Automatic chemical design using a data-driven continuous representation of molecules

7 October 2016

Rafael Gómez-Bombarelli

Jennifer N. Wei

David Duvenaud

José Miguel Hernández-Lobato

Benjamín Sánchez-Lengeling

Dennis Sheberla

J. Aguilera-Iparraguirre

Papers citing "Automatic chemical design using a data-driven continuous representation of molecules"

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Title
t-SMILES: A Scalable Fragment-based Molecular Representation Framework for De Novo Molecule Generation Juan-Ni Wu Tong Wang Yue (Eleanor) Chen Li-Juan Tang Hai-Long Wu Ru-Qin Yu 27 0 0 04 Jan 2023
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation Han Huang Leilei Sun Bowen Du Weifeng Lv 45 40 0 01 Jan 2023
Plug & Play Directed Evolution of Proteins with Gradient-based Discrete MCMC Patrick Emami Aidan Perreault Jeffrey N. Law David J. Biagioni Peter C. St. John 25 13 0 20 Dec 2022
Molecule optimization via multi-objective evolutionary in implicit chemical space Xin Xia Yansen Su Chunhou Zheng Xiangxiang Zeng 36 1 0 17 Dec 2022
Molecular Graph Generation by Decomposition and Reassembling Masatsugu Yamada M. Sugiyama 24 4 0 11 Dec 2022
The Role of AI in Drug Discovery: Challenges, Opportunities, and Strategies Alexandre Blanco-Gonzalez Alfonso Cabezon Alejandro Seco-Gonzalez Daniel Conde-Torres Paula Antelo-Riveiro Ángel Piñeiro R. García‐Fandiño 30 255 0 08 Dec 2022
GAUCHE: A Library for Gaussian Processes in Chemistry Ryan-Rhys Griffiths Leo Klarner Henry B. Moss Aditya Ravuri Sang T. Truong ... A. Lee Bingqing Cheng Alán Aspuru-Guzik P. Schwaller Jian Tang GP 30 40 0 06 Dec 2022
Improving Molecule Properties Through 2-Stage VAE Chenghui Zhou Barnabás Póczós DRL 28 1 0 06 Dec 2022
An open unified deep graph learning framework for discovering drug leads Yueming Yin Haifeng Hu Zhen Yang Jitao Yang Chun Jimmie Ye Jiansheng Wu W. Goh 19 0 0 06 Dec 2022
Accelerating Inverse Learning via Intelligent Localization with Exploratory Sampling Jiaxin Zhang Sirui Bi Victor Fung 35 3 0 02 Dec 2022
GrannGAN: Graph annotation generative adversarial networks Yoann Boget Magda Gregorova Alexandros Kalousis GAN 20 0 0 01 Dec 2022
A Deep Learning Approach to the Prediction of Drug Side-Effects on Molecular Graphs P. Bongini Elisa Messori Niccolò Pancino Monica Bianchini GNN OOD 23 2 0 30 Nov 2022
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 33 51 0 28 Nov 2022
BeGin: Extensive Benchmark Scenarios and An Easy-to-use Framework for Graph Continual Learning Jihoon Ko Shinhwan Kang Taehyung Kwon Heechan Moon Kijung Shin CLL 41 7 0 26 Nov 2022
BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation Zhen Wang Zheng Feng Yanjun Li Bowen Li Yongrui Wang C. Sha Min He Xiaolin Li AI4CE 35 9 0 25 Nov 2022
A Self-Attention Ansatz for Ab-initio Quantum Chemistry Ingrid von Glehn J. Spencer David Pfau 26 61 0 24 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 27 27 0 23 Nov 2022
Actively Learning Costly Reward Functions for Reinforcement Learning André Eberhard Houssam Metni G. Fahland A. Stroh Pascal Friederich OffRL 35 0 0 23 Nov 2022
Predicting Topological Maps for Visual Navigation in Unexplored Environments Huangying Zhan Hamid Rezatofighi Ian Reid 39 0 0 23 Nov 2022
Bidirectional Generation of Structure and Properties Through a Single Molecular Foundation Model Jinho Chang Jong Chul Ye AI4CE 22 30 0 19 Nov 2022
Molecular Fingerprints for Robust and Efficient ML-Driven Molecular Generation Ruslan N. Tazhigulov Joshua A. Schiller Jacob Oppenheim Max E Winston 14 1 0 16 Nov 2022
ParticleGrid: Enabling Deep Learning using 3D Representation of Materials Shehtab Zaman E. Ferguson Cécile Pereira D. Akhiyarov Mauricio Araya-Polo Kenneth Chiu DiffM AI4CE 29 2 0 15 Nov 2022
An Empirical Evaluation of Zeroth-Order Optimization Methods on AI-driven Molecule Optimization Elvin Lo Pin-Yu Chen 37 0 0 27 Oct 2022
Multi-Fidelity Bayesian Optimization with Unreliable Information Sources P. Mikkola Julien Martinelli Louis Filstroff Samuel Kaski 35 10 0 25 Oct 2022
Investigation of chemical structure recognition by encoder-decoder models in learning progress Katsuhisa Morita T. Mizuno Hiroyuki Kusuhara 19 8 0 24 Oct 2022
Bayesian Optimization with Conformal Prediction Sets Samuel Stanton Wesley J. Maddox A. Wilson 45 24 0 22 Oct 2022
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES E. Bjerrum Christian Margreitter Thomas Blaschke Raquel Lopez-Rios de Castro 40 12 0 22 Oct 2022
Deep Reinforcement Learning for Inverse Inorganic Materials Design Elton Pan Christopher Karpovich E. Olivetti AI4CE 27 11 0 21 Oct 2022
Discovering Many Diverse Solutions with Bayesian Optimization Natalie Maus Kaiwen Wu David Eriksson Jacob R. Gardner 24 23 0 20 Oct 2022
An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries Aryan Pedawi P. Gniewek Chao-Ling Chang Brandon M. Anderson H. V. D. Bedem 34 5 0 19 Oct 2022
Machine Learning for a Sustainable Energy Future Zhenpeng Yao Yanwei Lum Andrew K. Johnston L. M. Mejia-Mendoza Xiaoxia Zhou Yonggang Wen Alán Aspuru-Guzik E. Sargent Z. Seh 32 210 0 19 Oct 2022
A Transformer-based Generative Model for De Novo Molecular Design Wenlu Wang Ye Wang Honggang Zhao Simone Sciabola 16 0 0 17 Oct 2022
Pareto Set Learning for Expensive Multi-Objective Optimization Xi Lin Zhiyuan Yang Xiao-Yan Zhang Qingfu Zhang 39 54 0 16 Oct 2022
Computer-Aided Multi-Objective Optimization in Small Molecule Discovery Jenna C. Fromer Connor W. Coley 32 66 0 13 Oct 2022
Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design Ilia Igashov Hannes Stärk Clément Vignac Victor Garcia Satorras P. Frossard Max Welling Michael M. Bronstein B. Correia DiffM 44 84 0 11 Oct 2022
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 34 25 0 06 Oct 2022
Joint Entropy Search for Multi-objective Bayesian Optimization Ben Tu Axel Gandy N. Kantas B. Shafei 27 38 0 06 Oct 2022
When not to use machine learning: a perspective on potential and limitations Matthew R. Carbone 17 27 0 06 Oct 2022
Monte Carlo Tree Search based Variable Selection for High Dimensional Bayesian Optimization Lei Song Ke Xue Xiaobin Huang Chaojun Qian 14 34 0 04 Oct 2022
Spectral Augmentation for Self-Supervised Learning on Graphs Lu Lin Jinghui Chen Hongning Wang OOD 32 48 0 02 Oct 2022
Domain Generalization -- A Causal Perspective Paras Sheth Raha Moraffah K. S. Candan A. Raglin Huan Liu CML OOD 48 17 0 30 Sep 2022
ButterflyFlow: Building Invertible Layers with Butterfly Matrices Chenlin Meng Linqi Zhou Kristy Choi Tri Dao Stefano Ermon TPM 136 11 0 28 Sep 2022
GLSO: Grammar-guided Latent Space Optimization for Sample-efficient Robot Design Automation Jiaheng Hu Julian Whiman Howie Choset 42 16 0 23 Sep 2022
Distributed representations of graphs for drug pair scoring P. Scherer Pietro Lio M. Jamnik 39 2 0 19 Sep 2022
Meta-simulation for the Automated Design of Synthetic Overhead Imagery Handi Yu Simiao Ren L. Collins Jordan M. Malof 27 1 0 19 Sep 2022
Molecular Design Based on Integer Programming and Quadratic Descriptors in a Two-layered Model Jianshen Zhu Naveed Ahmed Azam Shengjuan Cao Ryota Ido Kazuya Haraguchi Liang Zhao H. Nagamochi Tatsuya Akutsu 24 3 0 13 Sep 2022
MDM: Molecular Diffusion Model for 3D Molecule Generation Lei Huang Hengtong Zhang Tingyang Xu Ka-Chun Wong DiffM 26 81 0 13 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 45 20 0 12 Sep 2022
A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language Bing-Huang Su Dazhao Du Zhao-Qing Yang Yujie Zhou Jiangmeng Li Anyi Rao Haoran Sun Zhiwu Lu Ji-Rong Wen 49 108 0 12 Sep 2022
Structured Q-learning For Antibody Design Alexander I. Cowen-Rivers P. Gorinski Aivar Sootla Asif R. Khan Liu Furui Jun Wang Jan Peters H. Ammar OffRL OnRL 32 3 0 10 Sep 2022