Recently, extensive literature has shown that the relationship between SC and FC is complex and not a simple one-to-one mapping.

Inthis work, we study Transformer-based models for brain network analysis.

Blind source separation, particularly through independent component analysis (ICA), is widely utilized across various signal processing domains for disentangling underlying components from observed mixed signals, owing to its fully data-driven nature that minimizes reliance on prior assumptions. However, conventional ICA methods rely on an assumption of linear mixing, limiting their ability to capture complex nonlinear relationships and to maintain robustness in noisy environments. In this work, we present deep deterministic nonlinear independent component analysis (DDICA), a novel deep neural network-based framework designed to address these limitations. DDICA leverages a matrix-based entropy function to directly optimize the independence criterion via stochastic gradient descent, bypassing the need for variational approximations or adversarial schemes. This results in a streamlined training process and improved resilience to noise. We validated the effectiveness and generalizability of DDICA across a range of applications, including simulated signal mixtures, hyperspectral image unmixing, modeling of primary visual receptive fields, and resting-state functional magnetic resonance imaging (fMRI) data analysis. Experimental results demonstrate that DDICA effectively separates independent components with high accuracy across a range of applications. These findings suggest that DDICA offers a robust and versatile solution for blind source separation in diverse signal processing tasks.

Traditional metrics of interbrain synchrony in social neuroscience typically depend on fixed, correlation-based approaches, restricting their explanatory capacity to descriptive observations. Inspired by the successful integration of geometric insights in network science, we propose leveraging discrete geometry to examine the dynamic reconfigurations in neural interactions during social exchanges. Unlike conventional synchrony approaches, our method interprets inter-brain connectivity changes through the evolving geometric structures of neural networks. This geometric framework is realized through a pipeline that identifies critical transitions in network connectivity using entropy metrics derived from curvature distributions. By doing so, we significantly enhance the capacity of hyperscanning methodologies to uncover underlying neural mechanisms in interactive social behavior.

Graph Transformer shows remarkable potential in brain network analysis due to its ability to model graph structures and complex node relationships. Most existing methods typically model the brain as a flat network, ignoring its modular structure, and their attention mechanisms treat all brain region connections equally, ignoring distance-related node connection patterns. However, brain information processing is a hierarchical process that involves local and long-range interactions between brain regions, interactions between regions and sub-functional modules, and interactions among functional modules themselves. This hierarchical interaction mechanism enables the brain to efficiently integrate local computations and global information flow, supporting the execution of complex cognitive functions. To address this issue, we propose BrainHGT, a hierarchical Graph Transformer that simulates the brain's natural information processing from local regions to global communities. Specifically, we design a novel long-short range attention encoder that utilizes parallel pathways to handle dense local interactions and sparse long-range connections, thereby effectively alleviating the over-globalizing issue. To further capture the brain's modular architecture, we designe a prior-guided clustering module that utilizes a cross-attention mechanism to group brain regions into functional communities and leverage neuroanatomical prior to guide the clustering process, thereby improving the biological plausibility and interpretability. Experimental results indicate that our proposed method significantly improves performance of disease identification, and can reliably capture the sub-functional modules of the brain, demonstrating its interpretability.

Brain processes occur at various timescales, ranging from milliseconds (neurons) to minutes and hours (behavior). Characterizing functional coupling among brain regions at these diverse timescales is key to understanding how the brain produces behavior. Here, we apply instantaneous and lag-based measures of conditional linear dependence, based on Granger-Geweke causality (GC), to infer network connections at distinct timescales from functional magnetic resonance imaging (fMRI) data. Due to the slow sampling rate of fMRI, it is widely held that GC produces spurious and unreliable estimates of functional connectivity when applied to fMRI data. We challenge this claim with simulations and a novel machine learning approach. First, we show, with simulated fMRI data, that instantaneous and lag-based GC identify distinct timescales and complementary patterns of functional connectivity. Next, we analyze fMRI scans from 500 subjects and show that a linear classifier trained on either instantaneous or lag-based GC connectivity reliably distinguishes task versus rest brain states, with ~80-85% cross-validation accuracy. Importantly, instantaneous and lag-based GC exploit markedly different spatial and temporal patterns of connectivity to achieve robust classification. Our approach enables identifying functionally connected networks that operate at distinct timescales in the brain.