4 citations · 14 across the 10 of their papers we have counts for
11 papers
Joint Discrete and SE(3) Diffusion for Protein Interface Design
Zhenqiao Song, Jianwen Xie, Lei Li
The design of high-affinity, target-specific protein binders is central to the development of modern therapeutics. However, existing protein-generation methods remain limited in th…
PPDiff: Diffusing in Hybrid Sequence-Structure Space for Protein-Protein Complex Design
Zhenqiao Song, Tiaoxiao Li, Lei Li +1
Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to…
InstructPro: Natural Language Guided Ligand-Binding Protein Design
Zhenqiao Song, Ramith Hettiarachchi, Chuan Li +2
The de novo design of ligand-binding proteins with tailored functions is essential for advancing biotechnology and molecular medicine, yet existing AI approaches are limited by sca…
SurfPro: Functional Protein Design Based on Continuous Surface
Zhenqiao Song, Tinglin Huang, Lei Li +1
How can we design proteins with desired functions? We are motivated by a chemical intuition that both geometric structure and biochemical properties are critical to a protein's fun…
Generative Enzyme Design Guided by Functionally Important Sites and Small-Molecule Substrates
Zhenqiao Song, Yunlong Zhao, Wenxian Shi +3
Enzymes are genetically encoded biocatalysts capable of accelerating chemical reactions. How can we automatically design functional enzymes? In this paper, we propose EnzyGen, an a…
Hire a Linguist!: Learning Endangered Languages with In-Context Linguistic Descriptions
Kexun Zhang, Yee Man Choi, Zhenqiao Song +3
How can large language models (LLMs) process and translate endangered languages? Many languages lack a large corpus to train a decent LLM; therefore existing LLMs rarely perform we…
Joint Design of Protein Sequence and Structure based on Motifs
Zhenqiao Song, Yunlong Zhao, Yufei Song +3
Designing novel proteins with desired functions is crucial in biology and chemistry. However, most existing work focus on protein sequence design, leaving protein sequence and stru…
Functional Geometry Guided Protein Sequence and Backbone Structure Co-Design
Zhenqiao Song, Yunlong Zhao, Wenxian Shi +2
Proteins are macromolecules responsible for essential functions in almost all living organisms. Designing reasonable proteins with desired functions is crucial. A protein's sequenc…
INSTRUCTSCORE: Explainable Text Generation Evaluation with Finegrained Feedback
Wenda Xu, Danqing Wang, Liangming Pan +4
Automatically evaluating the quality of language generation is critical. Although recent learned metrics show high correlation with human judgement, these metrics can not explain t…
Importance Weighted Expectation-Maximization for Protein Sequence Design
Zhenqiao Song, Lei Li
Designing protein sequences with desired biological function is crucial in biology and chemistry. Recent machine learning methods use a surrogate sequence-function model to replace…
MTG: A Benchmark Suite for Multilingual Text Generation
Yiran Chen, Zhenqiao Song, Xianze Wu +5
We introduce MTG, a new benchmark suite for training and evaluating multilingual text generation. It is the first-proposed multilingual multiway text generation dataset with the la…