Large Language Models for Structured Clinical Data Analysis: Dual-Agent Grounding and Validation

While interpretable prototype networks offer compelling case-based reasoning for clinical diagnostics, their raw continuous outputs lack the semantic structure required for medical documentation. Bridging this gap via standard Retrieval-Augmented Generation (RAG) routinely triggers ``retrieval sycophancy,'' where Large Language Models (LLMs) hallucinate post-hoc rationalizations to align with visual predictions. We introduce ProtoMedAgent, a framework that formalizes multimodal clinical reporting as an iterative, zero-gradient test-time optimization problem over a strict neuro-symbolic bottleneck. Operating on a frozen prototype backbone, we distill latent visual and tabular features into a discrete semantic memory. Online generation is strictly constrained by exact set-theoretic differentials and a reflective Scribe-Critic loop, mathematically precluding unsupported narrative claims. To safely bound data disclosure, we introduce a semantic privacy gate governed by $k$-anonymity and $\ell$-diversity. Evaluated on a 4,160-patient clinical cohort, ProtoMedAgent achieves 91.2% Comparison Set Faithfulness where it fundamentally outperforms standard RAG (46.2%). ProtoMedAgent additionally leverages a binding $\ell$-diversity phase transition to systematically reduce artifact-level membership inference risks by an absolute 9.8%.

Clinical data-science agents must transform heterogeneous longitudinal records into auditable analyses, yet existing benchmarks largely isolate medical question answering, structured-table reasoning, or generic scientific repositories. We introduce CLINLENS, a benchmark of 200 executable tasks over five linked MIMIC resources spanning structured electronic health records, notes, electrocardiograms, chest radiographs, and echocardiograms. A 4 x 5 taxonomy crosses four patient-time scopes with five analysis capabilities. Program-first reverse synthesis pairs each bounded semi-raw package with an evaluator-private reference workflow and checks required artifacts, cohort and temporal semantics, and the final answer. On a fixed 126-task suite, the strongest of 24 standardized model-scaffold configurations achieves 56.3% scope-macro STRICTPASS despite 100% EXECSUCCESS. For reference, a separately configured coding agent solves 83 of 126 tasks, while five biomedical systems adapted to GPT-4o-mini reach at most 2.9% scope-macro STRICTPASS. These results expose a substantial gap between runnable submissions and correct clinical analyses.

Deploying Large Language Models (LLMs) in high-stakes clinical settings remains limited by structural hallucinations, weak deterministic reasoning over tabular patient data, and omissions in vector retrieval. This paper presents the architecture and validation of Medi-Gemma, a Clinical Decision Support System (CDSS) for wound pathology triage and workflow automation. The platform introduces a decoupled framework that separates clinical perception from data orchestration while preserving traceable reasoning. Medi-Gemma uses a multi-stage pipeline coordinated by a centralized ClinicalOrchestrator. Data requests are handled without generative inference by a DataManager that cleans unstructured Electronic Medical Record (EMR) files through type coercion. Natural language queries are processed by a hierarchical IntentRouter, which routes requests to deterministic analytics paths executed by a PandasQueryEngine or to patient-specific reasoning managed by a ClinicalRAGEngine using a CPU-optimized vector store. A key contribution is the Ground Truth Injection Module, which intercepts patient-specific queries, extracts numeric identification tokens, queries the structured dataframe via Pandas, retrieves the latest validated clinical state, and embeds this snapshot as an overriding context block in the LLM prompt before generation. Safety compliance is enforced by a deterministic ProtocolManager that maps clinical terminology to fixed evidence-based risk pathways, while a SafetyVerifier phrase filter prevents output rule violations. Validation shows that this architecture eliminates semantic context drift, prevents database compilation crashes, and improves factual adherence to backend clinical repositories. These results support Medi-Gemma as a safer pattern for LLM-based clinical decision support where structured data fidelity, retrieval grounding, and deterministic safeguards are essential.