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This limitation hinders their ability to accurately represent the brain's structural and functional properties, thereby restricting the effectiveness of machine learning models in tasks such as brain disorder detection. In this work, we propose a novel Biologically Plausible Brain Graph Transformer (BioBGT) that encodes the small-world architecture inherent in brain graphs. Specifically, we present a network entanglement-based node importance encoding technique that captures the structural importance of nodes in global information propagation during brain graph communication, highlighting the biological properties of the brain structure. Furthermore, we introduce a functional module-aware self-attention to preserve the functional segregation and integration characteristics of brain graphs in the learned representations. Experimental results on three benchmark datasets demonstrate that BioBGT outperforms state-of-the-art models, enhancing biologically plausible brain graph representations for various brain graph analytical tasks","url_abs":"https://arxiv.org/abs/2502.08958v1","url_pdf":"https://arxiv.org/pdf/2502.08958v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"biologically-plausible-brain-graph","repo_url":"https://github.com/pcyyyy/BioBGT","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[],"methods":[{"method_slug":"absolute-position-encodings","method_name":"Absolute Position Encodings"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"graph-transformer","method_name":"Graph Transformer"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"lapeigen","method_name":"LapEigen"},{"method_slug":"laplacian-pe","method_name":"Laplacian PE"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"position-wise-feed-forward-layer","method_name":"Position-Wise Feed-Forward Layer"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"transformer","method_name":"Transformer"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2502.08958","atlas_url":"https://app.syntology.ai/?focus=2502.08958","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2502.08958"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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