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Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs


Sep 30, 2021
Zhao Xu, Youzhi Luo, Xuan Zhang, Xinyi Xu, Yaochen Xie, Meng Liu, Kaleb Dickerson, Cheng Deng, Maho Nakata, Shuiwang Ji


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Group Contrastive Self-Supervised Learning on Graphs


Jul 20, 2021
Xinyi Xu, Cheng Deng, Yaochen Xie, Shuiwang Ji


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


Jun 16, 2021
Meng Liu, Cong Fu, Xuan Zhang, Limei Wang, Yaochen Xie, Hao Yuan, Youzhi Luo, Zhao Xu, Shenglong Xu, Shuiwang Ji

* One of the winners of 2021 KDD Cup on OGB Large-Scale Challenge 

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Graph Neural Networks with Adaptive Frequency Response Filter


Apr 26, 2021
Yushun Dong, Kaize Ding, Brian Jalaian, Shuiwang Ji, Jundong Li


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Stochastic Optimization of Area Under Precision-Recall Curve for Deep Learning with Provable Convergence


Apr 18, 2021
Qi Qi, Youzhi Luo, Zhao Xu, Shuiwang Ji, Tianbao Yang

* 30 pages, 2 figures 

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


Mar 23, 2021
Meng Liu, Youzhi Luo, Limei Wang, Yaochen Xie, Hao Yuan, Shurui Gui, Zhao Xu, Haiyang Yu, Jingtun Zhang, Yi Liu, Keqiang Yan, Bora Oztekin, Haoran Liu, Xuan Zhang, Cong Fu, Shuiwang Ji


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Sent2Matrix: Folding Character Sequences in Serpentine Manifolds for Two-Dimensional Sentence


Mar 15, 2021
Hongyang Gao, Yi Liu, Xuan Zhang, Shuiwang Ji

* 8 pages 

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Adversarial Graph Disentanglement


Mar 12, 2021
Shuai Zheng, Zhenfeng Zhu, Zhizhe Liu, Shuiwang Ji, Yao Zhao

* In process 

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Spherical Message Passing for 3D Graph Networks


Feb 26, 2021
Yi Liu, Limei Wang, Meng Liu, Xuan Zhang, Bora Oztekin, Shuiwang Ji

* 16 pages, 8 figures, 8 tables 

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Self-Supervised Learning of Graph Neural Networks: A Unified Review


Feb 23, 2021
Yaochen Xie, Zhao Xu, Zhengyang Wang, Shuiwang Ji

* 17 pages, 6 figures 

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On Explainability of Graph Neural Networks via Subgraph Explorations


Feb 09, 2021
Hao Yuan, Haiyang Yu, Jie Wang, Kang Li, Shuiwang Ji


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GraphDF: A Discrete Flow Model for Molecular Graph Generation


Feb 01, 2021
Youzhi Luo, Keqiang Yan, Shuiwang Ji

* 14 pages, 4 figures 

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GraphEBM: Molecular Graph Generation with Energy-Based Models


Jan 31, 2021
Meng Liu, Keqiang Yan, Bora Oztekin, Shuiwang Ji

* 13 pages 

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A Multi-Stage Attentive Transfer Learning Framework for Improving COVID-19 Diagnosis


Jan 14, 2021
Yi Liu, Shuiwang Ji

* 12 pages, 4 figures, 6 tables 

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


Jan 12, 2021
Yi Liu, Shuiwang Ji

* 10 pages, 3 figures, 6 tables 

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Node2Seq: Towards Trainable Convolutions in Graph Neural Networks


Jan 06, 2021
Hao Yuan, Shuiwang Ji


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Explainability in Graph Neural Networks: A Taxonomic Survey


Dec 31, 2020
Hao Yuan, Haiyang Yu, Shurui Gui, Shuiwang Ji


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MoleculeKit: Machine Learning Methods for Molecular Property Prediction and Drug Discovery


Dec 02, 2020
Zhengyang Wang, Meng Liu, Youzhi Luo, Zhao Xu, Yaochen Xie, Limei Wang, Lei Cai, Shuiwang Ji

* Supplementary Material: https://documentcloud.adobe.com/link/track?uri=urn:aaid:scds:US:d0ca85d1-c6f9-428b-ae2b-c3bf3257196d 

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Towards Improved and Interpretable Deep Metric Learning via Attentive Grouping


Nov 19, 2020
Xinyi Xu, Zhengyang Wang, Cheng Deng, Hao Yuan, Shuiwang Ji


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Augmented Equivariant Attention Networks for Electron Microscopy Image Super-Resolution


Nov 06, 2020
Yaochen Xie, Yu Ding, Shuiwang Ji


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Noise2Same: Optimizing A Self-Supervised Bound for Image Denoising


Oct 22, 2020
Yaochen Xie, Zhengyang Wang, Shuiwang Ji

* 15 pages, NeurIPS 2020 

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


Oct 20, 2020
Lei Cai, Zhengyang Wang, Rob Kulathinal, Sudhir Kumar, Shuiwang Ji


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Line Graph Neural Networks for Link Prediction


Oct 20, 2020
Lei Cai, Jundong Li, Jie Wang, Shuiwang Ji


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Topology-Aware Graph Pooling Networks


Oct 19, 2020
Hongyang Gao, Yi Liu, Shuiwang Ji

* 8 pages, 4 figures, 5 tables 

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CorDEL: A Contrastive Deep Learning Approach for Entity Linkage


Sep 15, 2020
Zhengyang Wang, Bunyamin Sisman, Hao Wei, Xin Luna Dong, Shuiwang Ji

* Accepted by the 20th IEEE International Conference on Data Mining (ICDM 2020) 

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Global Voxel Transformer Networks for Augmented Microscopy


Aug 05, 2020
Zhengyang Wang, Yaochen Xie, Shuiwang Ji

* Supplementary Material: https://documentcloud.adobe.com/link/track?uri=urn:aaid:scds:US:967e80e2-d90e-49ad-b4f9-f6ca12379e1f 

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Machine Learning Explanations to Prevent Overtrust in Fake News Detection


Jul 27, 2020
Sina Mohseni, Fan Yang, Shiva Pentyala, Mengnan Du, Yi Liu, Nic Lupfer, Xia Hu, Shuiwang Ji, Eric Ragan


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Second-Order Pooling for Graph Neural Networks


Jul 20, 2020
Zhengyang Wang, Shuiwang Ji

* IEEE Transactions on Pattern Analysis and Machine Intelligence, 2020 
* 12 pages, 2 figures, https://www.computer.org/csdl/journal/tp/5555/01/09104936/1kj0O2A1yBa 

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Deep Learning of High-Order Interactions for Protein Interface Prediction


Jul 18, 2020
Yi Liu, Hao Yuan, Lei Cai, Shuiwang Ji

* 10 pages, 3 figures, 4 tables. KDD2020 

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