# MedGuideX: Internalizing Decision Logic from Executable Guidelines into Large Language Models for Clinical Reasoning

arXiv: https://arxiv.org/abs/2605.26567 · HTML: https://mlsanity.com/paper/2605.26567/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 34 of its 56 references that are in the map.
- First posted on arXiv 26 May 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 30 of 34)

- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Emergent Abilities of Large Language Models](https://mlsanity.com/paper/2206.07682/) (2022)
- [Search-R1: Training LLMs to Reason and Leverage Search Engines with Reinforcement Learning](https://mlsanity.com/paper/2503.09516/) (2025)
- [OpenAI GPT-5 System Card](https://mlsanity.com/paper/2601.03267/) (2025)
- [Solving math word problems with process- and outcome-based feedback](https://mlsanity.com/paper/2211.14275/) (2022)
- [DeepSeek-V3 Technical Report](https://mlsanity.com/paper/2412.19437/) (2024)
- [Kimi K2: Open Agentic Intelligence](https://mlsanity.com/paper/2507.20534/) (2025)
- [MedGemma Technical Report](https://mlsanity.com/paper/2507.05201/) (2025)
- [Scaling Relationship on Learning Mathematical Reasoning with Large Language Models](https://mlsanity.com/paper/2308.01825/) (2023)
- [MedAlpaca -- An Open-Source Collection of Medical Conversational AI Models and Training Data](https://mlsanity.com/paper/2304.08247/) (2023)
- [MEDITRON-70B: Scaling Medical Pretraining for Large Language Models](https://mlsanity.com/paper/2311.16079/) (2023)
- [HuatuoGPT-o1, Towards Medical Complex Reasoning with LLMs](https://mlsanity.com/paper/2412.18925/) (2024)
- [Lingshu: A Generalist Foundation Model for Unified Multimodal Medical Understanding and Reasoning](https://mlsanity.com/paper/2506.07044/) (2025)
- [MedReason: Eliciting Factual Medical Reasoning Steps in LLMs via Knowledge Graphs](https://mlsanity.com/paper/2504.00993/) (2025)
- [Hulu-Med: A Transparent Generalist Model towards Holistic Medical Vision-Language Understanding](https://mlsanity.com/paper/2510.08668/) (2025)
- [DeepRetrieval: Hacking Real Search Engines and Retrievers with Large Language Models via Reinforcement Learning](https://mlsanity.com/paper/2503.00223/) (2025)
- [MedCaseReasoning: Evaluating and learning diagnostic reasoning from clinical case reports](https://mlsanity.com/paper/2505.11733/) (2025)
- [ER-Reason: A Benchmark Dataset for LLM Clinical Reasoning in the Emergency Room](https://mlsanity.com/paper/2505.22919/) (2025)
- [CounterBench: Evaluating and Improving Counterfactual Reasoning in Large Language Models](https://mlsanity.com/paper/2502.11008/) (2025)
- [MedDM:LLM-executable clinical guidance tree for clinical decision-making](https://mlsanity.com/paper/2312.02441/) (2023)
- [Doctor-R1: Mastering Clinical Inquiry with Experiential Agentic Reinforcement Learning](https://mlsanity.com/paper/2510.04284/) (2025)
- [Executable Counterfactuals: Improving LLMs' Causal Reasoning Through Code](https://mlsanity.com/paper/2510.01539/) (2025)
- [The Aloe Family Recipe for Open and Specialized Healthcare LLMs](https://mlsanity.com/paper/2505.04388/) (2025)
- [Clinical-R1: Empowering Large Language Models for Faithful and Comprehensive Reasoning with Clinical Objective Relative Policy Optimization](https://mlsanity.com/paper/2512.00601/) (2025)
- [MACD: Multi-Agent Clinical Diagnosis with Self-Learned Knowledge for LLM](https://mlsanity.com/paper/2509.20067/) (2025)
- [EHR-RAG: Bridging Long-Horizon Structured Electronic Health Records and Large Language Models via Enhanced Retrieval-Augmented Generation](https://mlsanity.com/paper/2601.21340/) (2026)
- [Improving Clinical Diagnosis with Counterfactual Multi-Agent Reasoning](https://mlsanity.com/paper/2603.27820/) (2026)
- [Training and Evaluation of Guideline-Based Medical Reasoning in LLMs](https://mlsanity.com/paper/2512.03838/) (2025)

## Built on by (most cited first, 4 of 4)

- [GuideSkill: Evolving Executable LLM Agent Skills for Guideline-Grounded Clinical Reasoning](https://mlsanity.com/paper/2607.26160/) (2026)
- [Evaluating Counterfactual Sensitivity to Patient Information in Medication-Safety Reasoning](https://mlsanity.com/paper/2608.03028/) (2026)
- [MedRouter: Demystifying Knowledge Differences Across Medical LLMs for Routing-Based Reasoning](https://mlsanity.com/paper/2609.33119/) (2026)
- [More Reasoning Is Not Always Better: Executing Clinical Guidelines with LLMs and Rules](https://mlsanity.com/paper/2610.15912/) (2026)

## Abstract (arXiv)

Clinical practice guidelines (CPGs) encode evidence-based decision logic that clinicians apply by evaluating patient variables, conditional criteria, and recommendation rules. However, existing methods often use CPGs as free-text training data or retrieval sources, underutilizing their procedural decision structure. To better exploit this structure, we introduce a guideline-derived training pipeline that transforms CPG recommendations into executable clinical decision logic and uses it to generate factual and counterfactual question-answering data. Theses data teach models both guideline-supported decisions and how decisions change under different patient conditions. Post-training a medical LLM on the generated data yields MedGuideX. Across four clinical reasoning benchmarks, MedGuideX achieves a 10.28% relative improvement in average accuracy. Physician evaluation further shows that MedGuideX better recovers clinician authored reasoning steps and produces physician-preferred rationales in faithfulness, validity, completeness, and clarity. Overall, our results show that executable decision logic from CPGs can be transformed into scalable supervision for building reliable medical LLMs.