# When Language Models Meet NeuroGraphs: Exploring Enhanced Agentic LLM Framework Towards Brain Network Analysis

arXiv: https://arxiv.org/abs/2607.22082 · HTML: https://mlsanity.com/paper/2607.22082/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 34 of its 53 references that are in the map.
- First posted on arXiv 24 Jul 2026.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

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

- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Reflexion: Language Agents with Verbal Reinforcement Learning](https://mlsanity.com/paper/2303.11366/) (2023)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [Tree of Thoughts: Deliberate Problem Solving with Large Language Models](https://mlsanity.com/paper/2305.10601/) (2023)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day](https://mlsanity.com/paper/2306.00890/) (2023)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [GraphMAE: Self-Supervised Masked Graph Autoencoders](https://mlsanity.com/paper/2205.10803/) (2022)
- [Small Language Models are the Future of Agentic AI](https://mlsanity.com/paper/2506.02153/) (2025)
- [Capabilities of Gemini Models in Medicine](https://mlsanity.com/paper/2404.18416/) (2024)
- [GraphGPT: Graph Instruction Tuning for Large Language Models](https://mlsanity.com/paper/2310.13023/) (2023)
- [G-Retriever: Retrieval-Augmented Generation for Textual Graph Understanding and Question Answering](https://mlsanity.com/paper/2402.07630/) (2024)
- [When Attention Sink Emerges in Language Models: An Empirical View](https://mlsanity.com/paper/2410.10781/) (2024)
- [BrainGB: A Benchmark for Brain Network Analysis with Graph Neural Networks](https://mlsanity.com/paper/2204.07054/) (2022)
- [Interpretable Graph Neural Networks for Connectome-Based Brain Disorder Analysis](https://mlsanity.com/paper/2207.00813/) (2022)
- [Injecting New Knowledge into Large Language Models via Supervised Fine-Tuning](https://mlsanity.com/paper/2404.00213/) (2024)
- [Med-MoE: Mixture of Domain-Specific Experts for Lightweight Medical Vision-Language Models](https://mlsanity.com/paper/2404.10237/) (2024)
- [RAGraph: A General Retrieval-Augmented Graph Learning Framework](https://mlsanity.com/paper/2410.23855/) (2024)
- [SpreadsheetLLM: Encoding Spreadsheets for Large Language Models](https://mlsanity.com/paper/2407.09025/) (2024)
- [Medchain: Bridging the Gap Between LLM Agents and Clinical Practice with Interactive Sequence](https://mlsanity.com/paper/2412.01605/) (2024)
- [BrainNPT: Pre-training of Transformer networks for brain network classification](https://mlsanity.com/paper/2305.01666/) (2023)
- [MMGPL: Multimodal Medical Data Analysis with Graph Prompt Learning](https://mlsanity.com/paper/2312.14574/) (2023)
- [Multimodal Clinical Trial Outcome Prediction with Large Language Models](https://mlsanity.com/paper/2402.06512/) (2024)

## Abstract (arXiv)

Brain network analysis is crucial for understanding cognition and neurological disorders, yet existing deep learning methods mainly treat connectome analysis as a graph-to-logit classification problem, offering limited explanatory reasoning. Large language models (LLMs) provide a promising interface for knowledge-intensive scientific analysis, but directly applying general-purpose LLMs to brain networks remains challenging due to the structure-language gap, limited neuroscience grounding, and overconfident positive predictions. In this paper, we propose BrainAgent, an agentic LLM framework for knowledge-enhanced brain network analysis. BrainAgent reformulates connectome classification as an iterative process of topology-aware understanding, external retrieval, reasoning, and reflection. Specifically, it first converts raw brain networks into compact multi-level structural descriptions through brain-specific analysis tools, then retrieves relevant neuroscience knowledge and task-specific cases to ground the reasoning process, and finally generates structured predictions with reflective verification. Experiments on four public rs-fMRI datasets show that BrainAgent consistently improves different closed-source and open-source LLM backbones over direct prompting and standard reasoning baselines. Further ablation and interpretability analyses demonstrate the effectiveness of each component and show that BrainAgent produces more comprehensive, multi-level, and verifiable explanations.These results indicate that agentic LLMs provide a practical route toward interpretable and knowledge-grounded brain network analysis.