6 papers
Tokenizing Electron Cloud in Protein-Ligand Interaction Learning
Haitao Lin, Odin Zhang, Jia Xu +6
The affinity and specificity of protein-molecule binding directly impact functional outcomes, uncovering the mechanisms underlying biological regulation and signal transduction. Mo…
A Survey on Mixup Augmentations and Beyond
Xin Jin, Hongyu Zhu, Siyuan Li +6
As Deep Neural Networks have achieved thrilling breakthroughs in the past decade, data augmentations have garnered increasing attention as regularization techniques when massive la…
A Simple yet Effective DDG Predictor is An Unsupervised Antibody Optimizer and Explainer
Lirong Wu, Yunfan Liu, Haitao Lin +4
The proteins that exist today have been optimized over billions of years of natural evolution, during which nature creates random mutations and selects them. The discovery of funct…
FlowTS: Time Series Generation via Rectified Flow
Yang Hu, Xiao Wang, Zezhen Ding +7
Diffusion-based models have significant achievements in time series generation but suffer from inefficient computation: solving high-dimensional ODEs/SDEs via iterative numerical s…
PPFlow: Target-aware Peptide Design with Torsional Flow Matching
Haitao Lin, Odin Zhang, Huifeng Zhao +5
Therapeutic peptides have proven to have great pharmaceutical value and potential in recent decades. However, methods of AI-assisted peptide drug discovery are not fully explored.…
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
Haitao Lin, Guojiang Zhao, Odin Zhang +7
Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. How…