Ma, Jianzhu

40 publications

ICML 2025 Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling Xiangxin Zhou, Mingyu Li, Yi Xiao, Jiahan Li, Dongyu Xue, Zaixiang Zheng, Jianzhu Ma, Quanquan Gu

ICLR 2025 Group Ligands Docking to Protein Pockets Jiaqi Guan, Jiahan Li, Xiangxin Zhou, Xingang Peng, Sheng Wang, Yunan Luo, Jian Peng, Jianzhu Ma

ICLR 2025 Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension Jiahan Li, Tong Chen, Shitong Luo, Chaoran Cheng, Jiaqi Guan, Ruihan Guo, Sheng Wang, Ge Liu, Jian Peng, Jianzhu Ma

ICLR 2025 Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows Xiangxin Zhou, Yi Xiao, Haowei Lin, Xinheng He, Jiaqi Guan, Yang Wang, Qiang Liu, Feng Zhou, Liang Wang, Jianzhu Ma

ICML 2025 Safety-Polarized and Prioritized Reinforcement Learning Ke Fan, Jinpeng Zhang, Xuefeng Zhang, Yunze Wu, Jingyu Cao, Yuan Zhou, Jianzhu Ma

ICLR 2025 TFG-Flow: Training-Free Guidance in Multimodal Generative Flow Haowei Lin, Shanda Li, Haotian Ye, Yiming Yang, Stefano Ermon, Yitao Liang, Jianzhu Ma

ICML 2025 UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design Xiangzhe Kong, Zishen Zhang, Ziting Zhang, Rui Jiao, Jianzhu Ma, Wenbing Huang, Kai Liu, Yang Liu

ICML 2025 Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints Dapeng Jiang, Xiangzhe Kong, Jiaqi Han, Mingyu Li, Rui Jiao, Wenbing Huang, Stefano Ermon, Jianzhu Ma, Yang Liu

NeurIPS 2024 Enhancing Protein Mutation Effect Prediction Through a Retrieval-Augmented Framework Ruihan Guo, Rui Wang, Ruidong Wu, Zhizhou Ren, Jiahan Li, Shitong Luo, Zuofan Wu, Qiang Liu, Jian Peng, Jianzhu Ma

ICML 2024 FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames Ruidong Wu, Ruihan Guo, Rui Wang, Shitong Luo, Yue Xu, Jiahan Li, Jianzhu Ma, Qiang Liu, Yunan Luo, Jian Peng

ICML 2024 Full-Atom Peptide Design Based on Multi-Modal Flow Matching Jiahan Li, Chaoran Cheng, Zuofan Wu, Ruihan Guo, Shitong Luo, Zhizhou Ren, Jian Peng, Jianzhu Ma

ICLR 2024 InstaFlow: One Step Is Enough for High-Quality Diffusion-Based Text-to-Image Generation Xingchao Liu, Xiwen Zhang, Jianzhu Ma, Jian Peng, Qiang Liu

ICML 2024 Projecting Molecules into Synthesizable Chemical Spaces Shitong Luo, Wenhao Gao, Zuofan Wu, Jian Peng, Connor W. Coley, Jianzhu Ma

NeurIPS 2024 Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design Xiangxin Zhou, Jiaqi Guan, Yijia Zhang, Xingang Peng, Liang Wang, Jianzhu Ma

ICML 2024 Selecting Large Language Model to Fine-Tune via Rectified Scaling Law Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, Zihao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang

ICLRW 2024 Selecting Large Language Model to Fine-Tune via Rectified Scaling Law Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, Zihao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang

NeurIPS 2024 TFG: Unified Training-Free Guidance for Diffusion Models Haotian Ye, Haowei Lin, Jiaqi Han, Minkai Xu, Sheng Liu, Yitao Liang, Jianzhu Ma, James Zou, Stefano Ermon

ICLR 2023 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma

ICLR 2023 Boosting the Cycle Counting Power of Graph Neural Networks with I$^2$-GNNs Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang

ICML 2023 DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma, Qiang Liu, Liang Wang, Quanquan Gu

ICLR 2023 Learning Sparse Group Models Through Boolean Relaxation Yijie Wang, Yuan Zhou, Xiaoqing Huang, Kun Huang, Jie Zhang, Jianzhu Ma

NeurIPS 2023 LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion Jiaqi Guan, Xingang Peng, PeiQi Jiang, Yunan Luo, Jian Peng, Jianzhu Ma

NeurIPSW 2023 MCU: A Task-Centric Framework for Open-Ended Agent Evaluation in Minecraft Haowei Lin, Zihao Wang, Jianzhu Ma, Yitao Liang

ICML 2023 MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation Xingang Peng, Jiaqi Guan, Qiang Liu, Jianzhu Ma

NeurIPS 2023 ProBio: A Protocol-Guided Multimodal Dataset for Molecular Biology Lab Jieming Cui, Ziren Gong, Baoxiong Jia, Siyuan Huang, Zilong Zheng, Jianzhu Ma, Yixin Zhu

ICLR 2023 Rotamer Density Estimator Is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction Shitong Luo, Yufeng Su, Zuofan Wu, Chenpeng Su, Jian Peng, Jianzhu Ma

NeurIPS 2023 xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song

ICML 2022 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang

NeurIPS 2022 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma

NeurIPS 2022 Efficient Meta Reinforcement Learning for Preference-Based Fast Adaptation Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma

ICLR 2022 Energy-Inspired Molecular Conformation Optimization Jiaqi Guan, Wesley Wei Qian, Qiang Liu, Wei-Ying Ma, Jianzhu Ma, Jian Peng

CVPR 2022 Equivariant Point Cloud Analysis via Learning Orientations for Message Passing Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma

ICML 2022 Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma

ICML 2022 Proximal Exploration for Model-Guided Protein Sequence Design Zhizhou Ren, Jiahan Li, Fan Ding, Yuan Zhou, Jianzhu Ma, Jian Peng

NeurIPS 2021 A 3D Generative Model for Structure-Based Drug Design Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng

NeurIPS 2021 Fast Projection onto the Capped Simplex with Applications to Sparse Regression in Bioinformatics Man Shun Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang

UAI 2021 PALM: Probabilistic Area Loss Minimization for Protein Sequence Alignment Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue

ICML 2021 XOR-CD: Linearly Convergent Constrained Structure Generation Fan Ding, Jianzhu Ma, Jinbo Xu, Yexiang Xue

UAI 2015 Structure Learning Constrained by Node-Specific Degree Distribution Jianzhu Ma, Feng Zhao, Jinbo Xu

AISTATS 2013 Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu