1 citations · 2 across the 13 of their papers we have counts for
15 papers
CARD: Coarse-to-fine Autoregressive Modeling with Radix-based Decomposition for Transferable Free Energy Estimation
Ziyang Yu, Yi He, Wenbing Huang +2
Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, exis…
Lingshu-Cell: A generative cellular world model for transcriptome modeling toward virtual cells
Han Zhang, Guo-Hua Yuan, Chaohao Yuan +6
Modeling cellular states and predicting their responses to perturbations are central challenges in computational biology and the development of virtual cells. Existing foundation m…
Recurrent Reasoning with Vision-Language Models for Estimating Long-Horizon Embodied Task Progress
Yuelin Zhang, Sijie Cheng, Chen Li +4
Accurately estimating task progress is critical for embodied agents to plan and execute long-horizon, multi-step tasks. Despite promising advances, existing Vision-Language Models…
Experimental Powder X-ray Diffraction Crystal Structure Determination with RealPXRD-Solver
Qi Li, Mingyu Guo, Rui Jiao +14
Determining crystal structures from experimental powder X-ray diffraction data remains challenging because peak overlap, preferred orientation, and impurity phases obscure atomic a…
Unified Biomolecular Trajectory Generation via Pretrained Variational Bridge
Ziyang Yu, Wenbing Huang, Yang Liu
Molecular Dynamics (MD) simulations provide a fundamental tool for characterizing molecular behavior at full atomic resolution, but their applicability is severely constrained by t…
DMFlow: Disordered Materials Generation by Flow Matching
Liming Wu, Rui Jiao, Qi Li +4
The design of materials with tailored properties is crucial for technological progress. However, most deep generative models focus exclusively on perfectly ordered crystals, neglec…
Equivariant Diffusion for Crystal Structure Prediction
Peijia Lin, Pin Chen, Rui Jiao +6
In addressing the challenge of Crystal Structure Prediction (CSP), symmetry-aware deep learning models, particularly diffusion models, have been extensively studied, which treat CS…
Learning 3D Anisotropic Noise Distributions Improves Molecular Force Field Modeling
Xixian Liu, Rui Jiao, Zhiyuan Liu +6
Coordinate denoising has emerged as a promising method for 3D molecular pretraining due to its theoretical connection to learning molecular force field. However, existing denoising…
Latent Retrieval Augmented Generation of Cross-Domain Protein Binders
Zishen Zhang, Xiangzhe Kong, Wenbing Huang +1
Designing protein binders targeting specific sites, which requires to generate realistic and functional interaction patterns, is a fundamental challenge in drug discovery. Current…
Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints
Dapeng Jiang, Xiangzhe Kong, Jiaqi Han +6
Cyclic peptides, characterized by geometric constraints absent in linear peptides, offer enhanced biochemical properties, presenting new opportunities to address unmet medical need…
UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules
Ziyang Yu, Wenbing Huang, Yang Liu
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However…
StableToolBench-MirrorAPI: Modeling Tool Environments as Mirrors of 7,000+ Real-World APIs
Zhicheng Guo, Sijie Cheng, Yuchen Niu +4
The rapid advancement of large language models (LLMs) has spurred significant interest in tool learning, where LLMs are augmented with external tools to tackle complex tasks. Howev…
UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design
Xiangzhe Kong, Zishen Zhang, Ziting Zhang +5
The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restr…
Siamese Foundation Models for Crystal Structure Prediction
Liming Wu, Wenbing Huang, Rui Jiao +8
Predicting crystal structures from chemical compositions is a fundamental challenge in materials discovery, complicated by complex 3D geometries that distinguish it from fields lik…
Powder Diffraction Crystal Structure Determination Using Generative Models
Qi Li, Rui Jiao, Liming Wu +6
Accurate crystal structure determination is critical across all scientific disciplines involving crystalline materials. However, solving and refining inorganic crystal structures f…