MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design

28 March 2022

Jimeng Sun

Papers citing "MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design"

50 / 131 papers shown

Title
Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models Tomohide Masuda Matthew Ragoza D. Koes DiffM 64 53 0 16 Oct 2020
3DMolNet: A Generative Network for Molecular Structures V. Nesterov Mario Wieser Volker Roth AI4CE 221 33 0 08 Oct 2020
MIMOSA: Multi-constraint Molecule Sampling for Molecule Optimization Tianfan Fu Cao Xiao Xinhao Li Lucas Glass Jimeng Sun 87 81 0 05 Oct 2020
OrbNet: Deep Learning for Quantum Chemistry Using Symmetry-Adapted Atomic-Orbital Features Zhuoran Qiao Matthew Welborn Anima Anandkumar F. Manby Thomas F. Miller AI4CE 70 216 0 15 Jul 2020
Guiding Deep Molecular Optimization with Genetic Exploration SungSoo Ahn Junsup Kim Hankook Lee Jinwoo Shin 79 74 0 04 Jul 2020
Drug discovery with explainable artificial intelligence José Jiménez-Luna F. Grisoni G. Schneider 179 636 0 01 Jul 2020
Denoising Diffusion Probabilistic Models Jonathan Ho Ajay Jain Pieter Abbeel DiffM 625 18,096 0 19 Jun 2020
SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks F. Fuchs Daniel E. Worrall Volker Fischer Max Welling 3DPC 153 692 0 18 Jun 2020
MoFlow: An Invertible Flow Model for Generating Molecular Graphs Chengxi Zang Fei Wang BDL 122 293 0 17 Jun 2020
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation Simon Axelrod Rafael Gómez-Bombarelli 3DV AI4CE 90 217 0 09 Jun 2020
On the Bottleneck of Graph Neural Networks and its Practical Implications Uri Alon Eran Yahav GNN 88 688 0 09 Jun 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 64 83 0 18 May 2020
Principal Neighbourhood Aggregation for Graph Nets Gabriele Corso Luca Cavalleri Dominique Beaini Pietro Lio Petar Velickovic GNN 109 667 0 12 Apr 2020
Meta-Learning GNN Initializations for Low-Resource Molecular Property Prediction Cuong C. Nguyen Constantine Kreatsoulas K. Branson AI4CE 41 14 0 12 Mar 2020
Directional Message Passing for Molecular Graphs Johannes Klicpera Janek Groß Stephan Günnemann 122 875 0 06 Mar 2020
Exploiting Neuron and Synapse Filter Dynamics in Spatial Temporal Learning of Deep Spiking Neural Network Haowen Fang Amar Shrestha Ziyi Zhao Qinru Qiu 48 120 0 19 Feb 2020
Reinforcement Learning for Molecular Design Guided by Quantum Mechanics G. Simm Robert Pinsler José Miguel Hernández-Lobato AI4CE 62 85 0 18 Feb 2020
The Synthesizability of Molecules Proposed by Generative Models Wenhao Gao Connor W. Coley 63 256 0 17 Feb 2020
Hierarchical Generation of Molecular Graphs using Structural Motifs Wengong Jin Regina Barzilay Tommi Jaakkola 76 288 0 08 Feb 2020
GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation Chence Shi Minkai Xu Zhaocheng Zhu Weinan Zhang Ming Zhang Jian Tang 168 438 0 26 Jan 2020
Analyzing and Improving the Image Quality of StyleGAN Tero Karras S. Laine M. Aittala Janne Hellsten J. Lehtinen Timo Aila GAN 284 5,815 0 03 Dec 2019
CORE: Automatic Molecule Optimization Using Copy & Refine Strategy Tianfan Fu Cao Xiao Jimeng Sun 101 68 0 23 Nov 2019
SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery Shion Honda Shoi Shi H. Ueda MedIm 71 175 0 12 Nov 2019
Graph Residual Flow for Molecular Graph Generation Shion Honda Hirotaka Akita Katsuhiko Ishiguro Toshiki Nakanishi Kenta Oono 55 42 0 30 Sep 2019
Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space AkshatKumar Nigam Pascal Friederich Mario Krenn Alán Aspuru-Guzik AI4CE 50 131 0 25 Sep 2019
A Generative Model for Molecular Distance Geometry G. Simm José Miguel Hernández-Lobato GAN 77 107 0 25 Sep 2019
ChemBO: Bayesian Optimization of Small Organic Molecules with Synthesizable Recommendations Ksenia Korovina Sailun Xu Kirthevasan Kandasamy Willie Neiswanger Barnabás Póczós J. Schneider Eric Xing 92 123 0 05 Aug 2019
InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization Fan-Yun Sun Jordan Hoffmann Vikas Verma Jian Tang SSL 145 862 0 31 Jul 2019
Generative Modeling by Estimating Gradients of the Data Distribution Yang Song Stefano Ermon SyDa DiffM 258 3,916 0 12 Jul 2019
Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules Niklas W. A. Gebauer M. Gastegger Kristof T. Schütt 121 208 0 02 Jun 2019
MolecularRNN: Generating realistic molecular graphs with optimized properties Mariya Popova Mykhailo Shvets Junier Oliva Olexandr Isayev GNN 69 167 0 31 May 2019
Strategies for Pre-training Graph Neural Networks Weihua Hu Bowen Liu Joseph Gomes Marinka Zitnik Percy Liang Vijay S. Pande J. Leskovec SSL AI4CE 116 1,404 0 29 May 2019
GraphNVP: An Invertible Flow Model for Generating Molecular Graphs Kaushalya Madhawa Katushiko Ishiguro Kosuke Nakago Motoki Abe BDL 100 192 0 28 May 2019
Analyzing Learned Molecular Representations for Property Prediction Kevin Kaichuang Yang Kyle Swanson Wengong Jin Connor W. Coley Philipp Eiden ... Andrew Palmer Volker Settels Tommi Jaakkola K. Jensen Regina Barzilay 104 1,317 0 02 Apr 2019
Molecular geometry prediction using a deep generative graph neural network Elman Mansimov Omar Mahmood Seokho Kang Kyunghyun Cho 88 188 0 31 Mar 2019
Deep learning for molecular design - a review of the state of the art Daniel C. Elton Zois Boukouvalas M. Fuge Peter W. Chung AI4CE 3DV 73 329 0 11 Mar 2019
Mol-CycleGAN - a generative model for molecular optimization Łukasz Maziarka Agnieszka Pocha Jan Kaczmarczyk Krzysztof Rataj M. Warchoł 53 250 0 06 Feb 2019
A Style-Based Generator Architecture for Generative Adversarial Networks Tero Karras S. Laine Timo Aila 583 10,555 0 12 Dec 2018
Learning Multimodal Graph-to-Graph Translation for Molecular Optimization Wengong Jin Kevin Kaichuang Yang Regina Barzilay Tommi Jaakkola 85 229 0 03 Dec 2018
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models Daniil Polykovskiy Alexander Zhebrak Benjamín Sánchez-Lengeling Sergey Golovanov Oktai Tatanov ... Simon Johansson Hongming Chen Sergey I. Nikolenko Alán Aspuru-Guzik Alex Zhavoronkov ELM 257 651 0 29 Nov 2018
DEFactor: Differentiable Edge Factorization-based Probabilistic Graph Generation Rim Assouel Mohamed Ahmed Marwin H. S. Segler Amir Saffari Yoshua Bengio 67 55 0 24 Nov 2018
GuacaMol: Benchmarking Models for De Novo Molecular Design Nathan Brown Marco Fiscato Marwin H. S. Segler Alain C. Vaucher ELM 109 708 0 22 Nov 2018
Optimization of Molecules via Deep Reinforcement Learning Zhenpeng Zhou S. Kearnes Li Li R. Zare Patrick F. Riley AI4CE 84 540 0 19 Oct 2018
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding Jacob Devlin Ming-Wei Chang Kenton Lee Kristina Toutanova VLM SSL SSeg 1.8K 94,891 0 11 Oct 2018
How Powerful are Graph Neural Networks? Keyulu Xu Weihua Hu J. Leskovec Stefanie Jegelka GNN 240 7,653 0 01 Oct 2018
Glow: Generative Flow with Invertible 1x1 Convolutions Diederik P. Kingma Prafulla Dhariwal BDL DRL 295 3,134 0 09 Jul 2018
N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules Shengchao Liu M. F. Demirel Yingyu Liang GNN NAI 54 195 0 24 Jun 2018
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 287 902 0 07 Jun 2018
MolGAN: An implicit generative model for small molecular graphs Nicola De Cao Thomas Kipf GNN GAN 177 926 0 30 May 2018
Constrained Graph Variational Autoencoders for Molecule Design Qi Liu Miltiadis Allamanis Marc Brockschmidt Alexander L. Gaunt BDL 75 456 0 23 May 2018