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"

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Title
Towards Unified and Lossless Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Changhao Nai Kenji Kawaguchi Tat-Seng Chua Xiang Wang Yang Zhang Xiang Wang MedIm 126 0 0 19 Mar 2025
MOLLM: Multi-Objective Large Language Model for Molecular Design -- Optimizing with Experts Nian Ran Yue Wang Richard Allmendinger 125 1 0 18 Feb 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Changhao Nai Sihang Li Yaorui Shi Xiang Wang Kenji Kawaguchi Tat-Seng Chua 157 3 0 18 Feb 2025
3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery Xiuyuan Hu Guoqing Liu Can Chen Yang Zhao Jun Wang Xue Liu 96 2 0 07 Feb 2025
Reinforcement Learning for Generative AI: A Survey Yuanjiang Cao Quan.Z Sheng Julian McAuley Lina Yao SyDa 147 13 0 28 Aug 2023
Automated Scientific Discovery: From Equation Discovery to Autonomous Discovery Systems Stefan Kramer Mattia Cerrato Jannis Brugger Sašo Džeroski Ross King 72 12 0 03 May 2023
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 124 185 0 20 Mar 2022
A Survey on Deep Graph Generation: Methods and Applications Yanqiao Zhu Yuanqi Du Yinkai Wang Yichen Xu Jieyu Zhang Qiang Liu Shu Wu 3DV GNN 99 73 0 13 Mar 2022
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation Minkai Xu Lantao Yu Yang Song Chence Shi Stefano Ermon Jian Tang BDL DiffM 151 513 0 06 Mar 2022
Disentangled Spatiotemporal Graph Generative Models Yuanqi Du Xiaojie Guo Hengning Cao Yanfang Ye Liang Zhao 87 21 0 28 Feb 2022
Interpretable Molecular Graph Generation via Monotonic Constraints Yuanqi Du Xiaojie Guo Amarda Shehu Liang Zhao 88 19 0 28 Feb 2022
A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications Jun Xia Yanqiao Zhu Yuanqi Du Stan Z. Li VLM 57 42 0 16 Feb 2022
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk O. Ganea L. Pattanaik Regina Barzilay Tommi Jaakkola 82 267 0 07 Feb 2022
Direct Molecular Conformation Generation Jinhua Zhu Yingce Xia Chang-Shu Liu Lijun Wu Shufang Xie ... Tao Qin Wen-gang Zhou Houqiang Li Haiguang Liu Tie-Yan Liu 76 42 0 03 Feb 2022
Generative Coarse-Graining of Molecular Conformations Wujie Wang Minkai Xu Chen Cai Benjamin Kurt Miller Tess E. Smidt Yusu Wang Jian Tang Rafael Gómez-Bombarelli 47 36 0 28 Jan 2022
Local Latent Space Bayesian Optimization over Structured Inputs Natalie Maus Haydn Thomas Jones Juston Moore Matt J. Kusner John Bradshaw Jacob R. Gardner BDL 77 71 0 28 Jan 2022
Keeping it Simple: Language Models can learn Complex Molecular Distributions Daniel Flam-Shepherd Kevin Zhu A. Aspuru‐Guzik 207 148 0 06 Dec 2021
GFlowNet Foundations Yoshua Bengio Salem Lahlou T. Deleu J. E. Hu Mo Tiwari Emmanuel Bengio 48 230 0 17 Nov 2021
Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design Wenhao Gao Rocío Mercado Connor W. Coley 59 58 0 12 Oct 2021
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 172 317 0 07 Oct 2021
Geometric and Physical Quantities Improve E(3) Equivariant Message Passing Johannes Brandstetter Rob D. Hesselink Elise van der Pol Erik J. Bekkers Max Welling 82 242 0 06 Oct 2021
Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation Soojung Yang Doyeong Hwang Seul Lee Seongok Ryu Sung Ju Hwang 71 73 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 68 40 0 30 Sep 2021
Differentiable Scaffolding Tree for Molecular Optimization Tianfan Fu Wenhao Gao Cao Xiao Jacob Yasonik Connor W. Coley Jimeng Sun 75 78 0 22 Sep 2021
Inverse design of 3d molecular structures with conditional generative neural networks Niklas W. A. Gebauer M. Gastegger Stefaan S. P. Hessmann Klaus-Robert Muller Kristof T. Schütt AI4CE 225 173 0 10 Sep 2021
Improving black-box optimization in VAE latent space using decoder uncertainty Pascal Notin José Miguel Hernández-Lobato Y. Gal 123 62 0 30 Jun 2021
Rotation Invariant Graph Neural Networks using Spin Convolutions Muhammed Shuaibi Adeesh Kolluru Abhishek Das Aditya Grover Anuroop Sriram Zachary W. Ulissi C. L. Zitnick AI4CE 70 69 0 17 Jun 2021
Do Transformers Really Perform Bad for Graph Representation? Chengxuan Ying Tianle Cai Shengjie Luo Shuxin Zheng Guolin Ke Di He Yanming Shen Tie-Yan Liu GNN 95 441 0 09 Jun 2021
GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles O. Ganea L. Pattanaik Connor W. Coley Regina Barzilay K. Jensen W. Green Tommi Jaakkola AI4CE 86 136 0 08 Jun 2021
JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design AkshatKumar Nigam R. Pollice Alán Aspuru-Guzik 67 53 0 07 Jun 2021
GemNet: Universal Directional Graph Neural Networks for Molecules Johannes Klicpera Florian Becker Stephan Günnemann AI4CE 94 459 0 02 Jun 2021
An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming Minkai Xu Wujie Wang Shitong Luo Chence Shi Yoshua Bengio Rafael Gómez-Bombarelli Jian Tang 3DV 88 80 0 15 May 2021
Learning Gradient Fields for Molecular Conformation Generation Chence Shi Shitong Luo Minkai Xu Jian Tang DiffM AI4CE 75 215 0 09 May 2021
Learning to design drug-like molecules in three-dimensional space using deep generative models Yibo Li Jianfeng Pei L. Lai DiffM 84 113 0 17 Apr 2021
MARS: Markov Molecular Sampling for Multi-objective Drug Discovery Yutong Xie Chence Shi Hao Zhou Yuwei Yang Weinan Zhang Yong Yu Lei Li 88 144 0 18 Mar 2021
A Survey on Graph Structure Learning: Progress and Opportunities Yanqiao Zhu Weizhi Xu Jinghao Zhang Yuanqi Du Jieyu Zhang Qiang Liu Carl Yang Shu Wu GNN AI4CE 63 100 0 04 Mar 2021
High-Dimensional Bayesian Optimization with Sparse Axis-Aligned Subspaces David Eriksson M. Jankowiak 71 143 0 27 Feb 2021
E(n) Equivariant Graph Neural Networks Victor Garcia Satorras Emiel Hoogeboom Max Welling 108 1,020 0 19 Feb 2021
Spherical Message Passing for 3D Graph Networks Yi Liu Limei Wang Meng Liu Xuan Zhang Bora Oztekin Shuiwang Ji GNN 61 201 0 09 Feb 2021
HINT: Hierarchical Interaction Network for Trial Outcome Prediction Leveraging Web Data Tianfan Fu Kexin Huang Cao Xiao Lucas Glass Jimeng Sun 83 63 0 08 Feb 2021
Equivariant message passing for the prediction of tensorial properties and molecular spectra Kristof T. Schütt Oliver T. Unke M. Gastegger 107 534 0 05 Feb 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 230 199 0 01 Feb 2021
GraphEBM: Molecular Graph Generation with Energy-Based Models Meng Liu Keqiang Yan Bora Oztekin Shuiwang Ji 70 88 0 31 Jan 2021
How to Train Your Energy-Based Models Yang Song Diederik P. Kingma DiffM 67 259 0 09 Jan 2021
Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules Johannes Klicpera Shankari Giri Johannes T. Margraf Stephan Günnemann 79 323 0 28 Nov 2020
Score-Based Generative Modeling through Stochastic Differential Equations Yang Song Jascha Narain Sohl-Dickstein Diederik P. Kingma Abhishek Kumar Stefano Ermon Ben Poole DiffM SyDa 335 6,480 0 26 Nov 2020
Symmetry-Aware Actor-Critic for 3D Molecular Design G. Simm Robert Pinsler Gábor Csányi José Miguel Hernández-Lobato AI4CE 68 65 0 25 Nov 2020
Optimizing Molecules using Efficient Queries from Property Evaluations Samuel C. Hoffman Vijil Chenthamarakshan Kahini Wadhawan Pin-Yu Chen Payel Das 76 71 0 03 Nov 2020
An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale Alexey Dosovitskiy Lucas Beyer Alexander Kolesnikov Dirk Weissenborn Xiaohua Zhai ... Matthias Minderer G. Heigold Sylvain Gelly Jakob Uszkoreit N. Houlsby ViT 651 41,103 0 22 Oct 2020
ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction Seyone Chithrananda Gabriel Grand Bharath Ramsundar AI4CE 85 408 0 19 Oct 2020