A Human-in-the-Loop Large Language Model System Based on the Model Context Protocol for Differential Diagnosis from Electronic Medical Records and Literature

Abstract

Diagnostic errors, including misdiagnoses and delayed clinical diagnoses, could affect outcomes of a significant patient population, particularly individuals presenting with rare diseases or non-specific symptoms. From rule-based diagnostic decision supporting systems (DDSS) to large language model (LLM) based tools for clinical reasoning have been developed to address these limitations. However, existing DDSS are often proprietary and difficult to integrate, and recent LLM-based tools remain hindered by operational challenges such as cost, resources constraint, and privacy concerns. Moreover, existing systems interpret electronic medical records (EMR) and generate diagnoses separately, limiting continuous evidence-based analysis and imposing repeated clinician involvement. In this paper, we present DDx-Finder, an open-source framework that leverages Model Context Protocol (MCP) servers for direct EMR and literature access, enabling prompt-driven clinical state extraction and reliable case-report re- trieval via generating searching query by LLM, while addressing limitations related to resource demands and privacy concerns. A clinical case study demonstrates the systems feasibility and its potential to provide accessible, transparent, and systematic differential diagnostic support for complex cases.