Publications

Accepted Manuscripts

  • Zhengyang Wang and Shuiwang Ji
    Second-Order Pooling for Graph Neural Networks
    IEEE Transactions on Pattern Analysis and Machine Intelligence

  • Hongyang Gao, Zhengyang Wang, Lei Cai, and Shuiwang Ji
    ChannelNets: Compact and Efficient Convolutional Neural Networks via Channel-Wise Convolutions
    IEEE Transactions on Pattern Analysis and Machine Intelligence

2020

  • Yaochen Xie, Zhengyang Wang, and Shuiwang Ji
    Noise2Same: Optimizing A Self-Supervised Bound for Image Denoising
    The 34th Annual Conference on Neural Information Processing Systems (NeurIPS), x-x, 2020

  • Hao Yuan and Shuiwang Ji
    StructPool: Structured Graph Pooling via Conditional Random Fields
    The 8th International Conference on Learning Representations (ICLR), 2020

  • Hongyang Gao, Zhengyang Wang, and Shuiwang Ji
    Kronecker Attention Networks
    The 26th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 229-237, 2020

  • Meng Liu, Hongyang Gao, and Shuiwang Ji
    Towards Deeper Graph Neural Networks
    The 26th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 338-348, 2020

  • Hao Yuan, Jiliang Tang, Xia Hu, and Shuiwang Ji
    XGNN: Towards Model-Level Explanations of Graph Neural Networks
    The 26th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 430-438, 2020

  • Yi Liu, Hao Yuan, Lei Cai, and Shuiwang Ji
    Deep Learning of High-Order Interactions for Protein Interface Prediction
    The 26th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 679-687, 2020

  • Hongyang Gao, Lei Cai, and Shuiwang Ji
    Adaptive Convolutional ReLUs
    The 34th AAAI Conference on Artificial Intelligence (AAAI), 3914-3921, 2020

  • Zhengyang Wang, Na Zou, Dinggang Shen, and Shuiwang Ji
    Non-local U-Nets for Biomedical Image Segmentation
    The 34th AAAI Conference on Artificial Intelligence (AAAI), 6315-6322, 2020

  • Lei Cai and Shuiwang Ji
    A Multi-Scale Approach for Graph Link Prediction
    The 34th AAAI Conference on Artificial Intelligence (AAAI), 3308-3315, 2020

  • Hanzi Mao, Xi Liu, Nick Duffield, Hao Yuan, Shuiwang Ji, and Binayak Mohanty
    Context-Aware Deep Representation Learning for Geo-Spatiotemporal Analysis
    IEEE International Conference on Data Mining (ICDM), x-x, 2020

  • Zhengyang Wang, Bunyamin Sisman, Hao Wei, Xin Luna Dong, and Shuiwang Ji
    CorDEL: A Contrastive Deep Learning Approach for Entity Linkage
    IEEE International Conference on Data Mining (ICDM), x-x, 2020

  • Fan Yang, Ninghao Liu, Mengnan Du, Kaixiong Zhou, Shuiwang Ji, Xia Hu
    Deep Neural Networks with Knowledge Instillation
    SIAM International Conference on Data Mining (SDM), 370-378, 2020

  • Hongyang Gao, Hao Yuan, Zhengyang Wang, and Shuiwang Ji
    Pixel Transposed Convolutional Networks
    IEEE Transactions on Pattern Analysis and Machine Intelligence, 42(5): 1218-1227, 2020

2019

  • Debrup Banerjee, Kazi Islam, Keyi Xue, Gang Mei, Lemin Xiao, Guangfan Zhang, Roger Xu, Lei Cai, Shuiwang Ji, and Jiang Li
    A Deep Transfer Learning Approach for Improved Post Traumatic Stress Disorder Diagnosis
    Knowledge and Information Systems, 60(3): 1693-1724, 2019

  • Hongyang Gao and Shuiwang Ji
    Graph U-Nets
    The 36th International Conference on Machine Learning (ICML), 2083-2092, 2019
    [Code]

  • Hongyang Gao and Shuiwang Ji
    Graph Representation Learning via Hard and Channel-Wise Attention Networks
    The 25th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 741-749, 2019

  • Lei Cai and Shuiwang Ji
    An Efficient Policy Gradient Method for Conditional Dialogue Generation
    The 19th IEEE International Conference on Data Mining (ICDM), 31-40, 2019

  • Hao Yuan, Na Zou, Shaoting Zhang, Hanchuan Peng, and Shuiwang Ji
    Learning Hierarchical and Shared Features for Improving 3D Neuron Reconstruction
    The 19th IEEE International Conference on Data Mining (ICDM), 806-815, 2019

  • Yi Liu, Hao Yuan, and Shuiwang Ji
    Leaning Local and Global Multi-Context Representations for Document Classification
    The 19th IEEE International Conference on Data Mining (ICDM), 1234-1239, 2019

  • Hongyang Gao, Yongjun Chen, and Shuiwang Ji
    Learning Graph Pooling and Hybrid Convolutional Operations for Text Representations
    The Web Conference (WWW), 2743-2749, 2019

  • Mengnan Du, Ninghao Liu, Fan Yang, Shuiwang Ji, and Xia Hu
    On Attribution of Recurrent Neural Network Predictions via Additive Decomposition
    The Web Conference (WWW), 383-393, 2019

  • Fan Yang, Shiva Pentyala, Sina Mohseni, Mengnan Du, Hao Yuan, Rhema Linder, Eric Ragan, Shuiwang Ji, and Xia Hu
    XFake: Explainable Fake News Detector with Visualizations
    The Web Conference (WWW), Demonstrations Track, 3600-3604, 2019

  • Hao Yuan, Yongjun Chen, Xia Hu, and Shuiwang Ji
    Interpreting Deep Models for Text Analysis via Optimization and Regularization Methods
    The 33rd AAAI Conference on Artificial Intelligence (AAAI), 5717-5724, 2019

  • Jun Li, Yongjun Chen, Lei Cai, Ian Davidson, and Shuiwang Ji
    Dense Transformer Networks for Brain Electron Microscopy Image Segmentation
    The 28th International Joint Conference on Artificial Intelligence (IJCAI), 2894-2900, 2019

  • Zhengyang Wang, Hao Yuan, and Shuiwang Ji
    Spatial Variational Auto-Encoding via Matrix-Variate Normal Distributions
    The SIAM International Conference on Data Mining (SDM), 648-656, 2019

  • Lei Cai, Hongyang Gao, and Shuiwang Ji
    Multi-Stage Variational Auto-Encoders for Coarse-to-Fine Image Generation
    The SIAM International Conference on Data Mining (SDM), 630-638, 2019

  • Yin Zhang, Ninghao Liu, Shuiwang Ji, James Caverlee, Xia Hu
    An Interpretable Neural Model with Interactive Stepwise Influence
    The 23rd Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), 528-540, 2019

2018

  • Zhengyang Wang and Shuiwang Ji
    Smoothed Dilated Convolutions for Improved Dense Prediction
    The 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 2486-2495, 2018

  • Yongjun Chen, Hongyang Gao, Lei Cai, Min Shi, Dinggang Shen, and Shuiwang Ji
    Voxel Deconvolutional Networks for 3D Brain Image Labeling
    The 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 1226-1234, 2018

  • Hongyang Gao, Zhengyang Wang, and Shuiwang Ji
    Large-Scale Learnable Graph Convolutional Networks
    The 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 1416-1424, 2018
    [Code]

  • Lei Cai, Zhengyang Wang, Hongyang Gao, Dinggang Shen, and Shuiwang Ji
    Deep Adversarial Learning for Multi-Modality Missing Data Completion
    The 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 1158-1166, 2018

  • Zhengyang Wang and Shuiwang Ji
    Learning Convolutional Text Representations for Visual Question Answering
    The SIAM International Conference on Data Mining (SDM), 594-602, 2018
    [code]

  • Lei Cai, Bian Wu, and Shuiwang Ji
    Neuronal Activities in the Mouse Visual Cortex Predict Patterns of Sensory Stimuli
    Neuroinformatics, 16(3):473-488, 2018

  • Zhongyu Li, Erik Butler, Kang Li, Aidong Lu, Shuiwang Ji, and Shaoting Zhang
    Large-Scale Exploration of Neuronal Morphologies Using Deep Learning and Augmented Reality
    Neuroinformatics, 16(3):339-349, 2018

  • Lei Zhang, Yao Zhao, Zhenfeng Zhu, Dinggang Shen, and Shuiwang Ji
    Multi-View Missing Data Completion
    IEEE Transactions on Knowledge and Data Engineering, 30(7): 1296-1309, 2018

2017

  • Tao Zeng, Bian Wu, Jiayu Zhou, Ian Davidson and Shuiwang Ji
    Recurrent Encoder-Decoder Networks for Time-Varying Dense Prediction
    The IEEE International Conference on Data Mining (ICDM), 1165-1170, 2017

  • Hongyang Gao and Shuiwang Ji
    Efficient and Invariant Convolutional Neural Networks for Dense Prediction
    The IEEE International Conference on Data Mining (ICDM), 871-876, 2017

  • Debrup Banerjee, Kazi Islam, Gang Mei, Lemin Xiao, Roger Xu, Shuiwang Ji, and Jiang Li
    A Deep Transfer Learning Approach for Post Traumatic Stress Disorder Diagnosis
    The IEEE International Conference on Data Mining (ICDM), 11-20, 2017

  • Qi Wang, Mengying Sun, Liang Zhan, Paul Thompson, Shuiwang Ji, and Jiayu Zhou
    Multi-Modality Disease Modeling via Collective Deep Matrix Factorization
    The 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 1155-1164, 2017

  • Tao Zeng, Bian Wu, and Shuiwang Ji
    DeepEM3D: Approaching human-level performance on 3D anisotropic EM image segmentation
    Bioinformatics, 33(16): 2555-2562, 2017 (Impact factor: 7.307)

  • Rongjian Li, Tao Zeng, Hanchuan Peng, and Shuiwang Ji
    Deep Learning Segmentation of Optical Microscopy Images Improves 3-D Neuron Reconstruction
    IEEE Transactions on Medical Imaging, 36(7):1533-1541, 2017

2016

  • Ahmed Fakhry, Hanchuan Peng, and Shuiwang Ji
    Deep models for brain EM image segmentation: novel insights and improved performance
    Bioinformatics, 32: 2352-2358, 2016 (5-Yr impact factor: 7.685)

  • Rongjian Li, Dong Si, Tao Zeng, Shuiwang Ji, and Jing He
    Deep Convolutional Neural Networks for Detecting Secondary Structures in Protein Density Maps from Cryo-Electron Microscopy
    IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 41-46, 2016

  • Qingyang Li, Shuang Qiu, Shuiwang Ji, Paul Thompson, Jieping Ye, and Jie Wang
    Parallel Lasso Screening for Big Data Optimization
    The 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 1705-1714, 2016

  • Kaixiang Lin, Jianpeng Xu, Inci Baytas, Shuiwang Ji, and Jiayu Zhou
    Multi-Task Feature Interaction Learning
    The 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 1735-1744, 2016

  • Lei Zhang, Shupeng Wang, Xiaoyu Zhang, Yong Wang, Binbin Li, Dinggang Shen, and Shuiwang Ji
    Collaborative Multi-View Denoising
    The 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 2045-2054, 2016

2015

  • Tao Zeng and Shuiwang Ji
    Deep Convolutional Neural Networks for Multi-Instance Multi-Task Learning
    The IEEE International Conference on Data Mining (ICDM), 579-588, 2015

  • Wenlu Zhang, Rongjian Li, Tao Zeng, Qian Sun, Sudhir Kumar, Jieping Ye, and Shuiwang Ji
    Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis
    The 21st ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 1475-1484, 2015

  • Sen Yang, Qian Sun, Shuiwang Ji, Peter Wonka, Ian Davidson, Jieping Ye
    Structural Graphical Lasso for Learning Mouse Brain Connectivity
    The 21st ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 1385-1394, 2015

  • Rongjian Li, Wenlu Zhang, Yao Zhao, Zhenfeng Zhu, and Shuiwang Ji
    Sparsity Learning Formulations for Mining Time-Varying Data
    IEEE Transactions on Knowledge and Data Engineering, 27(5): 1411-1423, 2015

  • Tao Yang, Xinlin Zhao, Binbin Lin, Tao Zeng, Shuiwang Ji, and Jieping Ye
    Automated Gene Expression Pattern Annotation in the Mouse Brain
    The 20th Pacific Symposium on Biocomputing (PSB), 144-155, 2015

2014

  • Rongjian Li, Wenlu Zhang, Heung-Il Suk, Li Wang, Jiang Li, Dinggang Shen, and Shuiwang Ji
    Deep Learning Based Imaging Data Completion for Improved Brain Disease Diagnosis
    The Seventeenth International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 305-312, 2014

  • Feng Li, Loc Tran, Kim-Ham Thung, Shuiwang Ji, Dinggang Shen, and Jiang Li
    Robust Deep Learning for Improved Classification of AD/MCI Patients
    The Fifth MICCAI Workshop on Machine Learning in Medical Imaging (MLMI), 2014

2013

  • Wenlu Zhang, Shuiwang Ji, and Rui Zhang
    Evolutionary Soft Co-Clustering
    The 2013 SIAM International Conference on Data Mining (SDM 2013), 121-129, 2013

2012

  • Shuiwang Ji, Wenlu Zhang, and Jun Liu
    A Sparsity-Inducing Formulation for Evolutionary Co-Clustering
    The Eighteenth ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2012), 334-342, 2012

  • Shahram Mohrehkesh, Shuiwang Ji, Tamer Nadeem, and Michele C. Weigle
    Demographic Prediction of Mobile User from Phone Usage
    Mobile Data Challenge Workshop, Nokia Research Center, 2012
    Second Prize on Demographic Prediction

  • Dong Si, Shuiwang Ji, Kamal Al Nasr, and Jing He
    A Machine Learning Approach for the Identification of Protein Secondary Structure Elements from Electron Cryo-Microscopy Density Maps
    Biopolymers, 97(9):698-708, 2012

  • Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye and Zhi-Hua Zhou
    Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(1):98-112, 2012

2011

  • Shuiwang Ji
    Computational network analysis of the anatomical and genetic organizations in the mouse brain
    Bioinformatics, 27(23):3293-3299, 2011

  • Sudhir Kumar, Charlotte Konikoff, Bernard Van Emden, Christopher Busick, Kailah T. Davis, Shuiwang Ji, Lin-Wei Wu, Hector Ramos, Thomas Brody, Sethuraman Panchanathan, Jieping Ye, Timothy L. Karr, Kristyn Gerold, Michael McCutchan and Stuart J. Newfeld
    FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis
    Bioinformatics, 27(23):3319-3320, 2011

  • Liang Sun, Shuiwang Ji and Jieping Ye
    Canonical Correlation Analysis for Multilabel Classification: A Least-Squares Formulation, Extensions, and Analysis
    IEEE Transactions on Pattern Analysis and Machine Intelligence, 33(1):194-200, 2011

2010

  • Ting Kei Pong, Paul Tseng, Shuiwang Ji and Jieping Ye
    Trace Norm Regularization: Reformulations, Algorithms, and Multi-Task Learning
    SIAM Journal on Optimization, 20(6):3465-3489, 2010

  • Shuiwang Ji, Wei Xu, Ming Yang and Kai Yu
    3D Convolutional Neural Networks for Human Action Recognition
    The Twenty-Seventh International Conference on Machine Learning (ICML 2010), 495-502, 2010

  • Shuiwang Ji, Lei Tang, Shipeng Yu and Jieping Ye
    A Shared-Subspace Learning Framework for Multi-Label Classification
    ACM Transactions on Knowledge Discovery from Data, 4(2):1-29, 2010

2009

  • Jun Liu, Shuiwang Ji and Jieping Ye
    Multi-Task Feature Learning via Efficient L21-Norm Minimization
    The Twenty-Fifth Conference on Uncertainty in Artificial Intelligence (UAI 2009), 339-348, 2009

  • Shuiwang Ji and Jieping Ye
    An Accelerated Gradient Method for Trace Norm Minimization
    The Twenty-Sixth International Conference on Machine Learning (ICML 2009), 457-464, 2009

  • Liang Sun, Shuiwang Ji and Jieping Ye
    A Least Squares Formulation for a Class of Generalized Eigenvalue Problems in Machine Learning
    The Twenty-Sixth International Conference on Machine Learning (ICML 2009), 977-984, 2009

  • Shuiwang Ji, Lei Yuan, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar and Jieping Ye
    Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-term Interactions
    The Fifteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2009), 407-416, 2009

  • Bao-Hong Shen, Shuiwang Ji and Jieping Ye
    Mining Discrete Patterns via Binary Matrix Factorization
    The Fifteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2009), 757-766, 2009

  • Shuiwang Ji and Jieping Ye
    Linear Dimensionality Reduction for Multi-Label Classification
    The Twenty-First International Joint Conference on Artificial Intelligence (IJCAI 2009), 1077-1082, 2009

  • Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye and Zhi-Hua Zhou
    Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning
    The Twenty-First International Joint Conference on Artificial Intelligence (IJCAI 2009), 1445-1450, 2009

  • Liang Sun, Shuiwang Ji and Jieping Ye
    On the Equivalence Between Canonical Correlation Analysis and Orthonormalized Partial Least Squares
    The Twenty-First International Joint Conference on Artificial Intelligence (IJCAI 2009), 1230-1235, 2009

  • Ming Yang, Shuiwang Ji, Wei Xu, Jinjun Wang, Fengjun Lv, Kai Yu, Yihong Gong, Mert Dikmen, Dennis J. Lin and Thomas S. Huang
    Detecting Human Actions in Surveillance Videos
    TREC Video Retrieval Evaluation Workshop, 2009

  • Jieping Ye and Shuiwang Ji
    Discriminant Analysis for Dimensionality Reduction: An Overview of Recent Developments
    in N. Boulgouris and K. N. Plataniotis and E. Micheli-Tzanakou (Eds), Biometrics: Theory, Methods, and Applications, 1-19, Wiley-IEEE Press, New York, 2009

2008

  • Shuiwang Ji, Liang Sun, Rong Jin, Sudhir Kumar and Jieping Ye
    Automated Annotation of Drosophila Gene Expression Patterns Using a Controlled Vocabulary
    Bioinformatics, 24(17):1881-1888, 2008

  • Jieping Ye, Shuiwang Ji and Jianhui Chen
    Multi-class Discriminant Kernel Learning via Convex Programming
    Journal of Machine Learning Research, 9:719-758, 2008

  • Shuiwang Ji and Jieping Ye
    Kernel Uncorrelated and Regularized Discriminant Analysis: A Theoretical and Computational Study
    IEEE Transactions on Knowledge and Data Engineering, 20(10):1311-1321, 2008

  • Shuiwang Ji and Jieping Ye
    Generalized Linear Discriminant Analysis: A Unified Framework and Efficient Model Selection
    IEEE Transactions on Neural Networks, 19(10):1768-1782, 2008

  • Shuiwang Ji, Liang Sun, Rong Jin and Jieping Ye
    Multi-Label Multiple Kernel Learning
    The Twenty-Second Annual Conference on Neural Information Processing Systems (NIPS 2008), 777-784, 2008

  • Shuiwang Ji, Lei Tang, Shipeng Yu and Jieping Ye
    Extracting Shared Subspace for Multi-Label Classification
    The Fourteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2008), 381-389, 2008

  • Liang Sun, Shuiwang Ji and Jieping Ye
    Hypergraph Spectral Learning for Multi-Label Classification
    The Fourteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2008), 668-676, 2008

  • Jianhui Chen, Shuiwang Ji, Betul Ceran, Qi Li, Mingrui Wu and Jieping Ye
    Learning Subspace Kernels for Classification
    The Fourteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2008), 106-114, 2008

  • Liang Sun, Shuiwang Ji and Jieping Ye
    A Least Squares Formulation for Canonical Correlation Analysis
    The Twenty-Fifth International Conference on Machine Learning (ICML 2008), 1024-1031, 2008

  • Shuiwang Ji and Jieping Ye
    A Unified Framework for Generalized Linear Discriminant Analysis
    The IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2008), 1-7, 2008

2007

  • Jieping Ye, Shuiwang Ji and Jianhui Chen
    Learning the Kernel Matrix in Discriminant Analysis via Quadratically Constrained Quadratic Programming
    The Thirteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2007), 854-863, 2007

  • Jieping Ye, Jianhui Chen and Shuiwang Ji
    Discriminant Kernel and Regularization Parameter Learning via Semidefinite Programming
    The Twenty-Fourth International Conference on Machine Learning (ICML 2007), 1095-1102, 2007