrix and tensor based phenotyping can be successfully applied to the UC domain and to highly missing PRO data. We identify phenotypes useful to predict medication persistence - these phenotypes include several symptom variables, showing that PROs contain relevant infromation that is usually discarded.