# FCN-LLM: Empower LLM for Brain Functional Connectivity Network Understanding via Graph-level Multi-task Instruction Tuning

arXiv: https://arxiv.org/abs/2603.01135 · HTML: https://mlsanity.com/paper/2603.01135/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 34 of its 66 references that are in the map.
- First posted on arXiv 1 Mar 2026.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Microsoft COCO: Common Objects in Context](https://mlsanity.com/paper/1405.0312/) (2014)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [Qwen2.5 Technical Report](https://mlsanity.com/paper/2412.15115/) (2024)
- [BLIP: Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation](https://mlsanity.com/paper/2201.12086/) (2022)
- [VQA: Visual Question Answering](https://mlsanity.com/paper/1505.00468/) (2015)
- [Multitask Prompted Training Enables Zero-Shot Task Generalization](https://mlsanity.com/paper/2110.08207/) (2021)
- [Video-MME: The First-Ever Comprehensive Evaluation Benchmark of Multi-modal LLMs in Video Analysis](https://mlsanity.com/paper/2405.21075/) (2024)
- [Video-LLaVA: Learning United Visual Representation by Alignment Before Projection](https://mlsanity.com/paper/2311.10122/) (2023)
- [CoCa: Contrastive Captioners are Image-Text Foundation Models](https://mlsanity.com/paper/2205.01917/) (2022)
- [OK-VQA: A Visual Question Answering Benchmark Requiring External Knowledge](https://mlsanity.com/paper/1906.00067/) (2019)
- [M3-Embedding: Multi-Linguality, Multi-Functionality, Multi-Granularity Text Embeddings Through Self-Knowledge Distillation](https://mlsanity.com/paper/2402.03216/) (2024)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Self-Play Fine-Tuning Converts Weak Language Models to Strong Language Models](https://mlsanity.com/paper/2401.01335/) (2024)
- [ImageBind-LLM: Multi-modality Instruction Tuning](https://mlsanity.com/paper/2309.03905/) (2023)
- [AudioBench: A Universal Benchmark for Audio Large Language Models](https://mlsanity.com/paper/2406.16020/) (2024)
- [Multitask Prompt Tuning Enables Parameter-Efficient Transfer Learning](https://mlsanity.com/paper/2303.02861/) (2023)
- [Brain Network Transformer](https://mlsanity.com/paper/2210.06681/) (2022)
- [ATTEMPT: Parameter-Efficient Multi-task Tuning via Attentional Mixtures of Soft Prompts](https://mlsanity.com/paper/2205.11961/) (2022)
- [BrainGB: A Benchmark for Brain Network Analysis with Graph Neural Networks](https://mlsanity.com/paper/2204.07054/) (2022)
- [FBNETGEN: Task-aware GNN-based fMRI Analysis via Functional Brain Network Generation](https://mlsanity.com/paper/2205.12465/) (2022)
- [Multitask Vision-Language Prompt Tuning](https://mlsanity.com/paper/2211.11720/) (2022)
- [BrainMass: Advancing Brain Network Analysis for Diagnosis with Large-scale Self-Supervised Learning](https://mlsanity.com/paper/2403.01433/) (2024)
- [Advancing Fine-Grained Visual Understanding with Multi-Scale Alignment in Multi-Modal Models](https://mlsanity.com/paper/2411.09691/) (2024)

## Abstract (arXiv)

Large Language Models have achieved remarkable success in language understanding and reasoning, and their multimodal extensions enable comprehension of images, video, and audio. Inspired by this, foundation models for brain functional connectivity networks derived from resting-state fMRI have shown promise in clinical tasks. However, existing methods do not align FCNs with the text modality, limiting the ability of LLMs to directly understand FCNs. To address this, we propose FCN-LLM, a framework that enables LLMs to understand FCNs through graph-level, multi-task instruction tuning. Our approach employs a multi-scale FCN encoder capturing brain-region, functional subnetwork, and whole-brain features, projecting them into the semantic space of LLM. We design multi-paradigm instruction tasks covering 19 subject-specific attributes across demographics, phenotypes, and psychiatric conditions. A multi-stage learning strategy first aligns FCN embeddings with the LLM and then jointly fine-tunes the entire model to capture high-level semantic information. Experiments on a large-scale, multi-site FCN database show that FCN-LLM achieves strong zero-shot generalization on unseen datasets, outperforming conventional supervised and foundation models. This work introduces a new paradigm for integrating brain functional networks with LLMs, offering a flexible and interpretable framework for neuroscience.