Anna Lin | Searcharxiv

arXiv2026

Health System Scale Semantic Search Across Unstructured Clinical Notes

Introduction: Semantic search, which retrieves documents based on conceptual similarity rather than keywords, offers advantages for retrieval of clinical information. However, deploying semantic search across health systems, comprising hundreds of millions of clinical notes, presents formidable engineering, cost, and governance challenges that have prevented institutional adoption. Methods: We deployed a semantic search system at a large children's hospital indexing 166 million clinical notes (484 million embedding vectors) from 1.68 million patients. The system uses instruction-tuned qwen3-embedding-0.6B embeddings, stores vectors with storage-optimized indexing, maintains full-text metadata in a low-latency key-value store, and operates within a HIPAA-compliant governance framework. We evaluated the system by optimizing the model and chunking strategy using a physician-authored benchmark, characterizing full-scale performance (cost, latency, retrieval quality), and assessing clinical utility via chart abstraction efficiency and comparison to ICD-10 cohort generation. Results: The system delivers sub-second query latency with monthly operational costs of ~USD 4,000. Qwen3 embeddings with 300-token chunk size achieved 94.6% accuracy on the benchmark. In clinical utility evaluation across three abstraction tasks, semantic search reduced time-to-completion by 24 to 89% versus chart review while maintaining inter-rater agreement where assessable. During system-wide retrieval, semantic search recovered 98% of patients with molecularly confirmed genetic diseases, versus at most 75% by diagnosis codes. Conclusion: Health-system-scale semantic search is technically and operationally feasible. The system provides institutional infrastructure supporting interactive search, cohort generation, and downstream LLM-powered clinical applications without requiring specialized informatics expertise.

cs.IR↗

arXiv2025

COMPASS: Context-Modulated PID Attention Steering System for Hallucination Mitigation

Large language models (LLMs) often generate fluent but factually incorrect statements despite having access to relevant evidence, a failure mode rooted in how they allocate attention between contextual and parametric knowledge. Understanding and steering this internal behavior is key both for trustworthy deployment and for scientific interpretability of model mechanisms. We introduce COMPASS (Context-Modulated PID Attention Steering System), a lightweight, interpretable control framework that embeds a model-based feedback loop directly within decoding. COMPASS quantifies context reliance via a transparent metric, the Context Reliance Score (CRS), which serves as an online probe of how attention heads ground generation in evidence. Using this interpretable signal, a PID controller dynamically modulates attention heads to maintain factual consistency without retraining or multi-pass decoding. Across benchmarks (HotpotQA, XSum, HaluEval, RAGTruth), COMPASS consistently reduces contextual hallucination rates (2.8 to 5.8 percent absolute) while revealing how distinct attention heads contribute to evidence alignment. These results highlight feedback-driven interpretability as a pathway toward scientific understanding of LLM behavior.

cs.CL↗