FedPref: Federated Preference Learning for Structured Radiology Report Extraction

Radiology reports describe findings and locations in free text, but downstream search and analysis require these relations in a fixed schema. Learning this extraction requires labels that are unevenly distributed across institutions: smaller hospitals have less local evidence, and pooling data may be infeasible. We introduce FedPref: frozen public language models propose alternative JSON extractions, local annotations rank them, and sites collaboratively train compact Qwen3-8B adapters while sharing only model updates. A heterogeneous teacher pool provides cross-model contrast when repeated single-model samples collapse. On development data from six simulated hospitals with unequal data volume and disease prevalence, FedPref improves client-mean F1 by 2.49 points and worst-site F1 by 9.10 points compared with training each site in isolation, with the largest gains at the sites holding the least data. Central training on the pooled preference-pair union is 2.66 points higher on client-mean F1. On a locked, 400-report manually validated gold test set, FedPref reaches 68.68 F1 and pooled training 71.67, preserving that same ordering. FedPref thus lets institutions with unequal, unpooled data benefit from collaboration without ever sharing reports or annotations.

PVminerLLM2: Improving Structured Extraction of Patient Voice via Preference Optimization

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