5 citations · 6 across the 8 of their papers we have counts for
6 papers · 1 filter
SinAE: A Single-Architecture Flow-Matching Autoencoder for Cross-Domain Atomic Systems
Yuxuan Ren, Fan Yang, Jianhua Yao +1
Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its Small molecules, crystals, a…
Kempe Swap K-Means: A Scalable Near-Optimal Solution for Semi-Supervised Clustering
Yuxuan Ren, Shijie Deng
This paper presents a novel centroid-based heuristic algorithm, termed Kempe Swap K-Means, for constrained clustering under rigid must-link (ML) and cannot-link (CL) constraints. T…
EPO: Diverse and Realistic Protein Ensemble Generation via Energy Preference Optimization
Yuancheng Sun, Yuxuan Ren, Zhaoming Chen +3
Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computat…
Physical Consistency Bridges Heterogeneous Data in Molecular Multi-Task Learning
Yuxuan Ren, Dihan Zheng, Chang Liu +7
In recent years, machine learning has demonstrated impressive capability in handling molecular science tasks. To support various molecular properties at scale, machine learning mod…
Constraint Decoupled Latent Diffusion for Protein Backmapping
Xu Han, Yuancheng Sun, Kai Chen +3
Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (back…
Neural PM: A Long-Range Interaction Modeling Enhancer for Geometric GNNs
Yusong Wang, Chaoran Cheng, Shaoning Li +5
Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range inter…