Jianzhu Ma

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 75

Top Topics

Top Venues

Publications

Shitong Luo, Wenhao Gao, Zuofan Wu, Jian Peng, Connor W. Coley, Jianzhu Ma
Projecting Molecules into Synthesizable Chemical Spaces. CoRR (2024)
Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, Zihao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang
Selecting Large Language Model to Fine-tune via Rectified Scaling Law. CoRR (2024)
Ruidong Wu, Ruihan Guo, Rui Wang, Shitong Luo, Yue Xu, Jiahan Li, Jianzhu Ma, Qiang Liu, Yunan Luo, Jian Peng
FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames. CoRR (2024)
Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma, Qiang Liu, Liang Wang, Quanquan Gu
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design. CoRR (2024)
Xingchao Liu, Xiwen Zhang, Jianzhu Ma, Jian Peng, Qiang Liu
InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation. ICLR (2024)
Jiahan Li, Chaoran Cheng, Zuofan Wu, Ruihan Guo, Shitong Luo, Zhizhou Ren, Jian Peng, Jianzhu Ma
Full-Atom Peptide Design based on Multi-modal Flow Matching. CoRR (2024)
Yijie Wang, Yuan Zhou, Xiaoqing Huang, Kun Huang, Jie Zhang, Jianzhu Ma
Learning Sparse Group Models Through Boolean Relaxation. ICLR (2023)
Xingang Peng, Jiaqi Guan, Qiang Liu, Jianzhu Ma
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation. CoRR (2023)
Ruiyang Chen, Yingheng Tang, Jianzhu Ma, Weilu Gao
Scientific Computing with Diffractive Optical Neural Networks. Adv. Intell. Syst. 5 (12) (2023)
Jieming Cui, Ziren Gong, Baoxiong Jia, Siyuan Huang, Zilong Zheng, Jianzhu Ma, Yixin Zhu
ProBio: A Protocol-guided Multimodal Dataset for Molecular Biology Lab. CoRR (2023)
Xingchao Liu, Xiwen Zhang, Jianzhu Ma, Jian Peng, Qiang Liu
InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation. CoRR (2023)
Ruiyang Chen, Yingheng Tang, Jianzhu Ma, Weilu Gao
Scientific Computing with Diffractive Optical Neural Networks. CoRR (2023)
Jiaqi Guan, Xingang Peng, Peiqi Jiang, Yunan Luo, Jian Peng, Jianzhu Ma
LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion. NeurIPS (2023)
Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma, Qiang Liu, Liang Wang, Quanquan Gu
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design. ICML (2023)
Jieming Cui, Ziren Gong, Baoxiong Jia, Siyuan Huang, Zilong Zheng, Jianzhu Ma, Yixin Zhu
ProBio: A Protocol-guided Multimodal Dataset for Molecular Biology Lab. NeurIPS (2023)
Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. CoRR (2023)
Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang
Boosting the Cycle Counting Power of Graph Neural Networks with I$^2$-GNNs. ICLR (2023)
Xingang Peng, Yipin Lei, Peiyuan Feng, Lemei Jia, Jianzhu Ma, Dan Zhao, Jianyang Zeng
Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. Nat. Mac. Intell. 5 (4) (2023)
Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction. ICLR (2023)
Haowei Lin, Zihao Wang, Jianzhu Ma, Yitao Liang
MCU: A Task-centric Framework for Open-ended Agent Evaluation in Minecraft. CoRR (2023)
Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. NeurIPS (2023)
Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li
Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration. Bioinform. 39 (4) (2023)
Shitong Luo, Yufeng Su, Zuofan Wu, Chenpeng Su, Jian Peng, Jianzhu Ma
Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction. ICLR (2023)
Addie Woicik, Mingxin Zhang, Janelle Chan, Jianzhu Ma, Sheng Wang
Extrapolating heterogeneous time-series gene expression data using Sagittarius. Nat. Mac. Intell. 5 (7) (2023)
Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction. CoRR (2023)
Xingang Peng, Jiaqi Guan, Qiang Liu, Jianzhu Ma
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation. ICML (2023)
Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang, Sheng Wang
scPretrain: multi-task self-supervised learning for cell-type classification. Bioinform. 38 (6) (2022)
Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang
3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design. CoRR (2022)
Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma
Equivariant Point Cloud Analysis via Learning Orientations for Message Passing. CVPR (2022)
Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng, Jianzhu Ma
Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data. Briefings Bioinform. 23 (5) (2022)
Jiaqi Guan, Wesley Wei Qian, Qiang Liu, Wei-Ying Ma, Jianzhu Ma, Jian Peng
Energy-Inspired Molecular Conformation Optimization. ICLR (2022)
Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets. ICML (2022)
Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma
Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation. NeurIPS (2022)
Yingheng Tang, Princess Tara Zamani, Ruiyang Chen, Jianzhu Ma, Minghao Qi, Cunxi Yu, Weilu Gao
Device-system Co-design of Photonic Neuromorphic Processor using Reinforcement Learning. CoRR (2022)
Yubo Shao, Kaikai Zhao, Zhiwen Cao, Zhehao Peng, Xingang Peng, Pan Li, Yijie Wang, Jianzhu Ma
MobilePrune: Neural Network Compression via ℓ0 Sparse Group Lasso on the Mobile System. Sensors 22 (11) (2022)
Juan Shu, Bowei Xi, Yu Li, Fan Wu, Charles A. Kamhoua, Jianzhu Ma
Understanding Dropout for Graph Neural Networks. WWW (Companion Volume) (2022)
Zhizhou Ren, Jiahan Li, Fan Ding, Yuan Zhou, Jianzhu Ma, Jian Peng
Proximal Exploration for Model-guided Protein Sequence Design. ICML (2022)
Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma
Equivariant Point Cloud Analysis via Learning Orientations for Message Passing. CoRR (2022)
Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas J. Guibas, Jian Peng, Jianzhu Ma
Directed Weight Neural Networks for Protein Structure Representation Learning. CoRR (2022)
Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang
-GNNs. CoRR (2022)
Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng
A 3D Molecule Generative Model for Structure-Based Drug Design. CoRR (2022)
Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures. NeurIPS (2022)
Fan Ding, Yijie Wang, Jianzhu Ma, Yexiang Xue
Provable Constrained Stochastic Convex Optimization with XOR-Projected Gradient Descent. CoRR (2022)
Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets. CoRR (2022)
Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma, Satish V. Ukkusuri
Multiwave COVID-19 Prediction from Social Awareness Using Web Search and Mobility Data. KDD (2022)
Yingheng Tang, Jichao Fan, Xinwei Li, Jianzhu Ma, Minghao Qi, Cunxi Yu, Weilu Gao
Physics-informed recurrent neural network for time dynamics in optical resonances. Nat. Comput. Sci. 2 (3) (2022)
Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma
Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation. CoRR (2022)
Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang
3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design. ICML (2022)
Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Takahiro Yabe, Satish V. Ukkusuri, Jianzhu Ma
Quantifying the spatial homogeneity of urban road networks via graph neural networks. Nat. Mach. Intell. 4 (3) (2022)
Yunyu Liu, Jianzhu Ma, Pan Li
Neural Predicting Higher-order Patterns in Temporal Networks. WWW (2022)
Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma, Satish V. Ukkusuri
Multiwave COVID-19 Prediction via Social Awareness-Based Graph Neural Networks using Mobility and Web Search Data. CoRR (2021)
Andersen Man Shun Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang
Fast Projection onto the Capped Simplex with Applications to Sparse Regression in Bioinformatics. NeurIPS (2021)
Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Satish V. Ukkusuri, Jianzhu Ma
Quantifying spatial homogeneity of urban road networks via graph neural networks. CoRR (2021)
Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue
PALM: Probabilistic area loss Minimization for Protein Sequence Alignment. UAI (2021)
Xuesong Wang, Zhihang Hu, Tingyang Yu, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li
Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration. CoRR (2021)
Fan Ding, Jianzhu Ma, Jinbo Xu, Yexiang Xue
XOR-CD: Linearly Convergent Constrained Structure Generation. ICML (2021)
Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng
A 3D Generative Model for Structure-Based Drug Design. NeurIPS (2021)
Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma
Modeling gene regulatory networks using neural network architectures. Nat. Comput. Sci. 1 (7) (2021)
Yunyu Liu, Jianzhu Ma, Pan Li
Neural Higher-order Pattern (Motif) Prediction in Temporal Networks. CoRR (2021)
Juan Shu, Yu Li, Sheng Wang, Bowei Xi, Jianzhu Ma
Disease gene prediction with privileged information and heteroscedastic dropout. Bioinform. 37 (Supplement) (2021)
Andersen Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang
Fast Projection onto the Capped Simplex withApplications to Sparse Regression in Bioinformatics. CoRR (2021)
Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li, Jianzhu Ma
Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns. CoRR (2021)
Peiyuan Feng, Jianyang Zeng, Jianzhu Ma
Predicting MHC-peptide binding affinity by differential boundary tree. Bioinform. 37 (Supplement) (2021)
Yubo Shao, Tinghan Yang, He Wang, Jianzhu Ma
AirSign: Smartphone Authentication by Signing in the Air. Sensors 21 (1) (2021)
Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li, Jianzhu Ma
Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns. KDD (2021)
Yunan Luo, Jian Peng, Jianzhu Ma
When causal inference meets deep learning. Nat. Mach. Intell. 2 (8) (2020)
Qiuyu Lian, Hongyi Xin, Jianzhu Ma, Liza Konnikova, Wei Chen, Jin Gu, Kong Chen
Artificial-cell-type aware cell-type classification in CITE-seq. Bioinform. 36 (Supplement-1) (2020)
Wei Zhang, Jianzhu Ma, Trey Ideker
Classifying tumors by supervised network propagation. Bioinform. 35 (14) (2019)
Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng
Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. RECOMB (2019)
Wei Zhang, Jianzhu Ma, Trey Ideker
Classifying tumors by supervised network propagation. Bioinform. 34 (13) (2018)
Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng
Deciphering Signaling Specificity with Deep Neural Networks. RECOMB (2018)
Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker
Annotating gene sets by mining large literature collections with protein networks. PSB (2018)
Mingfu Shao, Jianzhu Ma, Sheng Wang
DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields. Bioinform. 33 (14) (2017)
Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu
ModuleAlign: module-based global alignment of protein-protein interaction networks. Bioinform. 32 (17) (2016)
Sheng Wang, Jianzhu Ma, Jinbo Xu
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. Bioinform. 32 (17) (2016)
Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage. BCB (2015)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. Bioinform. 31 (21) (2015)
Jianzhu Ma, Feng Zhao, Jinbo Xu
Structure Learning Constrained by Node-Specific Degree Distribution. UAI (2015)
Jianzhu Ma
Protein Structure Prediction by Protein Alignments. CoRR (2015)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning. RECOMB (2015)
Siqi Sun, Jianzhu Ma, Sheng Wang, Jinbo Xu
Predicting diverse M-best protein contact maps. BIBM (2015)
Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
Protein secondary structure prediction using deep convolutional neural fields. CoRR (2015)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. RECOMB (2014)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. PLoS Comput. Biol. 10 (3) (2014)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. CoRR (2014)
Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu
Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling. AISTATS (2013)
Jianzhu Ma, Sheng Wang, Feng Zhao, Jinbo Xu
Protein threading using context-specific alignment potential. Bioinform. 29 (13) (2013)
Jianzhu Ma, Sheng Wang, Jinbo Xu
Protein contact prediction by joint evolutionary coupling analysis across multiple families. CoRR (2013)
Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu
A conditional neural fields model for protein threading. Bioinform. 28 (12) (2012)
Jiyu Huang, Xuanzhe Liu, Qi Zhao, Jianzhu Ma, Gang Huang
A browser-based framework for data cache in Web-delivered service composition. SOCA (2010)