MARS: Markov Molecular Sampling for Multi-objective Drug Discovery

18 March 2021

Yong Yu

Lei Li

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Papers citing "MARS: Markov Molecular Sampling for Multi-objective Drug Discovery"

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Title
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 20 51 0 28 Nov 2022
Accelerating Antimicrobial Peptide Discovery with Latent Structure Danqing Wang Zeyu Wen Fei Ye Lei Li Hao Zhou MedIm 17 2 0 28 Nov 2022
Group SELFIES: A Robust Fragment-Based Molecular String Representation Austin H. Cheng Andy Cai Santiago Miret Gustavo Malkomes Mariano Phielipp Alán Aspuru-Guzik 19 27 0 23 Nov 2022
Multi-Objective GFlowNets Moksh Jain Sharath Chandra Raparthy Alex Hernandez-Garcia Jarrid Rector-Brooks Yoshua Bengio Santiago Miret Emmanuel Bengio 22 86 0 23 Oct 2022
Generative Augmented Flow Networks L. Pan Dinghuai Zhang Aaron Courville Longbo Huang Yoshua Bengio 104 42 0 07 Oct 2022
Learning GFlowNets from partial episodes for improved convergence and stability Kanika Madan Jarrid Rector-Brooks Maksym Korablyov Emmanuel Bengio Moksh Jain A. Nica Tom Bosc Yoshua Bengio Nikolay Malkin 21 87 0 26 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 41 20 0 12 Sep 2022
Retrieval-based Controllable Molecule Generation Zichao Wang Weili Nie Zhuoran Qiao Chaowei Xiao Richard Baraniuk Anima Anandkumar 6 36 0 23 Aug 2022
Improving Small Molecule Generation using Mutual Information Machine Daniel A. Reidenbach M. Livne Rajesh Ilango M. Gill Johnny Israeli 19 14 0 18 Aug 2022
Controllable Data Generation by Deep Learning: A Review Shiyu Wang Yuanqi Du Xiaojie Guo Bo Pan Zhaohui Qin Liang Zhao 29 28 0 19 Jul 2022
Discrete Langevin Sampler via Wasserstein Gradient Flow Haoran Sun H. Dai Bo Dai Haomin Zhou Dale Schuurmans BDL 34 19 0 29 Jun 2022
LIMO: Latent Inceptionism for Targeted Molecule Generation Peter Eckmann Kunyang Sun Bo-Lu Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 27 44 0 17 Jun 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo S. Hwang OODD 28 74 0 06 Jun 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 19 86 0 28 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 29 67 0 13 Mar 2022
Multi-Objective Latent Space Optimization of Generative Molecular Design Models Naﬁz Abeer Nathan M. Urban Ryan Weil Francis J. Alexander Byung-Jun Yoon 19 14 0 01 Mar 2022
Molecule Generation for Drug Design: a Graph Learning Perspective Nianzu Yang Huaijin Wu Xiaoyong Pan Ye Yuan Junchi Yan 14 13 0 18 Feb 2022
Graph Self-supervised Learning with Accurate Discrepancy Learning Dongki Kim Jinheon Baek Sung Ju Hwang SSL 8 36 0 07 Feb 2022
Trajectory balance: Improved credit assignment in GFlowNets Nikolay Malkin Moksh Jain Emmanuel Bengio Chen Sun Yoshua Bengio 145 165 0 31 Jan 2022
Biases in In Silico Evaluation of Molecular Optimization Methods and Bias-Reduced Evaluation Methodology Hiroshi Kajino Kohei Miyaguchi Takayuki Osogami 46 1 0 28 Jan 2022
Local Latent Space Bayesian Optimization over Structured Inputs N. Maus Haydn Jones Juston Moore Matt J. Kusner John Bradshaw J. Gardner BDL 47 69 0 28 Jan 2022
HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space Zhiyuan Chen Xiaomin Fang Zixu Hua Yueyang Huang Fan Wang Hua-Hong Wu MedIm 14 2 0 30 Nov 2021
GFlowNet Foundations Yoshua Bengio Salem Lahlou T. Deleu J. E. Hu Mo Tiwari Emmanuel Bengio 19 209 0 17 Nov 2021
Fragment-based Sequential Translation for Molecular Optimization Benson Chen Xiang Fu Regina Barzilay Tommi Jaakkola 19 7 0 26 Oct 2021
Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design Wenhao Gao Rocío Mercado Connor W. Coley 11 57 0 12 Oct 2021
Differentiable Scaffolding Tree for Molecular Optimization Tianfan Fu Wenhao Gao Cao Xiao Jacob Yasonik Connor W. Coley Jimeng Sun 20 74 0 22 Sep 2021
Edge Representation Learning with Hypergraphs Jaehyeong Jo Jinheon Baek Seul Lee Dongki Kim Minki Kang Sung Ju Hwang 8 63 0 30 Jun 2021
Molecule Generation by Principal Subgraph Mining and Assembling Xiangzhe Kong Wenbing Huang Zhixing Tan Yang Liu GNN 16 45 0 29 Jun 2021
Flow Network based Generative Models for Non-Iterative Diverse Candidate Generation Emmanuel Bengio Moksh Jain Maksym Korablyov Doina Precup Yoshua Bengio 24 304 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 14 51 0 07 Jun 2021
Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery Yulun Wu Mikaela Cashman Nicholas Choma E. Prates V. G. M. Vergara ... M. Head Rick L. Stevens Peter Nugent Daniel A. Jacobson James B. Brown GNN 33 10 0 04 Jun 2021
Realistic molecule optimization on a learned graph manifold Rémy Brossard Oriel Frigo David Dehaene 14 0 0 03 Jun 2021
Learning Gradient Fields for Molecular Conformation Generation Chence Shi Shitong Luo Minkai Xu Jian Tang DiffM AI4CE 17 210 0 09 May 2021
Learning to Extend Molecular Scaffolds with Structural Motifs Krzysztof Maziarz Henry Jackson-Flux Pashmina Cameron F. Sirockin Nadine Schneider N. Stiefl Marwin H. S. Segler Marc Brockschmidt AI4CE 8 69 0 05 Mar 2021
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 OOD LM&MA 25 259 0 18 Feb 2021
CF-GNNExplainer: Counterfactual Explanations for Graph Neural Networks Ana Lucic Maartje ter Hoeve Gabriele Tolomei Maarten de Rijke Fabrizio Silvestri 110 142 0 05 Feb 2021
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 189 884 0 07 Jun 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 219 1,332 0 12 Feb 2018