# Foundation models for discovering robust biomarkers of neurological disorders from dynamic functional connectivity

arXiv: https://arxiv.org/abs/2604.22018 · HTML: https://mlsanity.com/paper/2604.22018/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 49 references that are in the map.
- First posted on arXiv 23 Apr 2026.

## Builds on (most cited first, 14 of 14)

- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Explainability in Graph Neural Networks: A Taxonomic Survey](https://mlsanity.com/paper/2012.15445/) (2020)
- [From Anecdotal Evidence to Quantitative Evaluation Methods: A Systematic Review on Evaluating Explainable AI](https://mlsanity.com/paper/2201.08164/) (2022)
- [Learning Dynamic Graph Representation of Brain Connectome with Spatio-Temporal Attention](https://mlsanity.com/paper/2105.13495/) (2021)
- [Neuro-GPT: Towards A Foundation Model for EEG](https://mlsanity.com/paper/2311.03764/) (2023)
- [Brain-JEPA: Brain Dynamics Foundation Model with Gradient Positioning and Spatiotemporal Masking](https://mlsanity.com/paper/2409.19407/) (2024)
- [Spatio-Temporal Graph Convolution for Resting-State fMRI Analysis](https://mlsanity.com/paper/2003.10613/) (2020)
- [Rethinking Stability for Attribution-based Explanations](https://mlsanity.com/paper/2203.06877/) (2022)
- [Why are Saliency Maps Noisy? Cause of and Solution to Noisy Saliency Maps](https://mlsanity.com/paper/1902.04893/) (2019)
- [Brain Foundation Models: A Survey on Advancements in Neural Signal Processing and Brain Discovery](https://mlsanity.com/paper/2503.00580/) (2025)
- [F-Fidelity: A Robust Framework for Faithfulness Evaluation of Explainable AI](https://mlsanity.com/paper/2410.02970/) (2024)
- [Robustness tests for biomedical foundation models should tailor to specifications](https://mlsanity.com/paper/2502.10374/) (2025)
- [Discovering robust biomarkers of psychiatric disorders from resting-state functional MRI via graph neural networks: A systematic review](https://mlsanity.com/paper/2405.00577/) (2024)

## Abstract (arXiv)

Several brain foundation models (FM) have recently been proposed to predict brain disorders by modelling dynamic functional connectivity (FC). While they demonstrate remarkable model performance and zero- or few-shot generalization, the salient features identified as potential biomarkers are yet to be thoroughly evaluated. We propose RE-CONFIRM, a framework for evaluating the robustness of potential biomarker candidates elucidated by deep learning (DL) models including FMs. From experiments on five large datasets of Autism Spectrum Disorder (ASD), Attention-deficit Hyperactivity Disorder (ADHD), and Alzheimer's Disease (AD), we found that although commonly used performance metrics provide an intuitive assessment of model predictions, they are insufficient for evaluating the robustness of biomarkers identified by these models. RE-CONFIRM metrics revealed that simply finetuning FMs leads to models that fail to capture regional hubs effectively, even in disorders where hubs are known to be implicated, such as ASD and ADHD. In view of this, we propose Hub-LoRA (Low-Rank Adaptation) as a fine-tuning technique that enables FMs to not only outperform customised DL models but also produce neurobiologically faithful biomarkers supported by meta-analyses. RE-CONFIRM is generalizable and can be easily applied to ascertain the robustness of DL models trained on functional MRI datasets. Code is available at: https://github.com/SCSE-Biomedical-Computing-Group/RE-CONFIRM.