5 papers · 1 filter
Structure-Aligned Protein Language Model
Can Chen, David Heurtel-Depeiges, Robert M. Vernon +3
Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but often lack the structural knowledge essential for some biologica…
Lower Ricci Curvature for Hypergraphs
Shiyi Yang, Can Chen, Didong Li
Networks with higher-order interactions, prevalent in biological, social, and information systems, are naturally represented as hypergraphs, yet their structural complexity poses f…
Design Editing for Offline Model-based Optimization
Ye Yuan, Youyuan Zhang, Can Chen +5
Offline model-based optimization (MBO) aims to maximize a black-box objective function using only an offline dataset of designs and scores. These tasks span various domains, such a…
ParetoFlow: Guided Flows in Multi-Objective Optimization
Ye Yuan, Can Chen, Christopher Pal +1
In offline multi-objective optimization (MOO), we leverage an offline dataset of designs and their associated labels to simultaneously minimize multiple objectives. This setting mo…
AffinityFlow: Guided Flows for Antibody Affinity Maturation
Can Chen, Karla-Luise Herpoldt, Chenchao Zhao +4
Antibodies are widely used as therapeutics, but their development requires costly affinity maturation, involving iterative mutations to enhance binding affinity.This paper explores…