Miniformer: A Minimalist Transformer for Brain Functional Networks Analysis

Learning to estimate and classify brain functional networks (BFNs) has become an increasingly important way of predicting neurological or mental disorders at their early stages. The traditional methods conduct BFN estimation and classification in two separate steps, thus preventing the interaction and joint optimization. In contrast, Transformer provides a natural architecture to learn BFNs with downstream tasks in an end-to-end manner. Despite their great potential, Transformer-based methods involve a large number of parameters that need to be learnt from big data and often lead to poor model interpretability. Considering the challenge in acquiring data and the high demand for model interpretability in medical scenarios, in this paper, we propose a minimalist Transformer architecture, referred to as Miniformer, by simplifying the projection matrices in the self-attention module into a single diagonal matrix, which greatly reduces the number of parameters, alleviates the risk of overfitting, and improves the interpretability. Additionally, the clear physical meaning of parameters in Miniformer makes the integration of domain knowledge or prior easier and more natural. Therefore, we further develop two variants of Miniformer by incorporating sparsity for removing potentially noisy time points from fMRI signals, and smoothness for capturing the temporal correlations in fMRI signals, respectively. To evaluate the effectiveness of the proposed methods, we perform brain disease diagnosis experiments on three public datasets. The results show that Miniformer and its variants tend to achieve higher classification performance than comparison methods with good interpretability.