A browser-based framework for data cache in Web-delivered service composition. - Jiyu Huang; Xuanzhe Liu; Qi Zhao 005; Jianzhu Ma; Gang Huang 001 (SOCA, 2010)

A conditional neural fields model for protein threading. - Jianzhu Ma; Jian Peng 001; Sheng Wang 001; Jinbo Xu (Bioinform., 2012)

Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling. - Jianzhu Ma; Jian Peng 001; Sheng Wang 001; Jinbo Xu (AISTATS, 2013)

Protein threading using context-specific alignment potential. - Jianzhu Ma; Sheng Wang 001; Feng Zhao; Jinbo Xu (Bioinform., 2013)

Protein contact prediction by joint evolutionary coupling analysis across multiple families. - Jianzhu Ma; Sheng Wang 001; Jinbo Xu (CoRR, 2013)

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. - Jianzhu Ma; Sheng Wang 001; Zhiyong Wang 005; Jinbo Xu (PLoS Comput. Biol., 2014)

Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage. - Qingming Tang; Sheng Wang 001; Jian Peng 001; Jianzhu Ma; Jinbo Xu (BCB, 2015)

Predicting diverse M-best protein contact maps. - Siqi Sun; Jianzhu Ma; Sheng Wang 001; Jinbo Xu (BIBM, 2015)

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

Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. - Jianzhu Ma; Sheng Wang 001; Zhiyong Wang 005; Jinbo Xu (Bioinform., 2015)

Protein Structure Prediction by Protein Alignments. - Jianzhu Ma (CoRR, 2015)

Protein secondary structure prediction using deep convolutional neural fields. - Sheng Wang 001; Jian Peng 001; Jianzhu Ma; Jinbo Xu (CoRR, 2015)

Protein Homology Detection Through Alignment of Markov Random Fields - Using MRFalign - Jinbo Xu; Sheng Wang 001; Jianzhu Ma (Springer, 2015)

ModuleAlign: module-based global alignment of protein-protein interaction networks. - Somaye Hashemifar; Jianzhu Ma; Hammad Naveed; Stefan Canzar; Jinbo Xu (Bioinform., 2016)

AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. - Sheng Wang 001; Jianzhu Ma; Jinbo Xu (Bioinform., 2016)

DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields. - Mingfu Shao; Jianzhu Ma; Sheng Wang 001 (Bioinform., 2017)

Annotating gene sets by mining large literature collections with protein networks. - Sheng Wang 001; Jianzhu Ma; Michael Ku Yu; Fan Zheng; Edward W. Huang; Jiawei Han 001; Jian Peng 001; Trey Ideker (PSB, 2018)

Deciphering Signaling Specificity with Deep Neural Networks. - Yunan Luo; Jianzhu Ma; Yang Liu 097; Qing Ye; Trey Ideker; Jian Peng 001 (RECOMB, 2018)

Classifying tumors by supervised network propagation. - Wei Zhang 067; Jianzhu Ma; Trey Ideker (Bioinform., 2018)

Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. - Yunan Luo; Jianzhu Ma; Xiaoming Zhao 001; Yufeng Su; Yang Liu 097; Trey Ideker; Jian Peng 001 (RECOMB, 2019)

Artificial-cell-type aware cell-type classification in CITE-seq. - Qiuyu Lian; Hongyi Xin; Jianzhu Ma; Liza Konnikova; Wei Chen 074; Jin Gu; Kong Chen (Bioinform., 2020)

When causal inference meets deep learning. - Yunan Luo; Jian Peng 001; Jianzhu Ma (Nat. Mach. Intell., 2020)

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

Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns. - Susheel Suresh; Vinith Budde; Jennifer Neville; Pan Li 005; Jianzhu Ma (KDD, 2021)

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

A 3D Generative Model for Structure-Based Drug Design. - Shitong Luo; Jiaqi Guan; Jianzhu Ma; Jian Peng 001 (NeurIPS, 2021)

PALM: Probabilistic area loss Minimization for Protein Sequence Alignment. - Fan Ding; Nan Jiang 012; Jianzhu Ma; Jian Peng 001; Jinbo Xu; Yexiang Xue (UAI, 2021)

Predicting MHC-peptide binding affinity by differential boundary tree. - Peiyuan Feng; Jianyang Zeng 001; Jianzhu Ma (Bioinform., 2021)

Disease gene prediction with privileged information and heteroscedastic dropout. - Juan Shu; Yu Li 006; Sheng Wang 012; Bowei Xi; Jianzhu Ma (Bioinform., 2021)

Quantifying spatial homogeneity of urban road networks via graph neural networks. - Jiawei Xue; Nan Jiang 012; Senwei Liang; Qiyuan Pang; Satish V. Ukkusuri; Jianzhu Ma (CoRR, 2021)

Neural Higher-order Pattern (Motif) Prediction in Temporal Networks. - Yunyu Liu; Jianzhu Ma; Pan Li 005 (CoRR, 2021)

Fast Projection onto the Capped Simplex withApplications to Sparse Regression in Bioinformatics. - Andersen Ang; Jianzhu Ma; Nianjun Liu; Kun Huang; Yijie Wang (CoRR, 2021)

Multiwave COVID-19 Prediction via Social Awareness-Based Graph Neural Networks using Mobility and Web Search Data. - Jiawei Xue; Takahiro Yabe; Kota Tsubouchi; Jianzhu Ma; Satish V. Ukkusuri (CoRR, 2021)

Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration. - Xuesong Wang; Zhihang Hu; Tingyang Yu; Ruijie Wang; Yumeng Wei; Juan Shu; Jianzhu Ma; Yu Li 006 (CoRR, 2021)

Modeling gene regulatory networks using neural network architectures. - Hantao Shu; Jingtian Zhou; Qiuyu Lian; Han Li 018; Dan Zhao 004; Jianyang Zeng 001; Jianzhu Ma (Nat. Comput. Sci., 2021)

AirSign: Smartphone Authentication by Signing in the Air. - Yubo Shao; Tinghan Yang; He Wang 008; Jianzhu Ma (Sensors, 2021)

Equivariant Point Cloud Analysis via Learning Orientations for Message Passing. - Shitong Luo; Jiahan Li; Jiaqi Guan; Yufeng Su; Chaoran Cheng; Jian Peng 001; Jianzhu Ma (CVPR, 2022)

Energy-Inspired Molecular Conformation Optimization. - Jiaqi Guan; Wesley Wei Qian; Qiang Liu 001; Wei-Ying Ma; Jianzhu Ma; Jian Peng 001 (ICLR, 2022)

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

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets. - Xingang Peng; Shitong Luo; Jiaqi Guan; Qi Xie; Jian Peng 001; Jianzhu Ma (ICML, 2022)

Proximal Exploration for Model-guided Protein Sequence Design. - Zhizhou Ren; Jiahan Li; Fan Ding; Yuan Zhou 007; Jianzhu Ma; Jian Peng 001 (ICML, 2022)

Multiwave COVID-19 Prediction from Social Awareness Using Web Search and Mobility Data. - Jiawei Xue; Takahiro Yabe; Kota Tsubouchi; Jianzhu Ma; Satish V. Ukkusuri (KDD, 2022)

Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures. - Shitong Luo; Yufeng Su; Xingang Peng; Sheng Wang 001; Jian Peng 001; Jianzhu Ma (NeurIPS, 2022)

Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation. - Zhizhou Ren; Anji Liu; Yitao Liang; Jian Peng 001; Jianzhu Ma (NeurIPS, 2022)

Neural Predicting Higher-order Patterns in Temporal Networks. - Yunyu Liu; Jianzhu Ma; Pan Li 005 (WWW, 2022)

Understanding Dropout for Graph Neural Networks. - Juan Shu; Bowei Xi; Yu Li 006; Fan Wu; Charles A. Kamhoua; Jianzhu Ma (WWW (Companion Volume), 2022)

Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data. - Hantao Shu; Fan Ding; Jingtian Zhou; Yexiang Xue; Dan Zhao 004; Jianyang Zeng 001; Jianzhu Ma (Briefings Bioinform., 2022)

scPretrain: multi-task self-supervised learning for cell-type classification. - Ruiyi Zhang; Yunan Luo; Jianzhu Ma; Ming Zhang 004; Sheng Wang 012 (Bioinform., 2022)

Directed Weight Neural Networks for Protein Structure Representation Learning. - Jiahan Li; Shitong Luo; Congyue Deng; Chaoran Cheng; Jiaqi Guan; Leonidas J. Guibas; Jian Peng 001; Jianzhu Ma (CoRR, 2022)

Device-system Co-design of Photonic Neuromorphic Processor using Reinforcement Learning. - Yingheng Tang; Princess Tara Zamani; Ruiyang Chen; Jianzhu Ma; Minghao Qi; Cunxi Yu; Weilu Gao (CoRR, 2022)

A 3D Molecule Generative Model for Structure-Based Drug Design. - Shitong Luo; Jiaqi Guan; Jianzhu Ma; Jian Peng 001 (CoRR, 2022)

Provable Constrained Stochastic Convex Optimization with XOR-Projected Gradient Descent. - Fan Ding; Yijie Wang; Jianzhu Ma; Yexiang Xue (CoRR, 2022)

Boosting the Cycle Counting Power of Graph Neural Networks with I2-GNNs. - Yinan Huang; Xingang Peng; Jianzhu Ma; Muhan Zhang (CoRR, 2022)

Quantifying the spatial homogeneity of urban road networks via graph neural networks. - Jiawei Xue; Nan Jiang 012; Senwei Liang; Qiyuan Pang; Takahiro Yabe; Satish V. Ukkusuri; Jianzhu Ma (Nat. Mach. Intell., 2022)

Physics-informed recurrent neural network for time dynamics in optical resonances. - Yingheng Tang; Jichao Fan; Xinwei Li; Jianzhu Ma; Minghao Qi; Cunxi Yu; Weilu Gao (Nat. Comput. Sci., 2022)

MobilePrune: Neural Network Compression via ℓ0 Sparse Group Lasso on the Mobile System. - Yubo Shao; Kaikai Zhao; Zhiwen Cao; Zhehao Peng; Xingang Peng; Pan Li 005; Yijie Wang; Jianzhu Ma (Sensors, 2022)

3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction. - Jiaqi Guan; Wesley Wei Qian; Xingang Peng; Yufeng Su; Jian Peng 001; 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 (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 001; Jianzhu Ma (ICLR, 2023)

Learning Sparse Group Models Through Boolean Relaxation. - Yijie Wang; Yuan Zhou 007; Xiaoqing Huang; Kun Huang; Jie Zhang; Jianzhu Ma (ICLR, 2023)

DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design. - Jiaqi Guan; Xiangxin Zhou; Yuwei Yang; Yu Bao; Jian Peng 001; Jianzhu Ma; Qiang Liu 006; Liang Wang 001; Quanquan Gu (ICML, 2023)

MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation. - Xingang Peng; Jiaqi Guan; Qiang Liu 001; Jianzhu Ma (ICML, 2023)

ProBio: A Protocol-guided Multimodal Dataset for Molecular Biology Lab. - Jieming Cui; Ziren Gong; Baoxiong Jia; Siyuan Huang 001; Zilong Zheng; Jianzhu Ma; Yixin Zhu 001 (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 (NeurIPS, 2023)

LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion. - Jiaqi Guan; Xingang Peng; Peiqi Jiang; Yunan Luo; Jian Peng 001; Jianzhu Ma (NeurIPS, 2023)

InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation. - Xingchao Liu; Xiwen Zhang; Jianzhu Ma; Jian Peng 007; Qiang Liu 001 (CoRR, 2023)

MCU: A Task-centric Framework for Open-ended Agent Evaluation in Minecraft. - Haowei Lin; Zihao Wang; Jianzhu Ma; Yitao Liang (CoRR, 2023)

Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration. - Xuesong Wang; Zhihang Hu; Tingyang Yu; Yixuan Wang; Ruijie Wang; Yumeng Wei; Juan Shu; Jianzhu Ma; Yu Li 006 (Bioinform., 2023)

Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. - Xingang Peng; Yipin Lei; Peiyuan Feng; Lemei Jia; Jianzhu Ma; Dan Zhao 004; Jianyang Zeng 001 (Nat. Mac. Intell., 2023)

Extrapolating heterogeneous time-series gene expression data using Sagittarius. - Addie Woicik; Mingxin Zhang 008; Janelle Chan; Jianzhu Ma; Sheng Wang 012 (Nat. Mac. Intell., 2023)

Scientific Computing with Diffractive Optical Neural Networks. - Ruiyang Chen; Yingheng Tang; Jianzhu Ma; Weilu Gao (Adv. Intell. Syst., 2023)

InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation. - Xingchao Liu; Xiwen Zhang; Jianzhu Ma; Jian Peng 001; Qiang Liu 001 (ICLR, 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 001; 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 001; James Zou 001; Yitao Liang (ICML, 2024)

Projecting Molecules into Synthesizable Chemical Spaces. - Shitong Luo; Wenhao Gao 001; Zuofan Wu; Jian Peng 001; Connor W. Coley; 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 001; Yunan Luo; Jian Peng 001 (ICML, 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 001; Jian Peng 001; Jianzhu Ma (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 Y. Zou; Stefano Ermon (NeurIPS, 2024)

Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design. - Xiangxin Zhou; Jiaqi Guan; Yijia Zhang; Xingang Peng; Liang Wang 001; Jianzhu Ma (NeurIPS, 2024)

Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks. - Lingsheng Cai; Xiuli Ma; Jianzhu Ma (Briefings Bioinform., 2024)

Geometric Point Attention Transformer for 3D Shape Reassembly. - Jiahan Li; Chaoran Cheng; Jianzhu Ma; Ge Liu (CoRR, 2024)

Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension. - Jiahan Li; Tong Chen; Shitong Luo; Chaoran Cheng; Jiaqi Guan; Ruihan Guo; Sheng Wang 001; Ge Liu; Jian Peng 001; Jianzhu Ma (CoRR, 2024)

Group Ligands Docking to Protein Pockets. - Jiaqi Guan; Jiahan Li; Xiangxin Zhou; Xingang Peng; Sheng Wang 001; Yunan Luo; Jian Peng 001; 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)

TFG-Flow: Training-free Guidance in Multimodal Generative Flow. - Haowei Lin; Shanda Li; Haotian Ye; Yiming Yang; Stefano Ermon; Yitao Liang; 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 (ICLR, 2025)

Orientation-Aware Networks for Protein Structure Representation Learning. - Jiahan Li; Shitong Luo; Congyue Deng; Chaoran Cheng; Jiaqi Guan; Leonidas J. Guibas; Jian Peng 001; Jianzhu Ma (RECOMB, 2025)

Rag2Mol: structure-based drug design based on retrieval augmented generation. - Peidong Zhang; Xingang Peng; Rong Han; Ting Chen 006; Jianzhu Ma (Briefings Bioinform., 2025)

Data Mining in Transportation Networks with Graph Neural Networks: A Review and Outlook. - Jiawei Xue; Ruichen Tan; Jianzhu Ma; Satish V. Ukkusuri (CoRR, 2025)

PUGS: Zero-shot Physical Understanding with Gaussian Splatting. - Yinghao Shuai; Ran Yu; Yuantao Chen; Zijian Jiang; Xiaowei Song; Nan Wang; Jv Zheng; Jianzhu Ma; Meng Yang; Zhicheng Wang; Wenbo Ding; Hao Zhao 002 (CoRR, 2025)

MatterChat: A Multi-Modal LLM for Material Science. - Yingheng Tang; Wenbin Xu; Jie Cao 010; Jianzhu Ma; Weilu Gao; Steve Farrell; N. Benjamin Erichson; Michael W. Mahoney; Andy Nonaka; Zhi Yao (CoRR, 2025)

Predicting Individual Irregular Mobility via Web Search-Driven Bipartite Graph Neural Networks. - Jiawei Xue; Takahiro Yabe; Kota Tsubouchi; Jianzhu Ma; Satish V. Ukkusuri (IEEE Trans. Knowl. Data Eng., 2025)

A Neural Symbolic Model for Space Physics. - Jie Ying; Haowei Lin; Chao Yue; Yajie Chen; Chao Xiao; Quanqi Shi; Yitao Liang; Shing-Tung Yau; Yuan Zhou; Jianzhu Ma (CoRR, 2025)

UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design. - Xiangzhe Kong; Zishen Zhang; Ziting Zhang; Rui Jiao; Jianzhu Ma; Kai Liu; Wenbing Huang 001; Yang Liu 005 (CoRR, 2025)

Generative Evaluation of Complex Reasoning in Large Language Models. - Haowei Lin; Xiangyu Wang; Ruilin Yan; Baizhou Huang; Haotian Ye; Jianhua Zhu; Zihao Wang; James Zou 001; Jianzhu Ma; Yitao Liang (CoRR, 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 (CoRR, 2025)

Inference-time Scaling of Diffusion Models through Classical Search. - Xiangcheng Zhang; Haowei Lin; Haotian Ye; James Y. Zou; Jianzhu Ma; Yitao Liang; Yilun Du (CoRR, 2025)

Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints. - Dapeng Jiang; Xiangzhe Kong; Jiaqi Han; Mingyu Li; Rui Jiao; Wenbing Huang 001; Stefano Ermon; Jianzhu Ma; Yang Liu 005 (CoRR, 2025)

Morpheus: A Neural-driven Animatronic Face with Hybrid Actuation and Diverse Emotion Control. - Zongzheng Zhang; Jiawen Yang; Ziqiao Peng; Meng Yang; Jianzhu Ma; Lin Cheng; Huazhe Xu; Hang Zhao; Hao Zhao 002 (CoRR, 2025)

EvoSLD: Automated Neural Scaling Law Discovery With Large Language Models. - Haowei Lin; Xiangyu Wang; Jianzhu Ma; Yitao Liang (CoRR, 2025)