Papers citing 'Molecular Graph Convolutions: Moving Beyond Fingerprints'

Title
Bi-Level Graph Neural Networks for Drug-Drug Interaction Prediction Yunsheng Bai Ken Gu Luke Huan Wei Wang GNN 102 23 0 11 Jun 2020
A Tailored Convolutional Neural Network for Nonlinear Manifold Learning of Computational Physics Data using Unstructured Spatial DiscretizationsSIAM Journal on Scientific Computing (SIAM J. Sci. Comput.), 2020 John Tencer Kevin Potter AI4CE 221 13 0 11 Jun 2020
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation Simon Axelrod Rafael Gómez-Bombarelli 3DV AI4CE 373 274 0 09 Jun 2020
An Overview of Deep Semi-Supervised Learning Yassine Ouali C´eline Hudelot Myriam Tami SSL HAI 303 335 0 09 Jun 2020
Optimal Transport Graph Neural Networks Benson Chen Gary Bécigneul O. Ganea Regina Barzilay Tommi Jaakkola OT 342 48 0 08 Jun 2020
Convergence and Stability of Graph Convolutional Networks on Large Random GraphsNeural Information Processing Systems (NeurIPS), 2020 Nicolas Keriven A. Bietti Samuel Vaiter GNN 189 96 0 02 Jun 2020
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction Lior Hirschfeld Kyle Swanson Kevin Kaichuang Yang Regina Barzilay Connor W. Coley 215 217 0 20 May 2020
Deep Learning and Knowledge-Based Methods for Computer Aided Molecular Design -- Toward a Unified Approach: State-of-the-Art and Future Directions Abdulelah S. Alshehri R. Gani Fengqi You AI4CE 220 87 0 18 May 2020
Improved Protein-ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference Derek Jones Hyojin Kim Xiaohua Zhang A. Zemla Garrett A. Stevenson W. D. Bennett D. Kirshner Sergio E. Wong F. Lightstone Jonathan E. Allen AI4CE 106 208 0 17 May 2020
Multi-View Graph Neural Networks for Molecular Property Prediction Hehuan Ma Yatao Bian Yu Rong Wenbing Huang Qifeng Bai Wei-yang Xie Geyan Ye Junzhou Huang 187 45 0 17 May 2020
Foundations and modelling of dynamic networks using Dynamic Graph Neural Networks: A survey Joakim Skarding Bogdan Gabrys Katarzyna Musial AI4CE 252 286 0 13 May 2020
How hard is to distinguish graphs with graph neural networks? Andreas Loukas GNN 235 6 0 13 May 2020
MLSolv-A: A Novel Machine Learning-Based Prediction of Solvation Free Energies from Pairwise Atomistic Interactions Hyuntae Lim YounJoon Jung 126 41 0 13 May 2020
InteractionNet: Modeling and Explaining of Noncovalent Protein-Ligand Interactions with Noncovalent Graph Neural Network and Layer-Wise Relevance Propagation Hyeoncheol Cho E. Lee I. Choi GNN FAtt 133 6 0 12 May 2020
Autoencoding Pixies: Amortised Variational Inference with Graph Convolutions for Functional Distributional SemanticsAnnual Meeting of the Association for Computational Linguistics (ACL), 2020 Guy Edward Toh Emerson BDL 202 8 0 06 May 2020
Multi-View Self-Attention for Interpretable Drug-Target Interaction PredictionJournal of Biomedical Informatics (JBI), 2020 Brighter Agyemang Wei-Ping Wu Michael Y. Kpiebaareh Zhihua Lei Ebenezer Nanor Lei Chen 132 31 0 01 May 2020
ENT-DESC: Entity Description Generation by Exploring Knowledge GraphConference on Empirical Methods in Natural Language Processing (EMNLP), 2020 Liying Cheng Dekun Wu Lidong Bing Yan Zhang Zhanming Jie Wei Lu Luo Si 3DV 133 2 0 30 Apr 2020
Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement LearningACS Omega (ACS Omega), 2020 Julien Horwood Emmanuel Noutahi AI4CE 227 78 0 29 Apr 2020
LiDAR-based Online 3D Video Object Detection with Graph-based Message Passing and Spatiotemporal Transformer AttentionComputer Vision and Pattern Recognition (CVPR), 2020 Junbo Yin Jianbing Shen Chenye Guan Dingfu Zhou Ruigang Yang 3DPC 202 148 0 03 Apr 2020
Autonomous discovery in the chemical sciences part II: Outlook Connor W. Coley Natalie S. Eyke K. Jensen 155 185 0 30 Mar 2020
Detecting Symmetries with Neural Networks Sven Krippendorf Marc Syvaeri 121 70 0 30 Mar 2020
A Graph to Graphs Framework for Retrosynthesis PredictionInternational Conference on Machine Learning (ICML), 2020 Chence Shi Minkai Xu Hongyu Guo Ming Zhang Jian Tang 222 172 0 28 Mar 2020
A Survey of Deep Learning for Scientific Discovery M. Raghu Erica Schmidt OOD AI4CE 311 139 0 26 Mar 2020
Bridging the Gap Between Spectral and Spatial Domains in Graph Neural Networks M. Balcilar G. Renton Pierre Héroux Benoit Gaüzère Sébastien Adam P. Honeine 140 65 0 26 Mar 2020
A comprehensive study on the prediction reliability of graph neural networks for virtual screening Soojung Yang K. Lee Seongok Ryu 105 7 0 17 Mar 2020
Meta-Learning GNN Initializations for Low-Resource Molecular Property Prediction Cuong C. Nguyen Constantine Kreatsoulas K. Branson AI4CE 154 14 0 12 Mar 2020
PushNet: Efficient and Adaptive Neural Message PassingEuropean Conference on Artificial Intelligence (ECAI), 2020 Julian Busch Jiaxing Pi T. Seidl GNN 196 12 0 04 Mar 2020
An End-to-End Graph Convolutional Kernel Support Vector MachineApplied Network Science (Appl Netw Sci), 2020 P. Corcoran 121 6 0 29 Feb 2020
Assessing Graph-based Deep Learning Models for Predicting Flash PointMolecular Informatics (Mol. Inf.), 2020 Xiaoyu Sun Nathaniel J. Krakauer A. Politowicz Wei-Ting Chen Qiying Li ... Xianjia Shao Alfred Sunaryo Mingren Shen James Wang D. Morgan 102 25 0 26 Feb 2020
ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep LearningJournal of Chemical Information and Modeling (JCIM), 2020 M. Oldenhof Adam Arany Yves Moreau Jaak Simm GNN 118 56 0 23 Feb 2020
Molecule Attention Transformer Lukasz Maziarka Tomasz Danel Slawomir Mucha Krzysztof Rataj Jacek Tabor Stanislaw Jastrzebski 189 188 0 19 Feb 2020
Predicting drug properties with parameter-free machine learning: Pareto-Optimal Embedded Modeling (POEM) Andrew E. Brereton S. MacKinnon Z. Safikhani Shawn Reeves Sana Alwash V. Shahani A. Windemuth 125 10 0 11 Feb 2020
Hierarchical Generation of Molecular Graphs using Structural MotifsInternational Conference on Machine Learning (ICML), 2020 Wengong Jin Regina Barzilay Tommi Jaakkola 328 331 0 08 Feb 2020
Molecule Property Prediction and Classification with Graph Hypernetworks Eliya Nachmani Lior Wolf GNN 185 15 0 01 Feb 2020
Machine learning on DNA-encoded libraries: A new paradigm for hit-findingJournal of Medicinal Chemistry (J. Med. Chem.), 2020 Kevin McCloskey E. Sigel S. Kearnes L. Xue Xia Tian ... C. Hupp Anthony D. Keefe Christopher J. Mulhern Ying Zhang Patrick F. Riley 198 111 0 31 Jan 2020
GraphAF: a Flow-based Autoregressive Model for Molecular Graph GenerationInternational Conference on Learning Representations (ICLR), 2020 Chence Shi Minkai Xu Zhaocheng Zhu Weinan Zhang Ming Zhang Jian Tang 425 493 0 26 Jan 2020
Big-Data Science in Porous Materials: Materials Genomics and Machine LearningChemical Reviews (Chem. Rev.), 2020 Kevin Maik Jablonka D. Ongari S. M. Moosavi B. Smit AI4CE 239 404 0 18 Jan 2020
Geometric deep learning for computational mechanics Part I: Anisotropic HyperelasticityComputer Methods in Applied Mechanics and Engineering (CMAME), 2020 Nikolaos N. Vlassis R. Ma WaiChing Sun AI4CE 126 193 0 08 Jan 2020
TF3P: Three-dimensional Force Fields Fingerprint Learned by Deep Capsular NetworkJournal of Chemical Information and Modeling (JCIM), 2019 Yanxing Wang Jianxing Hu Junyong Lai Yibo Li Hongwei Jin L. Zhang L. Zhang Zhenming Liu MedIm 251 13 0 24 Dec 2019
libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning ApplicationsJournal of Chemical Information and Modeling (JCIM), 2019 Jocelyn Sunseri D. Koes AI4CE 134 37 0 10 Dec 2019
Drug-Target Indication Prediction by Integrating End-to-End Learning and Fingerprints Brighter Agyemang Wei-Ping Wu Michael Y. Kpiebaareh Ebenezer Nanor 142 3 0 03 Dec 2019
ASAP: Adaptive Structure Aware Pooling for Learning Hierarchical Graph RepresentationsAAAI Conference on Artificial Intelligence (AAAI), 2019 Ekagra Ranjan Soumya Sanyal Partha P. Talukdar GNN 384 373 0 18 Nov 2019
AMPL: A Data-Driven Modeling Pipeline for Drug DiscoveryJournal of Chemical Information and Modeling (JCIM), 2019 Amanda J. Minnich K. McLoughlin Margaret J. Tse Jason Deng Andrew Weber ... Bharath Ramsundar T. Rush Stacie Calad-Thomson J. Brase Jonathan E. Allen 177 70 0 13 Nov 2019
SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery Shion Honda Shoi Shi H. Ueda MedIm 178 216 0 12 Nov 2019
Generating valid Euclidean distance matrices Moritz Hoffmann Frank Noé 170 58 0 07 Oct 2019
Combining docking pose rank and structure with deep learning improves protein-ligand binding mode predictionJournal of Chemical Information and Modeling (JCIM), 2019 Joseph A. Morrone Matteo Terreran T. Huynh Heng Luo Wendy D. Cornell 101 78 0 07 Oct 2019
TransGCN:Coupling Transformation Assumptions with Graph Convolutional Networks for Link PredictionInternational Conference on Knowledge Capture (K-CAP), 2019 Ling Cai Bo Yan Gengchen Mai K. Janowicz Rui Zhu GNN 114 83 0 01 Oct 2019
A Multiple Filter Based Neural Network Approach to the Extrapolation of Adsorption Energies on Metal Surfaces for Catalysis ApplicationsJournal of Chemical Theory and Computation (JCTC), 2019 Asif J. Chowdhury Wenqiang Yang Kareem E. Abdelfatah M. Zare Andreas Heyden G. Terejanu 57 23 0 01 Oct 2019
Quantum Graph Neural Networks Guillaume Verdon Trevor McCourt Enxhell Luzhnica Vikas Singh Stefan Leichenauer Jack Hidary GNN 155 129 0 26 Sep 2019
A Generative Model for Molecular Distance GeometryInternational Conference on Machine Learning (ICML), 2019 G. Simm José Miguel Hernández-Lobato GAN 304 122 0 25 Sep 2019