From the 1 of 7 linked papers with an AI index.
7 papers
SinAE: A Single-Architecture Flow-Matching Autoencoder for Cross-Domain Atomic Systems
Yuxuan Ren, Fan Yang, Jianhua Yao +1
SinAE is a unified Transformer-based autoencoder that uses flow-matching decoding to reconstruct and generate atomic structures across molecules, crystals, and proteins with near-l…
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…
Riemannian Dueling Optimization
Yuxuan Ren, Abhishek Roy, Shiqian Ma
Dueling optimization considers optimizing an objective with access to only a comparison oracle of the objective function. It finds important applications in emerging fields such as…
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…
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…