Contrasformer: A Brain Network Contrastive Transformer for Neurodegenerative Condition Identification

Understanding neurological disorder is a fundamental problem in neuroscience, which often requires the analysis of brain networks derived from functional magnetic resonance imaging (fMRI) data. Despite the prevalence of Graph Neural Networks (GNNs) and Graph Transformers in various domains, applying them to brain networks faces challenges. Specifically, the datasets are severely impacted by the noises caused by distribution shifts across sub-populations and the neglect of node identities, both obstruct the identification of disease-specific patterns. To tackle these challenges, we propose Contrasformer, a novel contrastive brain network Transformer. It generates a prior-knowledge-enhanced contrast graph to address the distribution shifts across sub-populations by a two-stream attention mechanism. A cross attention with identity embedding highlights the identity of nodes, and three auxiliary losses ensure group consistency. Evaluated on 4 functional brain network datasets over 4 different diseases, Contrasformer outperforms the state-of-the-art methods for brain networks by achieving up to 10.8\% improvement in accuracy, which demonstrates its efficacy in neurological disorder identification. Case studies illustrate its interpretability, especially in the context of neuroscience. This paper provides a solution for analyzing brain networks, offering valuable insights into neurological disorders. Our code is available at \url{https://github.com/AngusMonroe/Contrasformer}.

Contrastive Graph Pooling for Explainable Classification of Brain Networks

Functional magnetic resonance imaging (fMRI) is a commonly used technique to measure neural activation. Its application has been particularly important in identifying underlying neurodegenerative conditions such as Parkinson's, Alzheimer's, and Autism. Recent analysis of fMRI data models the brain as a graph and extracts features by graph neural networks (GNNs). However, the unique characteristics of fMRI data require a special design of GNN. Tailoring GNN to generate effective and domain-explainable features remains challenging. In this paper, we propose a contrastive dual-attention block and a differentiable graph pooling method called ContrastPool to better utilize GNN for brain networks, meeting fMRI-specific requirements. We apply our method to 5 resting-state fMRI brain network datasets of 3 diseases and demonstrate its superiority over state-of-the-art baselines. Our case study confirms that the patterns extracted by our method match the domain knowledge in neuroscience literature, and disclose direct and interesting insights. Our contributions underscore the potential of ContrastPool for advancing the understanding of brain networks and neurodegenerative conditions.