Machine Learning Papers

 
  • NEW! Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models
    Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma
    NeurlPS 2022

     
  • NEW! Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation
    Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma
    NeurlPS 2022

     
  • NEW! 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, Yijie Wang, Jianzhu Ma
    Sensor 2022

     
  • NEW! 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 corresponding author Oral presentation

     
  • NEW! Proximal Exploration for Model-guided Biological Sequence Design
    Zhizhou Ren, Jiahan Li, Fan Ding, Yuan Zhou, Jianzhu Ma , Jian Peng
    ICML 2022 Short presentation

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

     
  • NEW! 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design
    Yinan Huang, Xingang Peng, Jianzhu Ma , Muhan Zhang
    ICML 2022 corresponding author Long presentation

     
  • NEW! Equivariant Point Set Analysis via Learning Orientations for Message Passing
    Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma
    CVPR 2022 Oral presentation

     
  • NEW! Physics-Guided and Physics-Explainable Recurrent Neural Network for Time Dynamics in Optical Resonances
    Yingheng Tang, Jichao Fan, Xinwei Li, Jianzhu Ma , Minghao Qi, Cunxi Yu, Weilu Gao
    Nature Computational Science 2022

     
  • NEW! Neural Energy Minimization for Molecular Conformation Optimization
    Jiaqi Guan, Wei Qian, Qiang Liu, Wei-ying Ma, Jianzhu Ma, Jian Peng
    ICLR 2022

     
  • NEW! Neural Predicting Higher-order Patterns in Temporal Networks
    Yuyun Liu, Jianzhu Ma, Pan Li
    WWW 2022

     
  • Quantifying spatial homogeneity of urban road networks via graph neural networks
    Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Takahiro Yabe, Satish Ukkusuri, Jianzhu Ma
    Nature Machine intelligence 2022 cover paper

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

     
  • Fast Projection onto the Capped Simplex withApplications to Sparse Regression in Bioinformatics
    Andersen Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang
    NeurlPS 2021

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

     
  • AirSign: Smartphone Authentication by Signing in the Air
    Yubo Shao, Tinghan Yang, He Wang, Jianzhu Ma
    Sensor 2021

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

     
  • Causality in machine learning: When causal inference meets deep neural networks
    Yunan Luo, Jian Peng, Jianzhu Ma
    Nature Machine intelligence 2020

     
  • Structure Learning Constrained by Node-Specific Degree Distribution
    Jianzhu Ma, Sheng Wang and Jinbo Xu
    UAI 2015

     
  • Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling
    Jianzhu Ma, Jian Peng, Sheng Wang and Jinbo Xu
    AI & Statistics 2013 oral presentation

     

Biology Papers

 
  • NEW! Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data
    Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng and Jianzhu Ma
    Briefings in Bioinformatics 2022

     
  • NEW! Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma
    Qi Xie, Zhilin Long, Chengfang Sun, Min Tang, Yin Wang, Jiayan Ma, Jichuan Yu, Jingchao Wei, Jianzhu Ma , Bohan Wang, and Jiaming Wen
    Cell Discovery 2022

     
  • NEW! Deep learning guided optimization of human antibody against SARS-Cov-2 variants with broad neutralization
    Sisi Shan, Shitong Luo, Ziqing Yang, Junxian Hong, Yufeng Su, Fan Ding, Chengyu Li, Peng Chen, Jianzhu Ma, Xuanling Shi, Qi Zhang, Bonnie Berger, Linqi Zhang, Jian Peng
    PNAS 2022

     
  • NEW! scPretrain: Multi-task self-supervised learning for cell type classification
    Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang, Sheng Wang
    Bioinformatics 2022

     
  • Next decade’s AI-based drug development features the tight integration of data and computation
    Yunan Luo, Jian Peng, Jianzhu Ma
    Health Data Science 2021

     
  • A multi-scale map of cell structure fusing protein images and interactions
    Yue Qin, Edward L. Huttlin, Casper F. Winsnes, Maya L. Gosztyla, Ludivine Wacheul, Marcus R. Kelly, Steven M. Blue, Fan Zheng, Michael Chen, Leah V. Schaffer, Katherine Licon, Anna Bäckström, Laura Pontano Vaites, John J. Lee, Wei Ouyang, Sophie N. Liu, Tian Zhang, Erica Silva, Jisoo Park, Adriana Pitea, Jason F. Kreisberg, Steven P. Gygi, Jianzhu Ma, J. Wade Harper, Gene W. Yeo, Denis L. J. Lafontaine, Emma Lundberg,Trey Ideker
    Nature 2021

     
  • SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through ACE2-independent interactions via C-type lectin receptors and TTYH2
    Qiao Lu, Jia Liu, Shuai Zhao, Maria Florencia Gomez Castro, Maudry Laurent-Rolle, Jianbo Dong, Xiaojuan Ran, Payal Damani-Yokota, Hongzheng Tang, Triantafyllia Karakousi, Juhee Son, Maria E. Kaczmarek, Ze Zhang, Stephen T. Yeung, Broc T. McCune, Rita E. Chen, Fei Tang, Xianwen Ren, Xufeng Chen, Jack C.C. Hsu, Marianna Teplova, Betty Huang, Haijing Deng, Zhilin Long, Tenny Mudianto, Shumin Jin, Peng Lin, Jasper Du, Ruochen Zang, Tina Tianjiao Su, Alberto Herrera, Ming Zhou, Renhong Yan, Jia Cui, James Zhu, Qiang Zhou, Tao Wang, Jianzhu Ma, Sergei B. Koralov, Zemin Zhang, Iannis Aifantis, Leopoldo N. Segal, Michael S. Diamond, Kamal M. Khanna, Kenneth A. Stapleford, Peter Cresswel, Yue Liu, Siyuan Ding, Qi Xie, Jun Wang
    Immunity 2021 (Impact Factor=22)

     
  • Modeling Gene Regulatory Networks Using Neural Network Architectures
    Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma
    Nature Computational Science 2021

     
  • ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways
    Xiaoqing Huang, Kun Huang, Travis Johnson, Milan Radovich, Jie Zhang, Jianzhu Ma, Yijie Wang
    NAR genomics and bioinformatics 2021 corresponding author

     
  • Predicting MHC-peptide binding affinity by differential boundary tree
    Peiyuan Feng, Jianyang Zeng and Jianzhu Ma
    ISMB 2021

     
  • Disease Gene Prediction with Privileged Information and Heteroscedastic Dropout
    Juan Shu, Yu Li, Sheng Wang, Bowei Xi and Jianzhu Ma
    ISMB 2021

     
  • Towards the prediction of higher-order genetic interactions
    Ruochi Zhang, Jianzhu Ma, Jian Ma
    RECOMB 2021 corresponding author

     
  • Predicting drug response and synergy using a deep learning model of a cancer cell
    Brent Kuenzi, Jisoo Park, Samson H. Fong, Kyle Salinas Sanchez, Jason F. Kreisberg, Jianzhu Ma, Trey Ideker
    Cancer Cell 2020

  • A conserved epigenetic progression aligns dog and human age
    Tina Wang, Jianzhu Ma, Andrew N. Hogan, Samson Fong, Katherine Licon, Brian Tsui, Jason F. Kreisberg, Peter D. Adams, Anne-Ruxandra Carvunis, Danika L. Bannasch, Elaine A. Ostrander and Trey Ideker
    Cell Systems 2020

     
  • Artificial-Cell-Type Aware Cell Type Classification in CITE-seq
    Qiuyu Lian, Hongyi Xin, Jianzhu Ma, Liza Konnikova, Wei Chen, Jin Gu and Kong Chen
    ISMB 2020

     
  • Learning predictive models of drug response that translate across biological contexts
    Jianzhu Ma, Samson Fong, Yunan Luo, Christopher Bakkenist, John Paul Shen, Soufiane Mourragui, Lodewyk Wessels, Marc Hafner, Roded Sharan, Jian Peng, Trey Ideker
    Nature Cancer 2020

     
  • Robust Single-Cell Hi-C Clustering by Convolution and Random Walk based Imputation
    Jingtian Zhou, Jianzhu Ma, Yusi Chen, Chuankai Cheng, Bokan Bao, Jian Peng, Terrence J. Sejnowski, Jesse R. Dixon, Joseph R. Ecker
    PNAS 2019 co-first author

  • DDOT: A Swiss-Army Knife for Investigating Data-Driven Biological Ontologies
    Michael Ku Yu, Jianzhu Ma, Keiichiro Ono, Fan Zheng, Samson H. Fong, Aaron Gary, Jing Chen, Barry Demchak, Dexter Pratt, Trey Ideker
    Cell Systems 2019 co-first author

     
  • Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning
    Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng
    RECOMB 2019 co-first author

     
  • Visible Machine Learning for Biomedicine
    Michael Ku Yu, Jianzhu Ma, Jasmin Fisher, Jason F. Kreisberg, Benjamin J. Raphael, Trey Ideker
    Cell 2018 co-first author

     
  • Typing tumors using pathways selected by somatic evolution
    Sheng Wang, Jianzhu Ma, Wei Zhang, John Shen, Justin Huang, Jian Peng, Trey Ideker
    Nature Communications 2018 co-first author

     
  • Classifying tumors by supervised network propagation
    Wei Zhang, Jianzhu Ma, Trey Ideker
    ISMB 2018 co-first author

     
  • Using deep learning to model the hierarchical structure and function of a cell
    Jianzhu Ma, Michael Ku Yu, Samson Fong, Keiichiro Ono, Eric Sage, Barry Demchak, Roded Sharan, Trey Ideker
    Nature Methods 2018

  • Deciphering signaling specificity with deep neural networks
    Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng
    RECOMB 2018 co-first author

     
  • Annotating gene sets by mining large literature collections with protein networks
    Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W Huang, Jiawei Han, Jian Peng, Trey Ideker
    Pacific Symposium on Biocomputing, 2018 co-first author

     
  • DeepBound: Accurate Identification of Transcript Boundaries via Deep Convolutional Neural Fields
    Mingfu Shao, Jianzhu Ma, Sheng Wang
    ISMB 2017 co-first author

     
  • AUCpreD: proteome-level protein disorder prediction by AUC-maximized Deep Convolutional Neural Fields
    Sheng Wang, Jianzhu Ma, Jinbo Xu
    ECCB 2016

     
  • ModuleAlign: Module-based global alignment of protein-protein interaction networks
    Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu
    ECCB 2016

     
  • Protein secondary structure prediction using deep convolutional neural fields
    Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
    Scientific Reports 2016

     
  • Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage
    Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
    ACM BCB 2016

     
  • AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multi-Task Learning Framework under the Conditional Random Fields Model
    Jianzhu Ma and Sheng Wang
    BioMed Research International 2015

     
  • Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning
    Jianzhu Ma, Sheng Wang, Zhiyong Wang and Jinbo Xu
    RECOMB and Biofinformatics 2015

     
  • MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
    Jianzhu Ma, Sheng Wang, Jinbo Xu
    RECOMB and PLOS Computational Biology 2014
    This work also won the following awards:

    • Best Paper Award of RECOMB 2014

    • Best Poster Award of 2nd Zing Conference on Protein and RNA Structure Prediction

    • Warren DeLano Award of 3DSIG 2014

  • Predicting diverse M-best protein contact maps
    Siqi Sun,Jianzhu Ma, Jinbo Xu
    BIBM 2015

     
  • DeepCNF-D: Predicting Protein Order/Disorder Regions by Weighted Deep Convolutional Neural Fields
    Sheng Wang, Jianzhu Ma, Jinbo Xu
    International Journal of Molecular Sciences 2015

     
  • An Integrative Computational Approach for Prioritization of Genomic Variants
    Inna Dubchak, Sandhya Balasubramanian, Sheng Wang, Cem Meyden, Dinanath Sulakhe, Alexander Poliakov, Daniela Börnigen, Bingqing Xie, Andrew Taylor, Jianzhu Ma, Alex R Paciorkowski, Ghayda M Mirzaa, Paul Dave, Gady Agam, Jinbo Xu, Lihadh Al-Gazali, Christopher E Mason, M Elizabeth Ross, Natalia Maltsev and T Conrad Gilliam
    PLOS ONE 2015

     
  • Algorithms, Applications and Challenges of Protein Structure Alignment
    Jianzhu Ma and Sheng Wang
    Journal of Advances in Protein Chemistry and Structural Biology 2014

     
  • Protein Threading Using Context-Specific Alignment Potential
    Jianzhu Ma, Sheng Wang and Jinbo Xu
    ISMB 2013

     
  • A Conditional Neural Fields Model for Protein Threading
    Jianzhu Ma, Jian Peng, Sheng Wang and Jinbo Xu
    ISMB 2012

     
  • Fast and Automatic Pairwise Structure Alignment Algorithm close to Manually-Curated Precision
    Scientific Reports and 3DSIG 2012. Warren DeLano Award

     
  • A Self-Adaptive Mechanism for Software Configuration Based on Case-based Reasoning and Policy
    Maoguang Wang, Hong Mei, Wenpin Jiao, Junjing Jie and Jianzhu Ma
    AICI 2010

     
  • An Empirical Study on the Impacts of Autonomy of Components on Qualities of Software Systems
    Shiting Xun, Jianzhu Ma, Wenpin Jiao and Fanjing Meng
    EASe 2011

     
  • A Two-way Selections based Approach to Automated Integration of Multi-Agent Systems
    Xi Fang, Jianzhu Ma, Maoguang Wang and Wenpin Jiao
    3rd National Conference on Agent Theory and Application 2010

     
  • A Browser-based Framework for Data Cache in Web-Delivered Service Composition
    Jiyu Huang, Xuanzhe Liu, Qi Zhao, Jianzhu Ma and Gang Huang
    SOCA 2010 (Best paper running up)

     
  • Design and Implementation of a Cooperate Framework for Autonomous Component based on Rule Injection
    Jianzhu Ma, Jiyu Huang and Wenpin Jiao
    NASAC 2009