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Molecular Graph Convolutions: Moving Beyond Fingerprints

2 March 2016

Papers citing "Molecular Graph Convolutions: Moving Beyond Fingerprints"

50 / 439 papers shown

Title
What Functions Can Graph Neural Networks Generate? Mohammad Fereydounian Hamed Hassani Amin Karbasi 178 5 0 17 Feb 2022
Knowledge-informed Molecular Learning: A Survey on Paradigm TransferKnowledge Science, Engineering and Management (KSEM), 2022 Yin Fang Zhuo Chen Xiaohui Fan Qiang Zhang 269 5 0 17 Feb 2022
MolNet: A Chemically Intuitive Graph Neural Network for Prediction of Molecular Properties Yeji Kim Yoonho Jeong Jihoo Kim E. Lee W. Kim I. Choi GNN 133 11 0 01 Feb 2022
Benchmarking Resource Usage for Efficient Distributed Deep LearningIEEE Conference on High Performance Extreme Computing (HPEC), 2022 Nathan C. Frey Baolin Li Joseph McDonald Dan Zhao Michael Jones David Bestor Devesh Tiwari V. Gadepally S. Samsi 186 13 0 28 Jan 2022
Molecule Generation from Input-Attributions over Graph Convolutional Networks Dylan Savoia Alessio Ragno Roberto Capobianco GNN 61 0 0 25 Jan 2022
DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery -- A Focus on Affinity Prediction Problems with Noise Annotations Yuanfeng Ji Jun Liu Jiaxiang Wu Bing Wu Long-Kai Huang ... Ping Luo Shuigeng Zhou Junzhou Huang Peilin Zhao Yatao Bian OOD 242 85 0 24 Jan 2022
GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules Mahdi Ghorbani Samarjeet Prasad Jeffery B. Klauda B. Brooks GNN 92 37 0 12 Jan 2022
Optimizing Diffusion Rate and Label Reliability in a Graph-Based Semi-supervised ClassifierBrazilian Conference on Intelligent Systems (BRACIS), 2022 B. Afonso Lilian Berton 81 4 0 10 Jan 2022
Model Stealing Attacks Against Inductive Graph Neural Networks Yun Shen Xinlei He Yufei Han Yang Zhang 204 80 0 15 Dec 2021
Bringing Atomistic Deep Learning to Prime Time Nathan C. Frey S. Samsi Bharath Ramsundar Connor W. Coley V. Gadepally AI4CE 168 0 0 09 Dec 2021
Graph Neural Networks Accelerated Molecular DynamicsJournal of Chemical Physics (JCP), 2021 Zijie Li Kazem Meidani Prakarsh Yadav A. Farimani GNN AI4CE 188 70 0 06 Dec 2021
Scalable Geometric Deep Learning on Molecular Graphs Nathan C. Frey S. Samsi Joseph McDonald Lin Li Connor W. Coley V. Gadepally GNN AI4CE 123 4 0 06 Dec 2021
Molecular Contrastive Learning with Chemical Element Knowledge Graph Yin Fang Qiang Zhang Haihong Yang Xiang Zhuang Shumin Deng Wen Zhang Minghai Qin Zhuo Chen Xiaohui Fan Huajun Chen 226 132 0 01 Dec 2021
Structure-Aware Label Smoothing for Graph Neural Networks Yiwei Wang Yujun Cai Yuxuan Liang Wei Wang Henghui Ding Muhao Chen Jing Tang Bryan Hooi 133 5 0 01 Dec 2021
Decoding the Protein-ligand Interactions Using Parallel Graph Neural Networks C. Knutson Mridula Bontha Jenna A. Bilbrey Neeraj Kumar 118 38 0 30 Nov 2021
AugLiChem: Data Augmentation Library of Chemical Structures for Machine Learning Rishikesh Magar Yuyang Wang Cooper Lorsung Chen Liang Hariharan Ramasubramanian Peiyuan Li A. Farimani 215 39 0 30 Nov 2021
Benchmarking Accuracy and Generalizability of Four Graph Neural Networks Using Large In Vitro ADME Datasets from Different Chemical SpacesMolecular Informatics (Mol. Inf.), 2021 F. Broccatelli Richard E Trager M. Reutlinger George Karypis Mufei Li GNN 94 20 0 27 Nov 2021
Reliable Graph Neural Networks for Drug Discovery Under Distributional Shift Kehang Han Balaji Lakshminarayanan J. Liu OOD GNN 180 38 0 25 Nov 2021
Improving Compound Activity Classification via Deep Transfer and Representation LearningACS Omega (ACS Omega), 2021 Vishal Dey R. Machiraju Xia Ning AAML 213 4 0 14 Nov 2021
Implicit vs Unfolded Graph Neural Networks Yongyi Yang Tang Liu Yangkun Wang Zengfeng Huang David Wipf 394 17 0 12 Nov 2021
MEGAN: Memory Enhanced Graph Attention Network for Space-Time Video Super-ResolutionIEEE Workshop/Winter Conference on Applications of Computer Vision (WACV), 2021 Chenyu You Lianyi Han Aosong Feng Ruihan Zhao Hui Tang Wei Fan 181 13 0 28 Oct 2021
Geometric Transformer for End-to-End Molecule Properties Prediction Yoni Choukroun Lior Wolf AI4CE ViT 229 19 0 26 Oct 2021
Transportation Scenario Planning with Graph Neural Networks Ana Alice Peregrino S. Pradhan Zhicheng Liu Nivan Ferreira Fabio Miranda AI4TS 167 2 0 25 Oct 2021
Relative Molecule Self-Attention TransformerJournal of Cheminformatics (J Cheminform), 2021 Lukasz Maziarka Dawid Majchrowski Tomasz Danel Piotr Gaiñski Jacek Tabor Igor T. Podolak Pawel M. Morkisz Stanislaw Jastrzebski MedIm 176 42 0 12 Oct 2021
Learning 3D Representations of Molecular Chirality with Invariance to Bond RotationsInternational Conference on Learning Representations (ICLR), 2021 Keir Adams L. Pattanaik Connor W. Coley 228 41 0 08 Oct 2021
Attentive Walk-Aggregating Graph Neural Networks M. F. Demirel Shengchao Liu Siddhant Garg Zhenmei Shi Yingyu Liang 234 11 0 06 Oct 2021
Inference Attacks Against Graph Neural Networks Zhikun Zhang Min Chen Michael Backes Yun Shen Yang Zhang MIACV AAML GNN 164 50 0 06 Oct 2021
Permute Me Softly: Learning Soft Permutations for Graph Representations Giannis Nikolentzos George Dasoulas Michalis Vazirgiannis GNN 260 9 0 05 Oct 2021
Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs Fang Wu Dragomir R. Radev Huabin Xing ViT 684 77 0 04 Oct 2021
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs Zhao Xu Youzhi Luo Xuan Zhang Xinyi Xu Yaochen Xie Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 176 45 0 30 Sep 2021
Chemical-Reaction-Aware Molecule Representation Learning Hongwei Wang Weijian Li Xiaomeng Jin Kyunghyun Cho Heng Ji Jiawei Han Martin D. Burke 255 73 0 21 Sep 2021
Graph-Convolutional Deep Learning to Identify Optimized Molecular Configurations Eshan Joshi S. Somuyiwa H. Jooya GNN 112 0 0 22 Aug 2021
Bridging the Gap between Spatial and Spectral Domains: A Unified Framework for Graph Neural NetworksACM Computing Surveys (CSUR), 2021 Zhiqian Chen Fanglan Chen Lei Zhang Taoran Ji Kaiqun Fu Bo Pan Feng Chen Lingfei Wu Charu C. Aggarwal Chang-Tien Lu 547 31 0 21 Jul 2021
Learning Attributed Graph Representations with Communicative Message Passing TransformerInternational Joint Conference on Artificial Intelligence (IJCAI), 2021 Jianwen Chen Shuangjia Zheng Ying Song Jiahua Rao Yuedong Yang 218 53 0 19 Jul 2021
Relational graph convolutional networks for predicting blood-brain barrier penetration of drug molecules Yan Ding Xiaoqian Jiang Yejin Kim GNN 143 22 0 04 Jul 2021
Molecular distance matrix prediction based on graph convolutional networksJournal of Molecular Structure (J. Mol. Struct.), 2021 Xiao Lin Yongquan Jiang Yan Yang GNN 155 4 0 01 Jul 2021
LiteGEM: Lite Geometry Enhanced Molecular Representation Learning for Quantum Property Prediction Shanzhuo Zhang Lihang Liu Sheng Gao Donglong He Xiaomin Fang Weibin Li Zhengjie Huang Weiyue Su Wenjin Wang 113 9 0 28 Jun 2021
DGL-LifeSci: An Open-Source Toolkit for Deep Learning on Graphs in Life ScienceACS Omega (ACS Omega), 2021 Mufei Li Jinjing Zhou Jiajing Hu Wenxuan Fan Yangkang Zhang Yaxin Gu George Karypis GNN AI4CE 153 188 0 27 Jun 2021
Geometric learning of the conformational dynamics of molecules using dynamic graph neural networks Michael Ashby Jenna A. Bilbrey 115 4 0 24 Jun 2021
Fea2Fea: Exploring Structural Feature Correlations via Graph Neural Networks Jiaqing Xie Rex Ying GNN 195 3 0 24 Jun 2021
Artificial Intelligence in Drug Discovery: Applications and Techniques Jianyuan Deng Zhibo Yang Iwao Ojima Dimitris Samaras Fusheng Wang AI4TS 417 139 0 09 Jun 2021
DAMSL: Domain Agnostic Meta Score-based Learning J. Cai B. Cai S. Shen 123 5 0 06 Jun 2021
MoleHD: Ultra-Low-Cost Drug Discovery using Hyperdimensional Computing Dongning Ma Rahul Thapa Xun Jiao 146 4 0 05 Jun 2021
SpreadGNN: Serverless Multi-task Federated Learning for Graph Neural Networks Chaoyang He Emir Ceyani Keshav Balasubramanian M. Annavaram Salman Avestimehr FedML 157 61 0 04 Jun 2021
Detect the Interactions that Matter in Matter: Geometric Attention for Many-Body Systems Thorben Frank Stefan Chmiela 249 3 0 04 Jun 2021
Materials Representation and Transfer Learning for Multi-Property PredictionApplied Physics Reviews (APR), 2021 Shufeng Kong D. Guevarra Daniel Schwalbe-Koda J. Gregoire AI4CE 165 48 0 04 Jun 2021
Multiresolution Equivariant Graph Variational Autoencoder Truong-Son Hy Risi Kondor 204 21 0 02 Jun 2021
Hashing-Accelerated Graph Neural Networks for Link PredictionThe Web Conference (WWW), 2021 Wei Wu Bin Li Chuan Luo Wolfgang Nejdl GNN 132 48 0 29 May 2021
An End-to-End Framework for Molecular Conformation Generation via Bilevel ProgrammingInternational Conference on Machine Learning (ICML), 2021 Minkai Xu Wujie Wang Shitong Luo Chence Shi Yoshua Bengio Rafael Gómez-Bombarelli Jian Tang 3DV 295 87 0 15 May 2021
Optimization of Graph Neural Networks: Implicit Acceleration by Skip Connections and More DepthInternational Conference on Machine Learning (ICML), 2021 Keyulu Xu Mozhi Zhang Stefanie Jegelka Kenji Kawaguchi GNN 218 84 0 10 May 2021