Analyzing Healthcare Interoperability Vulnerabilities: Formal Modeling and Graph-Theoretic Approach

Fast Healthcare Interoperability Resources (FHIR) is the dominant standard for interoperable exchange of healthcare data. In FHIR, electronic health records form a directed graph of resources. Answering clinically meaningful questions over FHIR requires agents to perform multi-step reasoning, filtering, and aggregation across multiple resource types. Prior work shows that even tool-augmented LLM agents (retrieval, code execution, multi-turn planning) often select the wrong resources or violate traversal constraints. We study this problem in the context of FHIR-AgentBench, a benchmark for realistic question answering over real-world hospital data, and frame reasoning on FHIR as a sequential decision-making problem over a queryable structured graph. We implement a multi-turn CodeAct agent and post-train it with reinforcement learning using a custom harness and tools. A LLM Judge provides execution-grounded rewards. Compared to prompt-based, closed-model baselines, RL post-training improves performance while enforcing data-integrity constraints. Empirically, our approach improves answer correctness from 50% (o4-mini) to 77% on FHIR-AgentBench using a smaller and cheaper Qwen3-8B model. We present an end-to-end post-training pipeline (environment building, harness construction, model training and custom evaluation) that reliably improves multi-turn reasoning over structured clinical graphs.

Electronic health-record interoperability is a boundary problem: legacy systems, generative models, terminology services, identity systems, and human reviewers may each expose rich internal states, while operational exchange requires a narrow shared interface of typed claims, bounded uncertainty, provenance, and explicit admission or abstention. This paper details a mathematical and engineering architecture for that interface. The organizing idea is the logit boundary: a discovery model may propose pre-threshold scores over a local categorical decision, but a deterministic judgment substrate decides whether the proposal is admissible, requires review, or must be quarantined before any Fast Healthcare Interoperability Resources (FHIR) transaction is constructed. The resulting Geometric Belief Interface (GBI) combines finite boundary semantics, local Dirichlet evidence, cellular-sheaf and mapping-cone diagnostics, advisory geometric audit charts, and a Decentralized Cryptographic Sheaf-Enclave (DCSE) protocol sketch for fail-closed deployment. The framework does not establish clinical truth, global representation alignment, or end-to-end safety; it defines certificate-producing checks at a model-to-system boundary. A companion frozen synthetic benchmark, GBI BoundaryBench v0.1, evaluated Qwen3-4B-Instruct-2507 on 256 held-out tasks across three evidence modes (768 canonical executions). All executions completed, but none produced an output accepted by the benchmark contract: 369 were rejected during safe parsing and 399 during schema validation, yielding zero coverage and deterministic quarantine. This empirical result is deliberately narrow - one 4B open-weight model under one frozen interface - and is reported as evidence about the admission boundary, not as a general claim about LLM capability or clinical safety. A Julia appendix verifies numerical certificates using standard libraries.

Though patients are increasingly granted digital access to their electronic health records (EHRs), existing interfaces may not support precise, trustworthy answers to patient-specific questions. Large language models (LLM) show promise in clinical question answering (QA), but retrieval-based approaches are computationally inefficient, prone to hallucination, and difficult to deploy over real-life EHRs. This work introduces FHIRPath-QA, the first open dataset and benchmark for patient-specific QA that includes open-standard FHIRPath queries over real-world clinical data. A text-to-FHIRPath QA paradigm is proposed that shifts reasoning from free-text generation to FHIRPath query synthesis. For o4-mini, this reduced average token usage by 391x relative to retrieval-first prompting (629,829 vs 1,609 tokens per question) and lowered failure rates from 0.36 to 0.09 on clinician-phrased questions. Built on MIMIC-IV on FHIR Demo, the dataset pairs over 14k natural language questions in patient and clinician phrasing with validated FHIRPath queries and answers. Empirically, the evaluated LLMs achieve at most 42% accuracy, highlighting the challenge of the task, but benefit strongly from supervised fine-tuning, with query synthesis accuracy improving from 27% to 79% for 4o-mini. These results highlight that text-to-FHIRPath synthesis has the potential to serve as a practical foundation for safe, efficient, and interoperable consumer health applications, and the FHIRPath-QA dataset and benchmark serve as a starting point for future research on the topic. The full dataset and generation code can be accessed at: https://github.com/mooshifrew/fhirpath-qa.