# overview
Shuiwang Ji is currently an Associate Professor in the Department of Computer Science & Engineering, Texas A&M University, leading the Data Integration, Visualization, and Exploration (DIVE) Laboratory. Ji received the Ph.D. degree in Computer Science from Arizona State University in 2010, advised by Prof. Jieping Ye. His research interests include machine learning, data mining, and computational neuroscience. Ji received the National Science Foundation CAREER Award in 2014. He has authored over 80 research articles and has coauthored a book. Currently, Ji serves as an Action Editor for Data Mining and Knowledge Discovery, and an Associate Editor for ACM Transactions on Knowledge Discovery from Data, IEEE Transactions on Neural Networks and Learning Systems, and BMC Bioinformatics. Ji is a Program Chair for the 2017 Bioimage Informatics Conference and a senior member of IEEE.

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Networking And Information Technology R&d

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5 Development Of Treatments And Therapeutic Interventions

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1.1 Normal Biological Development And Functioning

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3404 Medicinal And Biomolecular Chemistry

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3102 Bioinformatics And Computational Biology

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Networking And Information Technology R&d (nitrd)

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3102 Bioinformatics And Computational Biology

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Gene Expression Pattern Image Annotation

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Networking And Information Technology R&d

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Networking And Information Technology R&d

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Networking And Information Technology R&d

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4603 Computer Vision And Multimedia Computation

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Networking And Information Technology R&d (nitrd)

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4607 Graphics, Augmented Reality And Games

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Networking And Information Technology R&d

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Alzheimer's Disease Including Alzheimer's Disease Related Dementias (ad/adrd)

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Arizona State University - (Tempe, Arizona, United States)

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A Deep Learning Approach for Targeted Contrast-Enhanced Ultrasound Based Prostate Cancer Detection.

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Institute of Electrical and Electronics Engineers (IEEE)

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Deep convolutional neural networks for multi-modality isointense infant brain image segmentation.

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Learning Graph Pooling and Hybrid Convolutional Operations for Text Representations

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Association for Computing Machinery (ACM)

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Discriminant sparse neighborhood preserving embedding for face recognition

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XFake: Explainable Fake News Detector with Visualizations

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Hypergraph spectral learning for multi-label classification

# publications[].publisher
Association for Computing Machinery (ACM)

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Advanced Graph and Sequence Neural Networks for Molecular Property  Prediction and Drug Discovery

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How to Estimate the Regularization Parameter for Spectral Regression Discriminant Analysis and its Kernel Version?

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Institute of Electrical and Electronics Engineers (IEEE)

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Group Contrastive Self-Supervised Learning on Graphs.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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A least squares formulation for a class of generalized eigenvalue problems in machine learning

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Association for Computing Machinery (ACM)

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Global Pixel Transformers for Virtual Staining of Microscopy Images.

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Institute of Electrical and Electronics Engineers (IEEE)

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Fast Quantum Property Prediction via Deeper 2D and 3D Graph Networks

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CleftNet: Augmented Deep Learning for Synaptic Cleft Detection From Brain Electron Microscopy.

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Institute of Electrical and Electronics Engineers (IEEE)

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Allen mouse brain atlases reveal different neural connection and gene expression patterns in cerebellum gyri and sulci.

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Dense Transformer Networks for Brain Electron Microscopy Image Segmentation

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International Joint Conferences on Artificial Intelligence

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Advanced graph and sequence neural networks for molecular property prediction and drug discovery.

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Institute of Electrical and Electronics Engineers (IEEE)

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Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning.

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Spherical Message Passing for 3D Graph Networks

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An Interpretable Neural Model with Interactive Stepwise Influence

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Society for Industrial & Applied Mathematics (SIAM)

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Recurrent Encoder-Decoder Networks for Time-Varying Dense Prediction

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Institute of Electrical and Electronics Engineers (IEEE)

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Automated identification of cell-type-specific genes in the mouse brain by image computing of expression patterns.

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Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering.

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A bag-of-words approach for Drosophila gene expression pattern annotation.

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Deep Convolutional Neural Networks for Multi-Instance Multi-Task Learning

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Group Contrastive Self-Supervised Learning on Graphs

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Stochastic Optimization of Areas Under Precision-Recall Curves with  Provable Convergence

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Interpreting Image Classifiers by Generating Discrete Masks.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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A probabilistic latent semantic analysis model for coclustering the mouse brain atlas.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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A least squares formulation for a class of generalized eigenvalue problems in machine learning

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Generating 3D Molecules for Target Protein Binding

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Voxel Deconvolutional Networks for 3D Brain Image Labeling.

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Association for Computing Machinery (ACM)

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Parallel Lasso Screening for Big Data Optimization

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Association for Computing Machinery (ACM)

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Residual Deconvolutional Networks for Brain Electron Microscopy Image Segmentation.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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On Attribution of Recurrent Neural Network Predictions via Additive Decomposition

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Association for Computing Machinery (ACM)

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Institute of Electrical and Electronics Engineers (IEEE)

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ChannelNets: Compact and Efficient Convolutional Neural Networks via Channel-Wise Convolutions.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Global Voxel Transformer Networks for Augmented Microscopy

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Learning Local and Global Multi-Context Representations for Document Classification

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Adaptive diffusion kernel learning from biological networks for protein function prediction.

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A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis.

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Non-local U-Net for Biomedical Image Segmentation

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Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval.

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Drosophila gene expression pattern annotation through multi-instance multi-label learning.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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AdaGNN: Graph Neural Networks with Adaptive Frequency Response Filter

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Global analysis of gene expression and projection target correlations in the mouse brain.

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Graph and Geometry Generative Modeling for Drug Discovery

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Association for Computing Machinery (ACM)

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Learning subspace kernels for classification

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Association for Computing Machinery (ACM)

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Computational modeling of cellular structures using conditional deep generative networks.

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Deep Learning Segmentation of Optical Microscopy Images Improves 3-D Neuron Reconstruction.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Development of XantheneBased Fluorescent Dyes: Machine LearningAssisted Prediction vs. TDDFT Prediction and Experimental Validation

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Second-Order Pooling for Graph Neural Networks.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Workshop on Optimization Based Methods for Emerging Data Mining Problems

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].publisher
Association for Computing Machinery (ACM)

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Image-level and group-level models for Drosophila gene expression pattern annotation.

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Deep models for brain EM image segmentation: novel insights and improved performance.

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A Unified Framework for Generalized Linear Discriminant Analysis

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Institute of Electrical and Electronics Engineers (IEEE)

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CorDEL: A Contrastive Deep Learning Approach for Entity Linkage

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Automated annotation of Drosophila gene expression patterns using a controlled vocabulary.

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Multi-class discriminant kernel learning via convex programming

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Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression.

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Segmenting Delaminations in Carbon Fiber Reinforced Polymer Composite CT using Convolutional Neural Networks

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Machine Learning Explanations to Prevent Overtrust in Fake News  Detection

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XGNN: Towards Model-Level Explanations of Graph Neural Networks

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Association for Computing Machinery (ACM)

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GraphDF: A Discrete Flow Model for Molecular Graph Generation

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Smoothed Dilated Convolutions for Improved Dense Prediction

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Association for Computing Machinery (ACM)

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Sparsity Learning Formulations for Mining Time-Varying Data

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Learning the Kernel Matrix in Discriminant Analysis via Quadratically Constrained Quadratic Programming

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Association for Computing Machinery (ACM)

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Learning Task-relevant Representations for Generalization via Characteristic Functions of Reward Sequence Distributions

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Association for Computing Machinery (ACM)

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FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis.

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Deep Low-Shot Learning for Biological Image Classification and Visualization From Limited Training Samples.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Large-scale Exploration of Neuronal Morphologies Using Deep Learning and Augmented Reality.

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Multiview Partitioning via Tensor Methods

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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An accelerated gradient method for trace norm minimization

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Deep Convolutional Neural Networks for Detecting Secondary Structures in Protein Density Maps from Cryo-Electron Microscopy.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].publisher
Association for Computing Machinery (ACM)

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A Shared-Subspace Learning Framework for Multi-Label Classification

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Association for Computing Machinery (ACM)

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Deep Learning of High-Order Interactions for Protein Interface Prediction

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Association for Computing Machinery (ACM)

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3D convolutional neural networks for human action recognition

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Learning Hierarchical and Shared Features for Improving 3D Neuron Reconstruction

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Duality-Induced Regularizer for Semantic Matching Knowledge Graph Embeddings.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Frontiers of Graph Neural Networks with DIG

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Association for Computing Machinery (ACM)

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Automated Data Augmentations for Graph Classification

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Explainability in Graph Neural Networks: A Taxonomic Survey

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Automated gene expression pattern annotation in the mouse brain.

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Deep Low-Shot Learning for Biological Image Classification and  Visualization from Limited Training Samples

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Canonical correlation analysis for multilabel classification: a least-squares formulation, extensions, and analysis.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Line Graph Neural Networks for Link Prediction.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-Term Interactions.

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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An Efficient Policy Gradient Method for Conditional Dialogue Generation

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Explainability in Graph Neural Networks: A Taxonomic Survey.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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On the Equivalence Between Canonical Correlation Analysis and Orthonormalized Partial Least Squares

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Discriminant kernel and regularization parameter learning via semidefinite programming

# publications[].publisher
Association for Computing Machinery (ACM)

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Towards structured NLP interpretation via graph explainers

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Multi-Modality Disease Modeling via Collective Deep Matrix Factorization

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Association for Computing Machinery (ACM)

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Extracting shared subspace for multi-label classification

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Association for Computing Machinery (ACM)

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Three-dimensional protein shape similarity analysis based on hybrid features.

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Efficient and Invariant Convolutional Neural Networks for Dense Prediction

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Towards Improved and Interpretable Deep Metric Learning via Attentive Grouping.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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Preface to the Large Scale Visual Analytics Workshop

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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An accelerated gradient method for trace norm minimization

# publications[].publisher
Association for Computing Machinery (ACM)

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BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology

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Kernel uncorrelated and regularized discriminant analysis: A theoretical and computational study

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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TRACE NORM REGULARIZATION: REFORMULATIONS, ALGORITHMS, AND MULTI-TASK LEARNING

# publications[].publisher
Society for Industrial & Applied Mathematics (SIAM)

# publications[].label
On Explainability of Graph Neural Networks via Subgraph Explorations

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
GraphEBM: Molecular Graph Generation with Energy-Based Models

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DIG: A Turnkey Library for Diving into Graph Deep Learning Research

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A Deep Transfer Learning Approach for Improved Post-Traumatic Stress Disorder Diagnosis

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Structural Graphical Lasso for Learning Mouse Brain Connectivity

# publications[].publisher
Association for Computing Machinery (ACM)

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Deep Learning Based Imaging Data Completion for Improved Brain Disease Diagnosis

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Machine Learning Explanations to Prevent Overtrust in Fake News Detection

# publications[].publisher
Association for the Advancement of Artificial Intelligence (AAAI)

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Discriminant Analysis for Dimensionality Reduction: An Overview of Recent Developments

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Neuronal Activities in the Mouse Visual Cortex Predict Patterns of Sensory Stimuli.

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A Robust Deep Model for Improved Classification of AD/MCI Patients.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.

# publications[].label
CorDEL: A Contrastive Deep Learning Approach for Entity Linkage

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Mining Discrete Patterns via Binary Matrix Factorization

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Deep Adversarial Learning for Multi-Modality Missing Data Completion

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
FlowX: Towards Explainable Graph Neural Networks via Message Flows.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Augmented Equivariant Attention Networks for Microscopy Image Transformation.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Deep convolutional neural networks for annotating gene expression patterns in the mouse brain.

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Adversarial Attacks and Defenses on Graphs

# publications[].publisher
Association for Computing Machinery (ACM)

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Computational network analysis of the anatomical and genetic organizations in the mouse brain.

# publications[].label
Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

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DeepEM3D: approaching human-level performance on 3D anisotropic EM image segmentation.

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3D convolutional neural networks for human action recognition.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
A deep transfer learning approach for improved post-traumatic stress disorder diagnosis

# publications[].label
Multi-task feature learning via efficient <inf>2, 1</inf>-norm minimization

# publications[].label
Global voxel transformer networks for augmented microscopy

# publications[].label
Robust Deep Learning for Improved Classification of AD/MCI Patients

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Deep learning based imaging data completion for improved brain disease diagnosis.

# publications[].label
Learning Convolutional Text Representations for Visual Question Answering

# publications[].publisher
Society for Industrial and Applied Mathematics

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Feature Selection Based on Structured Sparsity: A Comprehensive Study.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Non-Local U-Nets for Biomedical Image Segmentation

# publications[].publisher
Association for the Advancement of Artificial Intelligence (AAAI)

# publications[].label
XFake: Explainable Fake News Detector with Visualizations

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
A machine learning approach for the identification of protein secondary structure elements from electron cryo-microscopy density maps.

# publications[].label
Self-Supervised Learning of Graph Neural Networks: A Unified Review

# publications[].publisher
Association for Computing Machinery (ACM)

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Graph Representation Learning via Hard and Channel-Wise Attention Networks

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
IDM 2017: Workshop on Interpretable Data Mining - Bridging the Gap between Shallow and Deep Models

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Integrative analysis of the connectivity and gene expression atlases in the mouse brain.

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New phenotype discovery method by unsupervised deep representation learning empowers genetic association studies of brain imaging

# publications[].label
Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Smoothed dilated convolutions for improved dense prediction

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Self-Supervised Learning of Graph Neural Networks: A Unified Review.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Generalized linear discriminant analysis: a unified framework and efficient model selection.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
A least squares formulation for canonical correlation analysis

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
High-resolution prediction of mouse brain connectivity using gene expression patterns.

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III: Small: Collaborative Research: Structured Methods for Multi-Task Learning

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Directorate for Computer & Information Science & Engineering - (Arlington, Virginia, United States)

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BIGDATA: Collaborative Research: F: Efficient and Exact Methods for Big Data Reduction

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Directorate for Computer & Information Science & Engineering - (Arlington, Virginia, United States)

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III: Small: Deep Learning for Gene Expression Pattern Image Analysis

# researcherOn[].awardedBy.label
Directorate for Computer & Information Science & Engineering - (Arlington, Virginia, United States)

# researcherOn[].label
III: Small: Collaborative Research: Demystifying Deep Learning on Graphs: From Basic Operations to Applications

# researcherOn[].awardedBy.label
Directorate for Computer & Information Science & Engineering - (Arlington, Virginia, United States)

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Collaborative Research: ABI Innovation: Towards Computational Exploration of Large-Scale Neuro-Morphological Datasets

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Directorate for Biological Sciences - (Arlington, Virginia, United States)

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III: Medium: Collaborative Research: Towards Scalable and Interpretable Graph Neural Networks

# researcherOn[].awardedBy.label
Directorate for Computer & Information Science & Engineering - (Arlington, Virginia, United States)

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CAREER: Towards the Next Generation of Data-Driven

# researcherOn[].awardedBy.label
Directorate for Biological Sciences - (Arlington, Virginia, United States)

# researcherOn[].awardedBy.label
National Institute of Neurological Disorders and Stroke - (Bethesda, Maryland, United States)

# etdChairOf[].label
Wang, Zhengyang (2020-10). Deep Attention Networks for Images and Graphs. Doctoral Dissertation.

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Gao, Hongyang (2020-06). Graph Neural Networks: A Feature and Structure Learning Approach. Doctoral Dissertation.

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Yuan, Hao (2021-06). Towards Explainable Deep Models for Images, Texts, and Graphs. Doctoral Dissertation.