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Motif-aware Attribute Masking for Molecular Graph Pre-training

8 September 2023

Papers citing "Motif-aware Attribute Masking for Molecular Graph Pre-training"

37 / 37 papers shown

Title
Pre-training Graph Neural Networks on 2D and 3D Molecular Structures by using Multi-View Conditional Information Bottleneck Van Thuy Hoang O-Joun Lee 56 0 0 23 Nov 2025
ProtoMol: Enhancing Molecular Property Prediction via Prototype-Guided Multimodal Learning Yingxu Wang Kunyu Zhang Jiaxin Huang Nan Yin Siwei Liu Eran Segal 100 2 0 19 Oct 2025
Equivariant Masked Position Prediction for Efficient Molecular RepresentationInternational Conference on Learning Representations (ICLR), 2025 Junyi An Chao Qu Yun-Fei Shi XinHao Liu Qianwei Tang Fenglei Cao Yuan Qi 236 1 0 12 Feb 2025
Revisiting Graph Neural Networks on Graph-level Tasks: Comprehensive Experiments, Analysis, and Improvements Haoyang Li Yongjun Xu C. Zhang Alexander Zhou Lei Chen Qing Li AI4CE 684 0 0 03 Jan 2025
Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information BottleneckAAAI Conference on Artificial Intelligence (AAAI), 2024 Van Thuy Hoang O-Joun Lee AI4CE 257 8 0 20 Dec 2024
Exploring Hierarchical Molecular Graph Representation in Multimodal LLMs Chengxin Hu Hao Li Yihe Yuan Jing Li Ivor Tsang 337 6 0 07 Nov 2024
Molecular Graph Representation Learning via Structural Similarity Information Chengyu Yao Hong Huang Hang Gao Fengge Wu Haiming Chen Junsuo Zhao 149 2 0 13 Sep 2024
TDNetGen: Empowering Complex Network Resilience Prediction with Generative Augmentation of Topology and DynamicsKnowledge Discovery and Data Mining (KDD), 2024 Chang Liu Jingtao Ding Yiwen Song Yong Li AI4CE 137 7 0 19 Aug 2024
HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignment Yongqiang Chen Quanming Yao Juzheng Zhang James Cheng Yatao Bian 275 4 0 20 Jun 2024
Learning Molecular Representation in a Cell Gang Liu Srijit Seal John Arevalo Zhenwen Liang Anne E Carpenter Meng Jiang Shantanu Singh 292 10 0 17 Jun 2024
Expressivity and Generalization: Fragment-Biases for Molecular GNNs Tom Wollschlager Niklas Kemper Leon Hetzel Johanna Sommer Stephan Günnemann 267 9 0 12 Jun 2024
Where to Mask: Structure-Guided Masking for Graph Masked Autoencoders Chuang Liu Yuyao Wang Yibing Zhan Xueqi Ma Dapeng Tao Hongzhi Zhang Wenbin Hu 200 11 0 24 Apr 2024
Data-Centric Learning from Unlabeled Graphs with Diffusion ModelNeural Information Processing Systems (NeurIPS), 2023 Gang Liu Eric Inae Tong Zhao Jiaxin Xu Te Luo Meng Jiang DiffM 169 30 0 17 Mar 2023
De Novo Molecular Generation via Connection-aware Motif MiningInternational Conference on Learning Representations (ICLR), 2023 Zijie Geng Shufang Xie Ziheng Lu Lijun Wu Tao Qin Jie Wang Yongdong Zhang Feng Wu Tie-Yan Liu 250 42 0 02 Feb 2023
Motif-based Graph Representation Learning with Application to Chemical Molecules Yifei Wang Shiyang Chen Guobin Chen Ethan Shurberg Hang Liu Pengyu Hong GNN 100 18 0 09 Aug 2022
A Survey on Masked Autoencoder for Self-supervised Learning in Vision and Beyond Chaoning Zhang Chenshuang Zhang Junha Song John Seon Keun Yi Kang Zhang In So Kweon SSL 165 92 0 30 Jul 2022
Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link PredictionNeural Information Processing Systems (NeurIPS), 2022 Seongjun Yun Seoyoon Kim Junhyun Lee Jaewoo Kang Hyunwoo J. Kim GNN 145 149 0 09 Jun 2022
GraphMAE: Self-Supervised Masked Graph AutoencodersKnowledge Discovery and Data Mining (KDD), 2022 Zhenyu Hou Xiao Liu Yukuo Cen Yuxiao Dong Hongxia Yang C. Wang Jie Tang SSL 512 734 0 22 May 2022
A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications Jun Xia Yanqiao Zhu Yuanqi Du Stan Z. Li VLM 137 42 0 16 Feb 2022
Graph Self-supervised Learning with Accurate Discrepancy LearningNeural Information Processing Systems (NeurIPS), 2022 Dongki Kim Jinheon Baek Sung Ju Hwang SSL 356 41 0 07 Feb 2022
Masked Autoencoders Are Scalable Vision LearnersComputer Vision and Pattern Recognition (CVPR), 2021 Kaiming He Xinlei Chen Saining Xie Yanghao Li Piotr Dollár Ross B. Girshick ViT TPM 1.6K 9,824 0 11 Nov 2021
Motif-based Graph Self-Supervised Learning for Molecular Property Prediction Zaixin Zhang Qi Liu Hao Wang Chengqiang Lu Chee-Kong Lee SSL AI4CE 200 314 0 03 Oct 2021
An Empirical Study of Graph Contrastive Learning Yanqiao Zhu Yichen Xu Qiang Liu Shu Wu 241 202 0 02 Sep 2021
Graph Contrastive Learning AutomatedInternational Conference on Machine Learning (ICML), 2021 Yuning You Tianlong Chen Yang Shen Zinan Lin 226 566 0 10 Jun 2021
Self-supervised Graph-level Representation Learning with Local and Global StructureInternational Conference on Machine Learning (ICML), 2021 Minghao Xu Hang Wang Bingbing Ni Hongyu Guo Jian Tang SSL 178 237 0 08 Jun 2021
MoCL: Data-driven Molecular Fingerprint via Knowledge-aware Contrastive Learning from Molecular GraphKnowledge Discovery and Data Mining (KDD), 2021 Mengying Sun Jing Xing Huijun Wang Bin Chen Jiayu Zhou 253 144 0 05 Jun 2021
GPT-GNN: Generative Pre-Training of Graph Neural Networks Ziniu Hu Yuxiao Dong Kuansan Wang Kai-Wei Chang Luke Huan SSL AI4CE 268 634 0 27 Jun 2020
On the Bottleneck of Graph Neural Networks and its Practical Implications Uri Alon Eran Yahav GNN 538 841 0 09 Jun 2020
Symmetric Graph Convolutional Autoencoder for Unsupervised Graph Representation LearningIEEE International Conference on Computer Vision (ICCV), 2019 Jiwoong Park Minsik Lee H. Chang Kyuewang Lee J. Choi SSL 226 264 0 07 Aug 2019
Strategies for Pre-training Graph Neural NetworksInternational Conference on Learning Representations (ICLR), 2019 Weihua Hu Bowen Liu Joseph Gomes Marinka Zitnik Abigail Z. Jacobs Vijay S. Pande J. Leskovec SSL AI4CE 349 1,620 0 29 May 2019
Graph Attention Auto-EncodersIEEE International Conference on Tools with Artificial Intelligence (ICTAI), 2019 Amin Salehi H. Davulcu GNN 97 151 0 26 May 2019
Discovering Molecular Functional Groups Using Graph Convolutional Neural Networks Phillip E. Pope Soheil Kolouri Mohammad Rostami Charles E. Martin Heiko Hoffmann GNN 330 16 0 01 Dec 2018
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding Jacob Devlin Ming-Wei Chang Kenton Lee Kristina Toutanova VLM SSL SSeg 2.8K 106,924 0 11 Oct 2018
How Powerful are Graph Neural Networks? Keyulu Xu Weihua Hu J. Leskovec Stefanie Jegelka GNN 790 8,888 0 01 Oct 2018
MoleculeNet: A Benchmark for Molecular Machine Learning Zhenqin Wu Bharath Ramsundar Evan N. Feinberg Joseph Gomes C. Geniesse Aneesh S. Pappu K. Leswing Vijay S. Pande OOD 890 2,148 0 02 Mar 2017
Variational Graph Auto-Encoders Thomas Kipf Max Welling GNN BDL SSL CML 463 4,051 0 21 Nov 2016
MADE: Masked Autoencoder for Distribution Estimation M. Germain Karol Gregor Iain Murray Hugo Larochelle OOD SyDa UQCV 405 914 0 12 Feb 2015