7 papers
Smoothing Dark Areas in Molecular Latent Diffusion
Xi Wang, Jiahan Li, Yuxuan Xia +3
Latent diffusion is a promising framework for scalable 3D molecular generation, but it requires a latent space that remains smooth, valid, and navigable beyond posterior samples. E…
Categorical Flow Matching on Statistical Manifolds
Chaoran Cheng, Jiahan Li, Jian Peng +1
We introduce Statistical Flow Matching (SFM), a novel and mathematically rigorous flow-matching framework on the manifold of parameterized probability measures inspired by the resu…
Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling
Xiangxin Zhou, Mingyu Li, Yi Xiao +5
Cyclic peptides offer inherent advantages in pharmaceuticals. For example, cyclic peptides are more resistant to enzymatic hydrolysis compared to linear peptides and usually exhibi…
Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension
Jiahan Li, Tong Chen, Shitong Luo +7
Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generativ…
-Flow: A Unified Framework for Continuous-State Discrete Flow Matching Models
Chaoran Cheng, Jiahan Li, Jiajun Fan +1
Recent efforts have extended the flow-matching framework to discrete generative modeling. One strand of models directly works with the continuous probabilities instead of discrete…
Group Ligands Docking to Protein Pockets
Jiaqi Guan, Jiahan Li, Xiangxin Zhou +5
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, t…