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SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks
v1v2 (latest)

SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks

Scientific Reports (Sci Rep), 2020
30 April 2020
Kexin Huang
C. Xiao
Lucas Glass
Marinka Zitnik
Jimeng Sun
    GNN
ArXiv (abs)PDFHTML

Papers citing "SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks"

45 / 45 papers shown
HeroFilter: Adaptive Spectral Graph Filter for Varying Heterophilic Relations
HeroFilter: Adaptive Spectral Graph Filter for Varying Heterophilic Relations
Shuaicheng Zhang
Haohui Wang
Junhong Lin
Xiaojie Guo
Yada Zhu
Si Zhang
Dongqi Fu
Dawei Zhou
167
2
0
13 Oct 2025
Graph Neural Networks in Modern AI-aided Drug Discovery
Graph Neural Networks in Modern AI-aided Drug DiscoveryChemical Reviews (Chem. Rev.), 2025
Odin Zhang
Haitao Lin
Xujun Zhang
Xiaorui Wang
Zhenxing Wu
...
Jike Wang
Kejun Ying
Yu Kang
Chang-Yu Hsieh
Tingjun Hou
GNNAI4CE
199
29
0
07 Jun 2025
Recent Developments in GNNs for Drug Discovery
Recent Developments in GNNs for Drug Discovery
Zhengyu Fang
Xiaoge Zhang
Anyin Zhao
Xiao Li
Huiyuan Chen
Jing Li
284
5
0
02 Jun 2025
Graph Data Selection for Domain Adaptation: A Model-Free Approach
Graph Data Selection for Domain Adaptation: A Model-Free Approach
Ting-Wei Li
Ruizhong Qiu
Hanghang Tong
OOD
330
4
0
22 May 2025
Adaptive Tokenization: On the Hop-Overpriority Problem in Tokenized Graph Learning Models
Adaptive Tokenization: On the Hop-Overpriority Problem in Tokenized Graph Learning Models
Zhibiao Wang
Yunlong Zhou
Ziwei Zhang
Mengmei Zhang
Shirui Pan
Chunming Hu
Xiao Wang
290
0
0
19 May 2025
Rethinking Federated Graph Learning: A Data Condensation Perspective
Rethinking Federated Graph Learning: A Data Condensation PerspectiveInternational Joint Conference on Artificial Intelligence (IJCAI), 2025
Hao Zhang
Miao Hu
Yinlin Zhu
Lianglin Hu
FedMLDDAI4CE
374
4
0
05 May 2025
Heterogeneous networks in drug-target interaction prediction
Heterogeneous networks in drug-target interaction prediction
Mohammad Molaee
Nasrollah Moghadam Charkari
Foad Ghaderi
397
0
0
22 Apr 2025
Customized Subgraph Selection and Encoding for Drug-drug Interaction
  Prediction
Customized Subgraph Selection and Encoding for Drug-drug Interaction PredictionNeural Information Processing Systems (NeurIPS), 2024
Haotong Du
Quanming Yao
Juzheng Zhang
Yong Liu
Zhen Wang
356
17
0
03 Nov 2024
Benchmarking drug-drug interaction prediction methods: a perspective of distribution changes
Benchmarking drug-drug interaction prediction methods: a perspective of distribution changesBioinformatics (Bioinformatics), 2024
Zhenqian Shen
Mingyuan Zhou
Yongqi Zhang
Quanming Yao
239
4
0
24 Oct 2024
A Survey of Mamba
A Survey of Mamba
Shuwei Shi
Shibing Chu
Rui An
Wenqi Fan
Yuee Xie
Hui Liu
Yuanping Chen
Qing Li
AI4CE
615
85
0
02 Aug 2024
Graph Neural Networks for Protein-Protein Interactions - A Short Survey
Graph Neural Networks for Protein-Protein Interactions - A Short Survey
Mingda Xu
Peisheng Qian
Ziyuan Zhao
Zeng Zeng
Jianguo Chen
Weide Liu
Xulei Yang
232
7
0
16 Apr 2024
Hierarchical Multi-Relational Graph Representation Learning for
  Large-Scale Prediction of Drug-Drug Interactions
Hierarchical Multi-Relational Graph Representation Learning for Large-Scale Prediction of Drug-Drug Interactions
Mengying Jiang
Guizhong Liu
Yuanchao Su
Weiqiang Jin
Biao Zhao
278
8
0
28 Feb 2024
Tensor-view Topological Graph Neural Network
Tensor-view Topological Graph Neural NetworkInternational Conference on Artificial Intelligence and Statistics (AISTATS), 2024
Tao Wen
Elynn Chen
Yuzhou Chen
540
19
0
22 Jan 2024
MotifPiece: A Data-Driven Approach for Effective Motif Extraction and
  Molecular Representation Learning
MotifPiece: A Data-Driven Approach for Effective Motif Extraction and Molecular Representation Learning
Zhaoning Yu
Hongyang Gao
307
2
0
24 Dec 2023
Robust Stochastic Graph Generator for Counterfactual Explanations
Robust Stochastic Graph Generator for Counterfactual Explanations
Mario Alfonso Prado-Romero
Bardh Prenkaj
Giovanni Stilo
CML
306
6
0
18 Dec 2023
Accurate and interpretable drug-drug interaction prediction enabled by
  knowledge subgraph learning
Accurate and interpretable drug-drug interaction prediction enabled by knowledge subgraph learningCommunications Medicine (Commun Med), 2023
Yaqing Wang
Zaifei Yang
Quanming Yao
215
43
0
25 Nov 2023
Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural
  Network with Biomedical Network
Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural Network with Biomedical NetworkNature Computational Science (Nat. Comput. Sci.), 2023
Yongqi Zhang
Quanming Yao
Ling Yue
Xian Wu
Ziheng Zhang
Zhenxi Lin
Yefeng Zheng
239
65
0
15 Nov 2023
ResMGCN: Residual Message Graph Convolution Network for Fast Biomedical
  Interactions Discovering
ResMGCN: Residual Message Graph Convolution Network for Fast Biomedical Interactions Discovering
Zecheng Yin
293
1
0
13 Nov 2023
Sheaf Hypergraph Networks
Sheaf Hypergraph NetworksNeural Information Processing Systems (NeurIPS), 2023
Iulia Duta
Giulia Cassara
Fabrizio Silvestri
Pietro Lio
410
44
0
29 Sep 2023
GPatcher: A Simple and Adaptive MLP Model for Alleviating Graph
  Heterophily
GPatcher: A Simple and Adaptive MLP Model for Alleviating Graph Heterophily
Shuaicheng Zhang
Haohui Wang
Si Zhang
Dawei Zhou
243
4
0
25 Jun 2023
Torsion Graph Neural Networks
Torsion Graph Neural NetworksIEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), 2023
Cong Shen
Xiang Liu
Jiawei Luo
Kelin Xia
264
1
0
23 Jun 2023
Curvature-enhanced Graph Convolutional Network for Biomolecular
  Interaction Prediction
Curvature-enhanced Graph Convolutional Network for Biomolecular Interaction PredictionComputational and Structural Biotechnology Journal (CSBJ), 2023
Cong Shen
Pingjian Ding
Junjie Wee
Jialin Bi
Jiawei Luo
Kelin Xia
GNN
368
15
0
23 Jun 2023
Comprehensive evaluation of deep and graph learning on drug-drug
  interactions prediction
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction
Xuan Lin
Lichang Dai
Yafang Zhou
Zunpeng Yu
Wen Zhang
...
Li Zeng
Hao-Heng Chen
Bosheng Song
Philip S. Yu
Xiangxiang Zeng
GNN
190
89
0
08 Jun 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey
  from Precision to Interpretability
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to InterpretabilityACM Computing Surveys (ACM Comput. Surv.), 2023
Zhiqiang Zhong
A. Barkova
Davide Mottin
289
17
0
16 Feb 2023
Simplifying Subgraph Representation Learning for Scalable Link
  Prediction
Simplifying Subgraph Representation Learning for Scalable Link Prediction
Paul Louis
Shweta Ann Jacob
Amirali Salehi-Abari
323
13
0
29 Jan 2023
Towards Training GNNs using Explanation Directed Message Passing
Towards Training GNNs using Explanation Directed Message PassingLOG IN (LOG IN), 2022
V. Giunchiglia
Chirag Varun Shukla
Guadalupe Gonzalez
Chirag Agarwal
228
11
0
30 Nov 2022
Predicting Biomedical Interactions with Probabilistic Model Selection for Graph Neural Networks
Predicting Biomedical Interactions with Probabilistic Model Selection for Graph Neural Networks
K. Kishan
Rui Li
Paribesh Regmi
Anne R. Haake
114
1
0
22 Nov 2022
EEGNN: Edge Enhanced Graph Neural Network with a Bayesian Nonparametric
  Graph Model
EEGNN: Edge Enhanced Graph Neural Network with a Bayesian Nonparametric Graph ModelInternational Conference on Artificial Intelligence and Statistics (AISTATS), 2022
Yirui Liu
Xinghao Qiao
Liying Wang
Jessica Lam
BDL
411
4
0
12 Aug 2022
Sampling Enclosing Subgraphs for Link Prediction
Sampling Enclosing Subgraphs for Link PredictionInternational Conference on Information and Knowledge Management (CIKM), 2022
Paul Louis
Shweta Ann Jacob
Amirali Salehi-Abari
GNN
349
20
0
23 Jun 2022
Ensemble Multi-Relational Graph Neural Networks
Ensemble Multi-Relational Graph Neural NetworksInternational Joint Conference on Artificial Intelligence (IJCAI), 2022
Yuling Wang
Haonan Xu
Yanhua Yu
Mengdi Zhang
Zhenhao Li
Yuji Yang
Wei Wu
155
11
0
24 May 2022
Discovering the Representation Bottleneck of Graph Neural Networks
Discovering the Representation Bottleneck of Graph Neural Networks
Fang Wu
Siyuan Li
Stan Z. Li
349
3
0
15 May 2022
BScNets: Block Simplicial Complex Neural Networks
BScNets: Block Simplicial Complex Neural Networks
Yuzhou Chen
Yulia R. Gel
H. Vincent Poor
GNN
261
46
0
13 Dec 2021
AugLiChem: Data Augmentation Library of Chemical Structures for Machine
  Learning
AugLiChem: Data Augmentation Library of Chemical Structures for Machine Learning
Rishikesh Magar
Yuyang Wang
Cooper Lorsung
Chen Liang
Hariharan Ramasubramanian
Peiyuan Li
A. Farimani
325
39
0
30 Nov 2021
STNN-DDI: A Substructure-aware Tensor Neural Network to Predict
  Drug-Drug Interactions
STNN-DDI: A Substructure-aware Tensor Neural Network to Predict Drug-Drug Interactions
Hui Yu
Shiyu Zhao
Jianyu Shi
207
53
0
10 Nov 2021
A Unified View of Relational Deep Learning for Drug Pair Scoring
A Unified View of Relational Deep Learning for Drug Pair ScoringInternational Joint Conference on Artificial Intelligence (IJCAI), 2021
Benedek Rozemberczki
Stephen Bonner
A. Nikolov
M. Ughetto
Sebastian Nilsson
Eliseo Papa
418
17
0
04 Nov 2021
MOOMIN: Deep Molecular Omics Network for Anti-Cancer Drug Combination
  Therapy
MOOMIN: Deep Molecular Omics Network for Anti-Cancer Drug Combination TherapyInternational Conference on Information and Knowledge Management (CIKM), 2021
Benedek Rozemberczki
A. Gogleva
S. Nilsson
G. Edwards
A. Nikolov
Eliseo Papa
GNN
294
21
0
28 Oct 2021
An In-depth Summary of Recent Artificial Intelligence Applications in
  Drug Design
An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design
Yi Zhang
AI4CE
285
7
0
10 Oct 2021
Machine Learning Applications for Therapeutic Tasks with Genomics Data
Machine Learning Applications for Therapeutic Tasks with Genomics DataPatterns (Patterns), 2021
Kexin Huang
Cao Xiao
Lucas Glass
C. Critchlow
G. Gibson
Jimeng Sun
LM&MAVLMSyDa
153
36
0
03 May 2021
Towards a Unified Framework for Fair and Stable Graph Representation
  Learning
Towards a Unified Framework for Fair and Stable Graph Representation LearningConference on Uncertainty in Artificial Intelligence (UAI), 2021
Chirag Agarwal
Himabindu Lakkaraju
Marinka Zitnik
407
193
0
25 Feb 2021
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug
  Discovery and Development
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development
Kexin Huang
Tianfan Fu
Wenhao Gao
Yue Zhao
Yusuf Roohani
J. Leskovec
Connor W. Coley
Cao Xiao
Jimeng Sun
Marinka Zitnik
OODLM&MA
350
401
0
18 Feb 2021
Binary Graph Neural Networks
Binary Graph Neural NetworksComputer Vision and Pattern Recognition (CVPR), 2020
Mehdi Bahri
Gaétan Bahl
Stefanos Zafeiriou
GNNAI4CE
314
58
0
31 Dec 2020
Predicting Biomedical Interactions with Higher-Order Graph Convolutional
  Networks
Predicting Biomedical Interactions with Higher-Order Graph Convolutional NetworksIEEE/ACM Transactions on Computational Biology & Bioinformatics (TCBB), 2020
K. Kishan
Rui Li
F. Cui
Anne R. Haake
GNN
173
36
0
16 Oct 2020
SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge
  Graph Summarization
SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization
Yue Yu
Kexin Huang
Chao Zhang
Lucas Glass
Jimeng Sun
Cao Xiao
299
163
0
04 Oct 2020
Layer-stacked Attention for Heterogeneous Network Embedding
Layer-stacked Attention for Heterogeneous Network Embedding
Nhat Chau Tran
Jean X. Gao
138
1
0
17 Sep 2020
Graph Meta Learning via Local Subgraphs
Graph Meta Learning via Local SubgraphsNeural Information Processing Systems (NeurIPS), 2020
Kexin Huang
Marinka Zitnik
431
188
0
14 Jun 2020
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