Jianzhu Ma - RankMe

137 papers A* 39A 3B 6Misc 1Journal 83Unranked 4

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	HAIC: Humanoid Agile Object Interaction Control via Dynamics-Aware World Model. CoRR Dongting Li, Xingyu Chen, Qianyang Wu, Bo Chen, Sikai Wu, Hanyu Wu, Guoyao Zhang, Liang Li, Mingliang Zhou, Diyun Xiang, Jianzhu Ma, Qiang Zhang, Renjing Xu
2026	J	`jnl`	Learning Protein Structure Representation with Orientation-Aware Networks. J. Comput. Biol. Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas J. Guibas, Jian Peng, Jianzhu Ma
2026	J	`jnl`	VecMol: Vector-Field Representations for 3D Molecule Generation. CoRR Yuchen Hua, Xingang Peng, Jianzhu Ma, Muhan Zhang
2025	J	`jnl`	A Neural Symbolic Model for Space Physics. CoRR Jie Ying, Haowei Lin, Chao Yue, Yajie Chen, Chao Xiao, Quanqi Shi, Yitao Liang, Shing-Tung Yau, Yuan Zhou, Jianzhu Ma
2025	J	`jnl`	Data Mining in Transportation Networks with Graph Neural Networks: A Review and Outlook. CoRR Jiawei Xue, Ruichen Tan, Jianzhu Ma, Satish V. Ukkusuri
2025	A*	`conf`	Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling. ICML Xiangxin Zhou, Mingyu Li, Yi Xiao, Jiahan Li, Dongyu Xue, Zaixiang Zheng, Jianzhu Ma, Quanquan Gu
2025	J	`jnl`	Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling. CoRR Xiangxin Zhou, Mingyu Li, Yi Xiao, Jiahan Li, Dongyu Xue, Zaixiang Zheng, Jianzhu Ma, Quanquan Gu
2025	J	`jnl`	Escaping the Drug-Bias Trap: Using Debiasing Design to Improve Interpretability and Generalization of Drug-Target Interaction Prediction. IEEE Trans. Comput. Biol. Bioinform. Peidong Zhang, Jianzhu Ma, Ting Chen
2025	J	`jnl`	EvoSLD: Automated Neural Scaling Law Discovery With Large Language Models. CoRR Haowei Lin, Xiangyu Wang, Jianzhu Ma, Yitao Liang
2025	J	`jnl`	Generative Evaluation of Complex Reasoning in Large Language Models. CoRR Haowei Lin, Xiangyu Wang, Ruilin Yan, Baizhou Huang, Haotian Ye, Jianhua Zhu, Zihao Wang, James Zou, Jianzhu Ma, Yitao Liang
2025	A*	`conf`	Group Ligands Docking to Protein Pockets. ICLR Jiaqi Guan, Jiahan Li, Xiangxin Zhou, Xingang Peng, Sheng Wang, Yunan Luo, Jian Peng, Jianzhu Ma
2025	J	`jnl`	Group Ligands Docking to Protein Pockets. CoRR Jiaqi Guan, Jiahan Li, Xiangxin Zhou, Xingang Peng, Sheng Wang, Yunan Luo, Jian Peng, Jianzhu Ma
2025	A*	`conf`	Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension. ICLR Jiahan Li, Tong Chen, Shitong Luo, Chaoran Cheng, Jiaqi Guan, Ruihan Guo, Sheng Wang, Ge Liu, Jian Peng, Jianzhu Ma
2025	J	`jnl`	Inference-time Scaling of Diffusion Models through Classical Search. CoRR Xiangcheng Zhang, Haowei Lin, Haotian Ye, James Y. Zou, Jianzhu Ma, Yitao Liang, Yilun Du
2025	A*	`conf`	Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows. ICLR Xiangxin Zhou, Yi Xiao, Haowei Lin, Xinheng He, Jiaqi Guan, Yang Wang, Qiang Liu, Feng Zhou, Liang Wang, Jianzhu Ma
2025	J	`jnl`	Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows. CoRR Xiangxin Zhou, Yi Xiao, Haowei Lin, Xinheng He, Jiaqi Guan, Yang Wang, Qiang Liu, Feng Zhou, Liang Wang, Jianzhu Ma
2025	J	`jnl`	Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks. Briefings Bioinform. Lingsheng Cai, Xiuli Ma, Jianzhu Ma
2025	J	`jnl`	LiteAT: A Data-Lightweight and User-Adaptive VR Telepresence System for Remote Education. IEEE Trans. Vis. Comput. Graph. Yuxin Shen, Wei Liang, Jianzhu Ma
2025	J	`jnl`	MatterChat: A Multi-Modal LLM for Material Science. CoRR Yingheng Tang, Wenbin Xu, Jie Cao, Jianzhu Ma, Weilu Gao, Steven Farrell, N. Benjamin Erichson, Michael W. Mahoney, Andy Nonaka, Zhi Yao
2025	J	`jnl`	Morpheus: A Neural-Driven Animatronic Face with Hybrid Actuation and Diverse Emotion Control. Int. J. Artif. Intell. Robotics Res. Zongzheng Zhang, Jiawen Yang, Ziqiao Peng, Meng Yang, Jianzhu Ma, Lin Cheng, Huazhe Xu, Hang Zhao, Hao Zhao
2025	J	`jnl`	Morpheus: A Neural-driven Animatronic Face with Hybrid Actuation and Diverse Emotion Control. CoRR Zongzheng Zhang, Jiawen Yang, Ziqiao Peng, Meng Yang, Jianzhu Ma, Lin Cheng, Huazhe Xu, Hang Zhao, Hao Zhao
2025	B	`conf`	Orientation-Aware Networks for Protein Structure Representation Learning. RECOMB Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas J. Guibas, Jian Peng, Jianzhu Ma
2025	A*	`conf`	PUGS: Zero-Shot Physical Understanding with Gaussian Splatting. ICRA Yinghao Shuai, Ran Yu, Yuantao Chen, Zijian Jiang, Xiaowei Song, Nan Wang, Jv Zheng, Jianzhu Ma, Meng Yang, Zhicheng Wang, Wenbo Ding, Hao Zhao
2025	J	`jnl`	PUGS: Zero-shot Physical Understanding with Gaussian Splatting. CoRR Yinghao Shuai, Ran Yu, Yuantao Chen, Zijian Jiang, Xiaowei Song, Nan Wang, Jv Zheng, Jianzhu Ma, Meng Yang, Zhicheng Wang, Wenbo Ding, Hao Zhao
2025	J	`jnl`	Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding. CoRR Xinheng He, Yijia Zhang, Haowei Lin, Xingang Peng, Xiangzhe Kong, Mingyu Li, Jianzhu Ma
2025	J	`jnl`	Predicting Individual Irregular Mobility via Web Search-Driven Bipartite Graph Neural Networks. IEEE Trans. Knowl. Data Eng. Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma, Satish V. Ukkusuri
2025	B	`conf`	Rag2Mol: Structure-Based Drug Design Based on Retrieval Augmented Generation. RECOMB Peidong Zhang, Xingang Peng, Rong Han, Ting Chen, Jianzhu Ma
2025	J	`jnl`	Rag2Mol: structure-based drug design based on retrieval augmented generation. Briefings Bioinform. Peidong Zhang, Xingang Peng, Rong Han, Ting Chen, Jianzhu Ma
2025	A*	`conf`	Safety-Polarized and Prioritized Reinforcement Learning. ICML Ke Fan, Jinpeng Zhang, Xuefeng Zhang, Yunze Wu, Jingyu Cao, Yuan Zhou, Jianzhu Ma
2025	A*	`conf`	TFG-Flow: Training-free Guidance in Multimodal Generative Flow. ICLR Haowei Lin, Shanda Li, Haotian Ye, Yiming Yang, Stefano Ermon, Yitao Liang, Jianzhu Ma
2025	J	`jnl`	TFG-Flow: Training-free Guidance in Multimodal Generative Flow. CoRR Haowei Lin, Shanda Li, Haotian Ye, Yiming Yang, Stefano Ermon, Yitao Liang, Jianzhu Ma
2025	A*	`conf`	UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design. ICML Xiangzhe Kong, Zishen Zhang, Ziting Zhang, Rui Jiao, Jianzhu Ma, Wenbing Huang, Kai Liu, Yang Liu
2025	J	`jnl`	UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design. CoRR Xiangzhe Kong, Zishen Zhang, Ziting Zhang, Rui Jiao, Jianzhu Ma, Kai Liu, Wenbing Huang, Yang Liu
2025	A*	`conf`	Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints. ICML Dapeng Jiang, Xiangzhe Kong, Jiaqi Han, Mingyu Li, Rui Jiao, Wenbing Huang, Stefano Ermon, Jianzhu Ma, Yang Liu
2025	J	`jnl`	Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints. CoRR Dapeng Jiang, Xiangzhe Kong, Jiaqi Han, Mingyu Li, Rui Jiao, Wenbing Huang, Stefano Ermon, Jianzhu Ma, Yang Liu
2024	J	`jnl`	DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design. CoRR Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma, Qiang Liu, Liang Wang, Quanquan Gu
2024	A*	`conf`	Enhancing Protein Mutation Effect Prediction through a Retrieval-Augmented Framework. NeurIPS Ruihan Guo, Rui Wang, Ruidong Wu, Zhizhou Ren, Jiahan Li, Shitong Luo, Zuofan Wu, Qiang Liu, Jian Peng, Jianzhu Ma
2024	A*	`conf`	FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames. ICML Ruidong Wu, Ruihan Guo, Rui Wang, Shitong Luo, Yue Xu, Jiahan Li, Jianzhu Ma, Qiang Liu, Yunan Luo, Jian Peng
2024	J	`jnl`	FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames. CoRR Ruidong Wu, Ruihan Guo, Rui Wang, Shitong Luo, Yue Xu, Jiahan Li, Jianzhu Ma, Qiang Liu, Yunan Luo, Jian Peng
2024	A*	`conf`	Full-Atom Peptide Design based on Multi-modal Flow Matching. ICML Jiahan Li, Chaoran Cheng, Zuofan Wu, Ruihan Guo, Shitong Luo, Zhizhou Ren, Jian Peng, Jianzhu Ma
2024	J	`jnl`	Full-Atom Peptide Design based on Multi-modal Flow Matching. CoRR Jiahan Li, Chaoran Cheng, Zuofan Wu, Ruihan Guo, Shitong Luo, Zhizhou Ren, Jian Peng, Jianzhu Ma
2024	J	`jnl`	Geometric Point Attention Transformer for 3D Shape Reassembly. CoRR Jiahan Li, Chaoran Cheng, Jianzhu Ma, Ge Liu
2024	J	`jnl`	Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension. CoRR Jiahan Li, Tong Chen, Shitong Luo, Chaoran Cheng, Jiaqi Guan, Ruihan Guo, Sheng Wang, Ge Liu, Jian Peng, Jianzhu Ma
2024	A*	`conf`	InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation. ICLR Xingchao Liu, Xiwen Zhang, Jianzhu Ma, Jian Peng, Qiang Liu
2024	A*	`conf`	Projecting Molecules into Synthesizable Chemical Spaces. ICML Shitong Luo, Wenhao Gao, Zuofan Wu, Jian Peng, Connor W. Coley, Jianzhu Ma
2024	J	`jnl`	Projecting Molecules into Synthesizable Chemical Spaces. CoRR Shitong Luo, Wenhao Gao, Zuofan Wu, Jian Peng, Connor W. Coley, Jianzhu Ma
2024	A*	`conf`	Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design. NeurIPS Xiangxin Zhou, Jiaqi Guan, Yijia Zhang, Xingang Peng, Liang Wang, Jianzhu Ma
2024	J	`jnl`	Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design. CoRR Xiangxin Zhou, Jiaqi Guan, Yijia Zhang, Xingang Peng, Liang Wang, Jianzhu Ma
2024	A*	`conf`	Selecting Large Language Model to Fine-tune via Rectified Scaling Law. ICML Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, Zihao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang
2024	J	`jnl`	Selecting Large Language Model to Fine-tune via Rectified Scaling Law. CoRR Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, Zihao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang
2024	A*	`conf`	TFG: Unified Training-Free Guidance for Diffusion Models. NeurIPS Haotian Ye, Haowei Lin, Jiaqi Han, Minkai Xu, Sheng Liu, Yitao Liang, Jianzhu Ma, James Y. Zou, Stefano Ermon
2024	J	`jnl`	TFG: Unified Training-Free Guidance for Diffusion Models. CoRR Haotian Ye, Haowei Lin, Jiaqi Han, Minkai Xu, Sheng Liu, Yitao Liang, Jianzhu Ma, James Zou, Stefano Ermon
2023	A*	`conf`	3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction. ICLR Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma
2023	J	`jnl`	3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction. CoRR Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma
2023	A*	`conf`	Boosting the Cycle Counting Power of Graph Neural Networks with I$^2$-GNNs. ICLR Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang
2023	J	`jnl`	Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. Nat. Mac. Intell. Xingang Peng, Yipin Lei, Peiyuan Feng, Lemei Jia, Jianzhu Ma, Dan Zhao, Jianyang Zeng
2023	J	`jnl`	Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration. Bioinform. Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li
2023	A*	`conf`	DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design. ICML Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma, Qiang Liu, Liang Wang, Quanquan Gu
2023	J	`jnl`	Extrapolating heterogeneous time-series gene expression data using Sagittarius. Nat. Mac. Intell. Addie Woicik, Mingxin Zhang, Janelle Chan, Jianzhu Ma, Sheng Wang
2023	J	`jnl`	InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation. CoRR Xingchao Liu, Xiwen Zhang, Jianzhu Ma, Jian Peng, Qiang Liu
2023	A*	`conf`	Learning Sparse Group Models Through Boolean Relaxation. ICLR Yijie Wang, Yuan Zhou, Xiaoqing Huang, Kun Huang, Jie Zhang, Jianzhu Ma
2023	A*	`conf`	LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion. NeurIPS Jiaqi Guan, Xingang Peng, Peiqi Jiang, Yunan Luo, Jian Peng, Jianzhu Ma
2023	J	`jnl`	MCU: A Task-centric Framework for Open-ended Agent Evaluation in Minecraft. CoRR Haowei Lin, Zihao Wang, Jianzhu Ma, Yitao Liang
2023	A*	`conf`	MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation. ICML Xingang Peng, Jiaqi Guan, Qiang Liu, Jianzhu Ma
2023	J	`jnl`	MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation. CoRR Xingang Peng, Jiaqi Guan, Qiang Liu, Jianzhu Ma
2023	A*	`conf`	ProBio: A Protocol-guided Multimodal Dataset for Molecular Biology Lab. NeurIPS Jieming Cui, Ziren Gong, Baoxiong Jia, Siyuan Huang, Zilong Zheng, Jianzhu Ma, Yixin Zhu
2023	J	`jnl`	ProBio: A Protocol-guided Multimodal Dataset for Molecular Biology Lab. CoRR Jieming Cui, Ziren Gong, Baoxiong Jia, Siyuan Huang, Zilong Zheng, Jianzhu Ma, Yixin Zhu
2023	A*	`conf`	Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction. ICLR Shitong Luo, Yufeng Su, Zuofan Wu, Chenpeng Su, Jian Peng, Jianzhu Ma
2023	J	`jnl`	Scientific Computing with Diffractive Optical Neural Networks. Adv. Intell. Syst. Ruiyang Chen, Yingheng Tang, Jianzhu Ma, Weilu Gao
2023	J	`jnl`	Scientific Computing with Diffractive Optical Neural Networks. CoRR Ruiyang Chen, Yingheng Tang, Jianzhu Ma, Weilu Gao
2023	A*	`conf`	xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. NeurIPS Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song
2023	J	`jnl`	xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. CoRR Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song
2022	A*	`conf`	3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design. ICML Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang
2022	J	`jnl`	3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design. CoRR Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang
2022	J	`jnl`	A 3D Molecule Generative Model for Structure-Based Drug Design. CoRR Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng
2022	A*	`conf`	Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures. NeurIPS Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma
2022	J	`jnl`	Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data. Briefings Bioinform. Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng, Jianzhu Ma
2022	J	`jnl`	Boosting the Cycle Counting Power of Graph Neural Networks with I CoRR Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang
2022	J	`jnl`	Device-system Co-design of Photonic Neuromorphic Processor using Reinforcement Learning. CoRR Yingheng Tang, Princess Tara Zamani, Ruiyang Chen, Jianzhu Ma, Minghao Qi, Cunxi Yu, Weilu Gao
2022	J	`jnl`	Directed Weight Neural Networks for Protein Structure Representation Learning. CoRR Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas J. Guibas, Jian Peng, Jianzhu Ma
2022	A*	`conf`	Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation. NeurIPS Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma
2022	J	`jnl`	Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation. CoRR Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma
2022	A*	`conf`	Energy-Inspired Molecular Conformation Optimization. ICLR Jiaqi Guan, Wesley Wei Qian, Qiang Liu, Wei-Ying Ma, Jianzhu Ma, Jian Peng
2022	A*	`conf`	Equivariant Point Cloud Analysis via Learning Orientations for Message Passing. CVPR Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma
2022	J	`jnl`	Equivariant Point Cloud Analysis via Learning Orientations for Message Passing. CoRR Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma
2022	J	`jnl`	MobilePrune: Neural Network Compression via ℓ0 Sparse Group Lasso on the Mobile System. Sensors Yubo Shao, Kaikai Zhao, Zhiwen Cao, Zhehao Peng, Xingang Peng, Pan Li, Yijie Wang, Jianzhu Ma
2022	A*	`conf`	Multiwave COVID-19 Prediction from Social Awareness Using Web Search and Mobility Data. KDD Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma, Satish V. Ukkusuri
2022	A*	`conf`	Neural Predicting Higher-order Patterns in Temporal Networks. WWW Yunyu Liu, Jianzhu Ma, Pan Li
2022	J	`jnl`	Physics-informed recurrent neural network for time dynamics in optical resonances. Nat. Comput. Sci. Yingheng Tang, Jichao Fan, Xinwei Li, Jianzhu Ma, Minghao Qi, Cunxi Yu, Weilu Gao
2022	A*	`conf`	Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets. ICML Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma
2022	J	`jnl`	Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets. CoRR Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma
2022	J	`jnl`	Provable Constrained Stochastic Convex Optimization with XOR-Projected Gradient Descent. CoRR Fan Ding, Yijie Wang, Jianzhu Ma, Yexiang Xue
2022	A*	`conf`	Proximal Exploration for Model-guided Protein Sequence Design. ICML Zhizhou Ren, Jiahan Li, Fan Ding, Yuan Zhou, Jianzhu Ma, Jian Peng
2022	J	`jnl`	Quantifying the spatial homogeneity of urban road networks via graph neural networks. Nat. Mach. Intell. Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Takahiro Yabe, Satish V. Ukkusuri, Jianzhu Ma
2022	—	`conf`	Understanding Dropout for Graph Neural Networks. WWW (Companion Volume) Juan Shu, Bowei Xi, Yu Li, Fan Wu, Charles A. Kamhoua, Jianzhu Ma
2022	J	`jnl`	scPretrain: multi-task self-supervised learning for cell-type classification. Bioinform. Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang, Sheng Wang
2021	A*	`conf`	A 3D Generative Model for Structure-Based Drug Design. NeurIPS Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng
2021	J	`jnl`	AirSign: Smartphone Authentication by Signing in the Air. Sensors Yubo Shao, Tinghan Yang, He Wang, Jianzhu Ma
2021	A*	`conf`	Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns. KDD Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li, Jianzhu Ma
2021	J	`jnl`	Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns. CoRR Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li, Jianzhu Ma
2021	J	`jnl`	Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration. CoRR Xuesong Wang, Zhihang Hu, Tingyang Yu, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li
2021	J	`jnl`	Disease gene prediction with privileged information and heteroscedastic dropout. Bioinform. Juan Shu, Yu Li, Sheng Wang, Bowei Xi, Jianzhu Ma
2021	A*	`conf`	Fast Projection onto the Capped Simplex with Applications to Sparse Regression in Bioinformatics. NeurIPS Andersen Man Shun Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang
2021	J	`jnl`	Fast Projection onto the Capped Simplex withApplications to Sparse Regression in Bioinformatics. CoRR Andersen Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang
2021	J	`jnl`	Modeling gene regulatory networks using neural network architectures. Nat. Comput. Sci. Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma
2021	J	`jnl`	Multiwave COVID-19 Prediction via Social Awareness-Based Graph Neural Networks using Mobility and Web Search Data. CoRR Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma, Satish V. Ukkusuri
2021	J	`jnl`	Neural Higher-order Pattern (Motif) Prediction in Temporal Networks. CoRR Yunyu Liu, Jianzhu Ma, Pan Li
2021	A	`conf`	PALM: Probabilistic area loss Minimization for Protein Sequence Alignment. UAI Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue
2021	J	`jnl`	Predicting MHC-peptide binding affinity by differential boundary tree. Bioinform. Peiyuan Feng, Jianyang Zeng, Jianzhu Ma
2021	J	`jnl`	Quantifying spatial homogeneity of urban road networks via graph neural networks. CoRR Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Satish V. Ukkusuri, Jianzhu Ma
2021	A*	`conf`	XOR-CD: Linearly Convergent Constrained Structure Generation. ICML Fan Ding, Jianzhu Ma, Jinbo Xu, Yexiang Xue
2020	J	`jnl`	Artificial-cell-type aware cell-type classification in CITE-seq. Bioinform. Qiuyu Lian, Hongyi Xin, Jianzhu Ma, Liza Konnikova, Wei Chen, Jin Gu, Kong Chen
2020	J	`jnl`	When causal inference meets deep learning. Nat. Mach. Intell. Yunan Luo, Jian Peng, Jianzhu Ma
2019	J	`jnl`	Classifying tumors by supervised network propagation. Bioinform. Wei Zhang, Jianzhu Ma, Trey Ideker
2019	B	`conf`	Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. RECOMB Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng
2018	Misc	`conf`	Annotating gene sets by mining large literature collections with protein networks. PSB Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker
2018	J	`jnl`	Classifying tumors by supervised network propagation. Bioinform. Wei Zhang, Jianzhu Ma, Trey Ideker
2018	B	`conf`	Deciphering Signaling Specificity with Deep Neural Networks. RECOMB Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng
2017	J	`jnl`	DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields. Bioinform. Mingfu Shao, Jianzhu Ma, Sheng Wang
2016	J	`jnl`	AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. Bioinform. Sheng Wang, Jianzhu Ma, Jinbo Xu
2016	J	`jnl`	ModuleAlign: module-based global alignment of protein-protein interaction networks. Bioinform. Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu
2015	—	`conf`	Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage. BCB Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
2015	—	`conf`	Predicting diverse M-best protein contact maps. BIBM Siqi Sun, Jianzhu Ma, Sheng Wang, Jinbo Xu
2015	B	`conf`	Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning. RECOMB Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
2015	—	`book`	Protein Homology Detection Through Alignment of Markov Random Fields - Using MRFalign Jinbo Xu, Sheng Wang, Jianzhu Ma
2015	J	`jnl`	Protein Structure Prediction by Protein Alignments. CoRR Jianzhu Ma
2015	J	`jnl`	Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. Bioinform. Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
2015	J	`jnl`	Protein secondary structure prediction using deep convolutional neural fields. CoRR Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
2015	A	`conf`	Structure Learning Constrained by Node-Specific Degree Distribution. UAI Jianzhu Ma, Feng Zhao, Jinbo Xu
2014	B	`conf`	MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. RECOMB Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
2014	J	`jnl`	MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. CoRR Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
2014	J	`jnl`	MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. PLoS Comput. Biol. Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
2013	A	`conf`	Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling. AISTATS Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu
2013	J	`jnl`	Protein contact prediction by joint evolutionary coupling analysis across multiple families. CoRR Jianzhu Ma, Sheng Wang, Jinbo Xu
2013	J	`jnl`	Protein threading using context-specific alignment potential. Bioinform. Jianzhu Ma, Sheng Wang, Feng Zhao, Jinbo Xu
2012	J	`jnl`	A conditional neural fields model for protein threading. Bioinform. Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu
2010	—	`conf`	A browser-based framework for data cache in Web-delivered service composition. SOCA Jiyu Huang, Xuanzhe Liu, Qi Zhao, Jianzhu Ma, Gang Huang