arXiv:2605.29158v1 Announce Type: new Abstract: Protein homology search underlies function annotation, structure prediction, and evolutionary analysis, but remains challenging in the "twilight zone," where global sequence similarity is weak and classical alignment methods lose sensitivity. Protein language models provide context-aware representations that could improve alignment sensitivity in this regime. However, prior protein embedding-based retrieval pipelines often pool these representations into a single vector, potentially obscuring local motifs, domains, or conserved residues that reve
Source: arXiv cs.LG — read the full report at the original publisher.