5 papers
Evolutionary Profiles for Protein Fitness Prediction
Jigang Fan, Xiaoran Jiao, Shengdong Lin +5
Predicting the fitness impact of mutations is central to protein engineering but constrained by limited assays relative to the size of sequence space. Protein language models (pLMs…
TriAttention: Efficient Long Reasoning with Trigonometric KV Compression
Weian Mao, Xi Lin, Wei Huang +5
Extended reasoning in large language models (LLMs) creates severe KV cache memory bottlenecks. Leading KV cache compression methods estimate KV importance using attention scores fr…
scPPDM: A Diffusion Model for Single-Cell Drug-Response Prediction
Zhaokang Liang, Shuyang Zhuang, Xiaoran Jiao +3
This paper introduces the Single-Cell Perturbation Prediction Diffusion Model (scPPDM), the first diffusion-based framework for single-cell drug-response prediction from scRNA-seq…
Revisiting Convolution Architecture in the Realm of DNA Foundation Models
Yu Bo, Weian Mao, Yanjun Shao +6
In recent years, a variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there…
Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions
Xiaoran Jiao, Weian Mao, Wengong Jin +3
Predicting the change in binding free energy () is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarc…