Shirin Amiraslani

Shirin Amiraslani, Xin Gao

Transformer self-attention computes pairwise token interactions, yet protein sequence to phenotype relationships often involve cooperative dependencies among three or more residues that dot product attention does not capture explicitly. We introduce Higher-Order Modular Attention, HOMA, a unified attention operator that fuses pairwise attention with an explicit triadic interaction pathway. To make triadic attention practical on long sequences, HOMA employs block-structured, windowed triadic attention. We evaluate on three TAPE benchmarks for Secondary Structure, Fluorescence, and Stability. Our attention mechanism yields consistent improvements across all tasks compared with standard self-attention and efficient variants including block-wise attention and Linformer. These results suggest that explicit triadic terms provide complementary representational capacity for protein sequence prediction at controllable additional computational cost.

Xin Gao, Xingming Xu, Shirin Amiraslani et al.

The Transformer, with its scaled dot-product attention mechanism, has become a foundational architecture in modern AI. However, this mechanism is computationally intensive and incurs substantial energy costs. We propose a new Transformer architecture EcoTransformer, in which the output context vector is constructed as the convolution of the values using a Laplacian kernel, where the distances are measured by the L1 metric between the queries and keys. Compared to dot-product based attention, the new attention score calculation is free of matrix multiplication. It performs on par with, or even surpasses, scaled dot-product attention in NLP, bioinformatics, and vision tasks, while consuming significantly less energy. (This version (v2) supersedes v1 and reflects the intended release and licensing.)