5 papers
Retrieval-Augmented Multimodal Learning for Enzyme-Substrate Interaction Prediction Under Low-Homology Shift
Chen Liu, Bingxin Zhou, Xinyuan Wang +3
Enzyme substrate interaction (ESI) prediction is a fundamental computational task for biocatalyst discovery and reaction screening in large biochemical spaces. In practical setting…
Rank-and-Reason: Multi-Agent Collaboration Accelerates Zero-Shot Protein Mutation Prediction
Yang Tan, Yuanxi Yu, Can Wu +7
Zero-shot mutation prediction is vital for low-resource protein engineering, yet existing protein language models (PLMs) often yield statistically confident results that ignore fun…
Sequence-Only Prediction of Binding Affinity Changes: A Robust and Interpretable Model for Antibody Engineering
Chen Liu, Mingchen Li, Yang Tan +3
A pivotal area of research in antibody engineering is to find effective modifications that enhance antibody-antigen binding affinity. Traditional wet-lab experiments assess mutants…
An extensive simulation study evaluating the interaction of resampling techniques across multiple causal discovery contexts
Ritwick Banerjee, Bryan Andrews, Erich Kummerfeld
Despite the accelerating presence of exploratory causal analysis in modern science and medicine, the available non-experimental methods for validating causal models are not well ch…
A PLMs based protein retrieval framework
Yuxuan Wu, Xiao Yi, Yang Tan +3
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search…