Institution-Specific LLM Prompting Recovers PHI That De-identification Systems and Their Gold Standards Both Miss

Abstract:Secondary use of electronic health records requires de-identification, yet existing systems miss \emph{institutionally situated} protected health information (PHI) such as hospital abbreviations, building names, and internal codes whose status is locally determined. We ask whether large language models (LLMs) with in-context learning (ICL) can close this gap and control the precision--recall trade-off. On 100 annotated pediatric oncology notes (5,322 PHI spans) from Texas Children's Hospital, we benchmarked eight LLMs against two purpose-built systems (Stanford TiDE, OpenMed PII) and two pattern-based baselines. Each LLM ran under three prompts of increasing specificity: (1) a HIPAA-aligned baseline, (2) baseline plus the institutional PHI categories it missed, and (3) prompt 2 plus instructions against over-redacting clinical content. We then compared 14~multi-agent and ensemble configurations against the best single prompt, with recall the primary safety metric. LLMs outperformed the purpose-built systems (best F1=0.918$\pm$0.001 vs.\ TiDE 0.779), with advantages concentrated in contextual categories. Naming the missed categories recovered 79\% (48/61) of them, and discouraging over-redaction restored precision. No agentic architecture beat calibrated single-pass prompting (F1 0.906--0.907), but LLM outputs surfaced 414~candidate annotation gaps; re-annotation confirmed 227~PHI spans, against which the final prompt reached recall=0.981 (F1=0.907$\pm$0.002). Well-calibrated ICL resolves both the institutional PHI gap and the precision--recall trade-off in one LLM call per note. LLMs cost more to run than traditional methods, but that cost buys a way to audit the reference standard. LLMs are a legitimate, adaptable alternative to purpose-built de-identification systems; institution-specific prompt development should be the primary adaptation strategy.

Computation and Language (cs.CL); Artificial Intelligence (cs.AI)

arXiv:2608.17051 [cs.CL]

(or arXiv:2608.17051v1 [cs.CL] for this version)

https://doi.org/10.48550/arXiv.2608.17051 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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