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
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Improving Small Molecule Generation using Mutual Information Machine Daniel A. Reidenbach M. Livne Rajesh Ilango M. Gill Johnny Israeli 28 14 0 18 Aug 2022
Quantum Machine Learning for Material Synthesis and Hardware Security Collin Beaudoin Satwik Kundu R. Topaloglu Swaroop Ghosh 27 5 0 16 Aug 2022
Active Learning Exploration of Transition Metal Complexes to Discover Method-Insensitive and Synthetically Accessible Chromophores Chenru Duan Aditya Nandy Gianmarco G. Terrones D. Kastner Heather J. Kulik 34 9 0 10 Aug 2022
Semi-Supervised Junction Tree Variational Autoencoder for Molecular Property Prediction Atia Hamidizadeh Tony Shen Martin Ester DRL 30 0 0 10 Aug 2022
Bayesian Optimization with Informative Covariance Afonso Eduardo Michael U. Gutmann 24 3 0 04 Aug 2022
Atomic structure generation from reconstructing structural fingerprints Victor Fung Shuyi Jia Jiaxin Zhang Sirui Bi Junqi Yin P. Ganesh 35 11 0 27 Jul 2022
Controllable Data Generation by Deep Learning: A Review Shiyu Wang Yuanqi Du Xiaojie Guo Bo Pan Zhaohui Qin Liang Zhao 33 28 0 19 Jul 2022
Graph Neural Network Bandits Parnian Kassraie Andreas Krause Ilija Bogunovic 26 11 0 13 Jul 2022
Unsupervised Learning for Combinatorial Optimization with Principled Objective Relaxation Haoyu Wang Nan Wu Hang Yang Cong Hao Pan Li 37 30 0 13 Jul 2022
Accelerating Material Design with the Generative Toolkit for Scientific Discovery Matteo Manica Jannis Born Joris Cadow Dimitrios Christofidellis A. Dave ... Lauren N. McHugh Alexy Khrabrov Payel Das Seiji Takeda John Smith 22 26 0 08 Jul 2022
Multisymplectic Formulation of Deep Learning Using Mean--Field Type Control and Nonlinear Stability of Training Algorithm Nader Ganaba 16 0 0 07 Jul 2022
Hyperbolic Molecular Representation Learning for Drug Repositioning K. Yu Shyam Visweswaran Kayhan Batmanghelich 18 0 0 06 Jul 2022
Graph Learning based Generative Design for Resilience of Interdependent Network Systems Jiaxin Wu Pingfeng Wang AI4CE 31 6 0 03 Jul 2022
PGMG: A Pharmacophore-Guided Deep Learning Approach for Bioactive Molecular Generation Hui Zhu Renyi Zhou Jing Tang Min Li BDL 21 4 0 02 Jul 2022
Optimizing Training Trajectories in Variational Autoencoders via Latent Bayesian Optimization Approach Arpan Biswas Rama K Vasudevan M. Ziatdinov Sergei V. Kalinin BDL DRL 19 10 0 30 Jun 2022
HyGNN: Drug-Drug Interaction Prediction via Hypergraph Neural Network Khaled Mohammed Saifuddin Bri Bumgardnerr Farhan Tanvir Esra Akbas 17 27 0 25 Jun 2022
Understanding and Extending Subgraph GNNs by Rethinking Their Symmetries Fabrizio Frasca Beatrice Bevilacqua Michael M. Bronstein Haggai Maron 43 125 0 22 Jun 2022
LIMO: Latent Inceptionism for Targeted Molecule Generation Peter Eckmann Kunyang Sun Bo Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 43 44 0 17 Jun 2022
GOOD: A Graph Out-of-Distribution Benchmark Shurui Gui Xiner Li Limei Wang Shuiwang Ji OOD 33 116 0 16 Jun 2022
High-Dimensional Bayesian Optimization with Constraints: Application to Powder Weighing Shoki Miyagawa Atsuyoshi Yano N. Sawada Isamu Ogawa 27 0 0 13 Jun 2022
Recent Advances in Bayesian Optimization Xilu Wang Yaochu Jin Sebastian Schmitt Markus Olhofer 40 200 0 07 Jun 2022
Recent Advances for Quantum Neural Networks in Generative Learning Jinkai Tian Xiaoyun Sun Yuxuan Du Shanshan Zhao Qing Liu ... Xingyao Wu Min-hsiu Hsieh Tongliang Liu Wen-Bin Yang Dacheng Tao AI4CE 31 82 0 07 Jun 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo Sung Ju Hwang OODD 30 75 0 06 Jun 2022
An Unpooling Layer for Graph Generation Yi Guo Dongmian Zou Gilad Lerman 16 2 0 04 Jun 2022
Graph Machine Learning for Design of High-Octane Fuels Jan G. Rittig Martin Ritzert Artur M. Schweidtmann Stefanie Winkler Jana M. Weber P. Morsch K. Heufer Martin Grohe Alexander Mitsos Manuel Dahmen 31 23 0 01 Jun 2022
Probabilistic Transformer: Modelling Ambiguities and Distributions for RNA Folding and Molecule Design Jörg Franke Frederic Runge Frank Hutter 17 14 0 27 May 2022
Sample-Efficient Optimisation with Probabilistic Transformer Surrogates A. Maraval Matthieu Zimmer Antoine Grosnit Rasul Tutunov Jun Wang H. Ammar 30 2 0 27 May 2022
Associative Learning Mechanism for Drug-Target Interaction Prediction Zhiqin Zhu Zheng Yao Guanqiu Qi Neal Mazur Baisheng Cong OOD 14 30 0 24 May 2022
Tyger: Task-Type-Generic Active Learning for Molecular Property Prediction Kuangqi Zhou Kaixin Wang Jiashi Feng Jian Tang Tingyang Xu Xinchao Wang 29 1 0 23 May 2022
3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design Yinan Huang Xing Peng Jianzhu Ma Muhan Zhang BDL 30 48 0 15 May 2022
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets Xingang Peng Shitong Luo Jiaqi Guan Qi Xie Jian-wei Peng Jianzhu Ma 27 176 0 15 May 2022
GPN: A Joint Structural Learning Framework for Graph Neural Networks Qianggang Ding Deheng Ye Tingyang Xu P. Zhao 26 0 0 12 May 2022
Conditional $β$ -VAE for De Novo Molecular Generation Ryan J. Richards A. Groener BDL DRL 24 10 0 01 May 2022
3D pride without 2D prejudice: Bias-controlled multi-level generative models for structure-based ligand design Lucian Chan Rajendra Kumar M. Verdonk C. Poelking DiffM AI4CE 24 2 0 22 Apr 2022
Accelerating Inhibitor Discovery With A Deep Generative Foundation Model: Validation for SARS-CoV-2 Drug Targets Vijil Chenthamarakshan Samuel C. Hoffman C. Owen P. Lukacik C. Strain-Damerell ... Aleksandra Mojsilović J. Crain Martin A. Walsh David I. Stuart Payel Das 26 0 0 19 Apr 2022
Generating 3D Molecules for Target Protein Binding Meng Liu Youzhi Luo Kanji Uchino Koji Maruhashi Shuiwang Ji 16 113 0 19 Apr 2022
Diagnosing and Fixing Manifold Overfitting in Deep Generative Models G. Loaiza-Ganem Brendan Leigh Ross Jesse C. Cresswell Anthony L. Caterini GAN DRL 19 28 0 14 Apr 2022
Accelerated Design and Deployment of Low-Carbon Concrete for Data Centers Xiou Ge Richard Goodwin Haizi Yu Pablo Romero Omar Abdelrahman Amruta Sudhalkar Julius Kusuma Ryan Cialdella Nakul Garg L. Varshney 22 10 0 11 Apr 2022
In-Pocket 3D Graphs Enhance Ligand-Target Compatibility in Generative Small-Molecule Creation Seung-gu Kang J. Weber Joseph A. Morrone Leili Zhang T. Huynh Wendy D. Cornell DiffM 21 3 0 05 Apr 2022
Generative Enriched Sequential Learning (ESL) Approach for Molecular Design via Augmented Domain Knowledge M. S. Ghaemi Karl Grantham Isaac Tamblyn Yifeng Li H. K. Ooi 33 3 0 05 Apr 2022
SELFIES and the future of molecular string representations Mario Krenn Qianxiang Ai Senja Barthel Nessa Carson Angelo Frei ... Andrew Wang Andrew D. White Adamo Young Rose Yu A. Aspuru‐Guzik 38 149 0 31 Mar 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 36 86 0 28 Mar 2022
Inverse Design and Experimental Verification of a Bianisotropic Metasurface Using Optimization and Machine Learning Stewart Pearson Parinaz Naseri S. Hum 11 0 0 28 Mar 2022
Meaningful machine learning models and machine-learned pharmacophores from fragment screening campaigns C. Poelking G. Chessari C. Murray Richard J. Hall Lucy J. Colwell M. Verdonk 19 5 0 25 Mar 2022
Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders Samuel Stanton Wesley J. Maddox Nate Gruver Phillip M. Maffettone E. Delaney Peyton Greenside A. Wilson BDL 38 89 0 23 Mar 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 69 178 0 20 Mar 2022
Learning Representation for Bayesian Optimization with Collision-free Regularization Fengxue Zhang Brian D. Nord Yuxin Chen OOD BDL 19 2 0 16 Mar 2022
Data-Efficient Graph Grammar Learning for Molecular Generation Minghao Guo Veronika Thost Beichen Li Payel Das Jie Chen Wojciech Matusik 43 36 0 15 Mar 2022