FastOMOP: A Foundational Architecture for Reliable Agentic Real-World Evidence Generation on OMOP CDM data

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.

Large Language Models (LLMs) show great potential as clinical agents, yet existing benchmarks reduce clinical workflows to static predictions or unconstrained Markov Decision Processes (MDPs) with coarse action sets. To address this, we introduce GPAgentBench-2K, the first Constrained MDP (CMDP) LLM-agent benchmark for primary-care clinical decision-making, constructed from expert-validated records of real-world GP encounters. Our environment models a full spectrum of six foundational clinical actions, imposes a topological workflow prior over the action space, and operationalizes safety-informed abstention as a first-class outcome. Evaluating 16 state-of-the-art LLMs reveals a significant performance degradation as the action space scales. Crucially, we uncover a clinical quality-safety gap: even frontier models with the highest diagnosis accuracy violate safety constraints in over half of high-risk cases. Finally, we establish a reference point using Constrained Group Relative Policy Optimization (C-GRPO), and show that while explicitly modeling constraints improves performance over unconstrained RL methods, it remains far from clinically acceptable safety.

Operations Research (OR) provides a rigorous framework for high-stakes decision-making, but effective OR modeling requires substantial domain knowledge, mathematical abstraction, and solver expertise. Recent LLM-based systems automate parts of this pipeline, yet remain limited by low accuracy on complex problems, opaque outputs, and narrow solver support. We propose COOPA (COoperative OPerations Agent), a modular LLM-agent architecture for interpretable and scalable OR decision support. It combines three components: iterative confidence-based modeling, which generates multiple candidate formulations, self-evaluates them across modeling dimensions, and selects one using a max-min confidence criterion; element-level provenance and confidence explanations, which link variables, parameters, constraints, and objectives to quoted source text and provide an audit trail for human verification; and multi-solver routing to specialized optimizer agents for different OR problem classes. Across three OR benchmarks, eight LLM backbones, and four baselines under identical conditions, COOPA achieves the best macro-average accuracy on six of eight backbones and improves over the strongest baseline by up to 6.7 percentage points. A within-system ablation isolates the contribution of iterative confidence-based modeling, while additional analyses and case studies illustrate the value of source traceability and multi-solver dispatch.