9 citations · 15 across the 20 of their papers we have counts for
8 papers · 1 filter
NoiseRater: Meta-Learned Noise Valuation for Diffusion Model Training
Fang Wu, Haokai Zhao, Da Xing +18
Training a diffusion model involves two sources of randomness for each data sample: the timestep and the Gaussian noise realization. The timestep has been studied extensively throu…
Proteo-R1: Reasoning Foundation Models for De Novo Protein Design
Fang Wu, Weihao Xuan, Heli Qi +26
Deep learning in de novo protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries…
RiboSphere: Learning Unified and Efficient Representations of RNA Structures
Zhou Zhang, Hanqun Cao, Cheng Tan +3
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures a…
From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?
Hanqun Cao, Hongrui Zhang, Junde Xu +12
Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has…
A deep reinforcement learning platform for antibiotic discovery
Hanqun Cao, Marcelo D. T. Torres, Jingjie Zhang +8
Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here we present ApexAmphion, a deep…
Position: The Hidden Costs and Measurement Gaps of Reinforcement Learning with Verifiable Rewards
Fang Wu, Aaron Tu, Weihao Xuan +21
Reinforcement learning with verifiable rewards (RLVR) is a practical, scalable way to improve large language models on math, code, and other structured tasks. However, we argue tha…
Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings
Hanqun Cao, Xinyi Zhou, Zijun Gao +7
Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA desi…
DEL-Ranking: Ranking-Correction Denoising Framework for Elucidating Molecular Affinities in DNA-Encoded Libraries
Hanqun Cao, Mutian He, Ning Ma +3
DNA-encoded library (DEL) screening has revolutionized the detection of protein-ligand interactions through read counts, enabling rapid exploration of vast chemical spaces. However…