# Uncertainty Reasoning with Large Language Models for Explainable Disease Diagnosis

arXiv: https://arxiv.org/abs/2605.25566 · HTML: https://mlsanity.com/paper/2605.25566/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 17 of its 44 references that are in the map.
- First posted on arXiv 25 May 2026.

## Placed in

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

## Builds on (most cited first, 17 of 17)

- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [On Calibration of Modern Neural Networks](https://mlsanity.com/paper/1706.04599/) (2017)
- [Survey of Hallucination in Natural Language Generation](https://mlsanity.com/paper/2202.03629/) (2022)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Neural Probabilistic Logic Programming in DeepProbLog](https://mlsanity.com/paper/1907.08194/) (2019)
- [ChatDoctor: A Medical Chat Model Fine-Tuned on a Large Language Model Meta-AI (LLaMA) Using Medical Domain Knowledge](https://mlsanity.com/paper/2303.14070/) (2023)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [End-to-End Differentiable Proving](https://mlsanity.com/paper/1705.11040/) (2017)
- [GRAM: Graph-based Attention Model for Healthcare Representation Learning](https://mlsanity.com/paper/1611.07012/) (2016)
- [DeID-GPT: Zero-shot Medical Text De-Identification by GPT-4](https://mlsanity.com/paper/2303.11032/) (2023)
- [RoentGen: Vision-Language Foundation Model for Chest X-ray Generation](https://mlsanity.com/paper/2211.12737/) (2022)
- [Recitation-Augmented Language Models](https://mlsanity.com/paper/2210.01296/) (2022)
- [MedExQA: Medical Question Answering Benchmark with Multiple Explanations](https://mlsanity.com/paper/2406.06331/) (2024)
- [Instruction Tuning and CoT Prompting for Contextual Medical QA with LLMs](https://mlsanity.com/paper/2506.12182/) (2025)

## Abstract (arXiv)

Clinical decision-making requires reasoning over incomplete, imprecise, and linguistically expressed patient narratives. While large language models (LLMs) excel at extracting latent information from natural language, they lack the verifiability and interpretability essential for trustworthy medical AI. We propose a neuro-symbolic reasoning framework that aligns LLMs with formal logic to enable explainable and formally verifiable medical diagnosis. Patient descriptions and clinical guidelines are embedded into a neural knowledge base, where LLMs extract structured medical entities, temporal relations, and fuzzy symptom patterns, which are decoded into a symbolic knowledge base expressed in fuzzy logic and declarative rules. We perform two-stage reasoning: (1) inductive symbolic generalization to capture diagnostic patterns from encoded narratives, and (2) inference verification via a logic programming engine to derive and validate diagnoses consistent with clinical standards. Each symptom is treated as a fuzzy predicate with probabilistic weights, and inference paths are auditable, adjustable, and compatible with physician feedback. Unlike purely statistical methods, our system supports iterative refinement: misalignment between LLM-generated diagnoses and ground truth can be traced, explained, and corrected through formal rules. By combining logic-based transparency, LLM adaptability, and probabilistic robustness, the framework enables human-aligned healthcare inference with strong generalization and verifiable, step-by-step reasoning chains. We validate our framework on public benchmarks, demonstrating effective reconciliation of symbolic reasoning and LLMs with real-world clinical narratives. Results show performance comparable to state-of-the-art LLMs, while additionally providing interpretable reasoning paths and formally verifiable diagnostic conclusions.