3 papers
q-bio.BM2026
TopoLIA: Topology-Inspired Latent Interaction Attention for Drug Discovery
Xiang Liu, Yiming Ren, Mustafa Hajij +2
The growing sophistication of drug discovery calls for new advances in artificial intelligence (AI). Transformers have underpinned recent breakthroughs in AI, yet their conventiona…
q-bio.QM2025
Fast and Interpretable Protein Substructure Alignment via Optimal Transport
Zhiyu Wang, Bingxin Zhou, Jing Wang +4
Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure…
cs.LG2025
Topotein: Topological Deep Learning for Protein Representation Learning
Zhiyu Wang, Arian Jamasb, Mustafa Hajij +3
Protein representation learning (PRL) is crucial for understanding structure-function relationships, yet current sequence- and graph-based methods fail to capture the hierarchical…