FHIRBench: Benchmarking FHIR Clinical Data Serialization Strategies for Large Language Models
TL;DR
It is established that clinical AI systems require model-aware serialization middleware, multi-layer evaluation frameworks, and capacity verification before deployment, as well as a patient-safety gap where AI fails for the patients who need it most.
Abstract
We present FHIRBench, a benchmark evaluating six FHIR clinical data serialization strategies across four frontier LLMs (Claude Sonnet 4.5, GPT-5.4, DeepSeek V3.2, Qwen3 32B) on three clinical tasks using 100 stratified synthetic FHIR R4 patient bundles. We employ two evaluation layers: token-level F1 and LLM-as-judge rubric on four clinical dimensions, yielding 7,200 evaluations per layer. Our findings reveal four results. First, serialization significantly impacts quality but the direction diverges between layers: Condensed outperforms Raw JSON on F1 for 3/4 models (Wilcoxon p < 10^-17), while Raw JSON achieves higher judge scores for 3/4 models (p < 10^-7). Narrative achieves 95% of Raw JSON's quality at 83% fewer tokens. Second, model rankings completely reverse between layers -- Claude ranks last on F1 but first on clinical quality (p = 1.0 x 10^-6), demonstrating that single-metric evaluation produces misleading model selection. Third, a significant Model x Serializer interaction (Friedman p = 0.0009) precludes universal format recommendations, with GPT-5.4 favoring Raw JSON while open-weight models favor compressed formats. Fourth, Llama 3.1 70B exhibits 100% inference failure on complex patients despite operating within its nominal context window, revealing a patient-safety gap where AI fails for the patients who need it most. These findings establish that clinical AI systems require model-aware serialization middleware, multi-layer evaluation frameworks, and capacity verification before deployment. Code and data publicly available.