EPPC-OASIS: Ontology-Aware Adaptation and Structured Inference Refinement for Electronic Patient-Provider Communication Mining in Secure Messages
Authors: Samah Fodeh, Sreeraj Ramachandran, Elyas Irankhah, Muhammad Arif, Afshan Khan, Ganesh Puthiaraju, Linhai Ma, Srivani Talakokkul, +2 more
Organizations: Yale University, New Haven, CT, USA · Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, OH, USA · Medical Oncology, Yale School of Medicine, New Haven, CT, USA
Secure patient-provider messages contain clinically important communication behaviors that are difficult to characterize manually at scale. The Electronic Patient-Provider Communication (EPPC) framework provides an ontology for coding these behaviors, but automated extraction remains challenging because predictions must preserve fine-grained code/sub-code structure while grounding annotations in message text. We developed EPPC-OASIS, an ontology-aware adaptation approach for structured EPPC extraction, and combined it with deployable inference-refinement procedures designed to improve the coherence of final annotations. EPPC-OASIS augments supervised fine-tuning with a Wasserstein alignment objective that encourages alignment between model representation neighborhoods and EPPC ontology-derived neighborhoods, while inference refinement uses verification, self-consistency, hybrid correction, and selection or ensembling to address residual prediction errors. We evaluated the framework on a de-identified corpus of secure patient-provider messages against prompting, supervised fine-tuning, preference-based, and robustness-oriented baselines across multiple open-weight language models. Across model families, the best deployable pipeline achieved 77.13% Code+Sub-code F1 and 63.83% Triplet F1, corresponding to modest but consistent absolute gains of +1.39 and +2.12 F1 points over the strongest supervised fine-tuning baseline. These results suggest that ontology-aware adaptation with structured inference refinement can support scalable retrospective EPPC mining, although external validation is needed before operational use.
Motivation: Patient-generated text contains critical information on patients' lived experiences, social context, and care engagement, but remains largely unstructured, limiting its use in patient-centered outcomes research. Prior work introduced the PV-Miner benchmark and PVMinerLLM models for structured extraction. However, supervised fine-tuning (SFT) alone struggles with rare, fine-grained, and unevenly distributed errors, particularly in token-critical structured outputs. Results: We present PVminerLLM2, an improved set of LLMs for structured patient voice extraction that applies preference optimization to address token-critical errors beyond the reach of supervised fine-tuning. Our method introduces (i) a preference objective with token-level gated stabilization term that prevents degradation of absolute token likelihood under preference optimization, and (ii) confusion-aware preference pair construction to better capture low-separation distinctions. We further incorporate token-importance weighting and inverse-frequency reweighing to address token imbalance and class skew. Across multiple model sizes, PVMinerLLM2 consistently outperforms strong baselines, achieving gains of up to 4.43% (Code), 3.50% (Sub-code), and 1.55% (Span), and outperforms baseline LLM trained with existing preference optimization methods. Availability and Implementation: The supplementary material, code, evaluation scripts, and trained models for PVminerLLM2 are publicly available at: https://github.com/Data-Mining-Lab-Yale/PVminerLLM2
Large Language Models (LLMs) have shown strong promise for mining Electronic Health Records (EHRs) by reasoning over longitudinal clinical information to capture context-rich patient trajectories. However, leveraging LLMs for structured EHRs (e.g., standardized diagnosis and medication codes) presents two key challenges. First, translating time-stamped EHR sequences into plain text can obscure both temporal structure and code identities, weakening the ability to capture code co-occurrence and longitudinal regularities. Second, unlike cohort-trained predictive models that learn a shared, task-aligned representation space across patients, LLMs are often applied in a case-isolated inference setting where each patient is processed independently without leveraging population-level patterns. To address these challenges, we introduce RePrompT, a time-aware LLM framework that integrates structured EHR encoders through prompt tuning, without modifying underlying architectures. Specifically, RePrompT recurrently incorporates latent states from prior visits to preserve longitudinal information, and injects population-level information through trainable prompt tokens derived from a cohort-trained, task-aligned EHR encoder. Experiments on MIMIC-III and MIMIC-IV demonstrate that RePrompT consistently outperforms both EHR-based and LLM-based baselines across multiple clinical prediction tasks.
Many modern AI systems analyze conversational traces to infer aspects of human interaction and state, implicitly assuming that such information is recoverable from conversation. We study observability: whether a target is recoverable from conversational transcripts alone. Observability is difficult to assess because transcripts may provide only a partial view of many targets, and large-scale analysis requires model-based annotation, making true limits of the conversational signal hard to distinguish from annotator error. We therefore study clinical encounters, where patient-reported outcome measures (PROMs) provide an external anchor for patient state, and visits follow broadly structured patterns. We study observability of patient state and conversational phase structure using 439 real-world clinical encounter transcripts spanning 134 hours, including 245 ENT transcripts paired with 273 PROM surveys. We operationalize patient state using PROM scores for voice, cough, and swallowing; phase structure using conversational phase segmentation. To make these analyses credible at scale, we use a PHI-compliant GPT-5 deployment for transcript annotation and conduct 40 hours of manual validation, reducing the risk that apparent limits of observability simply reflect annotator error. Our core finding is an observability asymmetry: phase structure is observable and useful for characterizing clinical encounter organization, while patient state is only partially observable, even in a setting designed to elicit patient symptoms and experiences, cautioning against transcript-only inference of human state.