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"

50 / 832 papers shown

Title
GPT-MolBERTa: GPT Molecular Features Language Model for molecular property prediction Suryanarayanan Balaji Rishikesh Magar Yayati Jadhav and Amir Barati Farimani 21 13 0 20 Sep 2023
Neural Network Driven, Interactive Design for Nonlinear Optical Molecules Based on Group Contribution Method Jinmin Fan Chao Qian Shaodong Zhou 15 0 0 15 Sep 2023
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation Gregory W. Kyro Anton Morgunov Rafael I. Brent Victor S. Batista 35 12 0 11 Sep 2023
Diffusion Generative Inverse Design Marin Vlastelica Tatiana López-Guevara Kelsey R. Allen Peter Battaglia Arnaud Doucet Kimberley L. Stachenfeld DiffM 29 1 0 05 Sep 2023
Objective-Agnostic Enhancement of Molecule Properties via Multi-Stage VAE Chenghui Zhou Barnabás Póczós 33 0 0 24 Aug 2023
Will More Expressive Graph Neural Networks do Better on Generative Tasks? Xian-Quan Zou Xiangyu Zhao Pietro Lio Yiren Zhao 15 2 0 23 Aug 2023
Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models Ziqi Chen B. Peng Srinivas Parthasarathy Xia Ning DiffM 39 11 0 23 Aug 2023
Conditional Sampling of Variational Autoencoders via Iterated Approximate Ancestral Sampling Vaidotas Šimkus Michael U. Gutmann BDL DRL 36 3 0 17 Aug 2023
Atom-by-atom protein generation and beyond with language models Daniel Flam-Shepherd Kevin Zhu Alán Aspuru-Guzik 33 2 0 16 Aug 2023
Expressivity of Spiking Neural Networks Manjot Singh Adalbert Fono Gitta Kutyniok 29 2 0 16 Aug 2023
Evaluating the diversity and utility of materials proposed by generative models Alexander New Michael Pekala Elizabeth A. Pogue Nam Q. Le Janna Domenico C. Piatko Christopher D. Stiles AI4CE 33 1 0 09 Aug 2023
Target-aware Variational Auto-encoders for Ligand Generation with Multimodal Protein Representation Learning Haoxiang Luo Gang Sun 40 2 0 02 Aug 2023
DBGSA: A Novel Data Adaptive Bregman Clustering Algorithm Ying Xiao Hou-Biao Li Yu-pu Zhang 13 7 0 25 Jul 2023
Prior Based Online Lane Graph Extraction from Single Onboard Camera Image Y. Can Alexander Liniger D. Paudel Luc Van Gool 29 2 0 25 Jul 2023
CTAGE: Curvature-Based Topology-Aware Graph Embedding for Learning Molecular Representations Yili Chen Zhengyu Li Zheng Wan Hui Yu Xian Wei 23 0 0 25 Jul 2023
Continuation Path Learning for Homotopy Optimization Xi Lin Zhiyuan Yang Xiao-Yan Zhang Qingfu Zhang 23 9 0 24 Jul 2023
Extracting Molecular Properties from Natural Language with Multimodal Contrastive Learning Romain Lacombe Andrew Gaut Jeff He D. Lüdeke Kateryna Pistunova 28 2 0 22 Jul 2023
Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions Leo Klarner Tim G. J. Rudner M. Reutlinger Torsten Schindler Garrett M. Morris Charlotte M. Deane Yee Whye Teh OOD BDL 15 9 0 14 Jul 2023
Graph Positional and Structural Encoder Semih Cantürk Renming Liu Olivier Lapointe-Gagné Vincent Létourneau Guy Wolf Dominique Beaini Ladislav Rampášek 41 15 0 14 Jul 2023
DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins Lei Huang Zheng Yuan Huihui Yan Rong Sheng Linjing Liu ... Nanjun Chen Fei Huang Songfang Huang Ka-Chun Wong Yaoyun Zhang 25 0 0 24 Jun 2023
Sampling from Gaussian Process Posteriors using Stochastic Gradient Descent J. Lin Javier Antorán Shreyas Padhy David Janz José Miguel Hernández-Lobato Alexander Terenin 23 22 0 20 Jun 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 42 1 0 20 Jun 2023
ChatGPT Chemistry Assistant for Text Mining and Prediction of MOF Synthesis Zhiling Zheng Oufan Zhang C. Borgs J. Chayes O. Yaghi 24 212 0 20 Jun 2023
Discrete Graph Auto-Encoder Yoann Boget Magda Gregorova Alexandros Kalousis 21 4 0 13 Jun 2023
Multi-objective Molecular Optimization for Opioid Use Disorder Treatment Using Generative Network Complex Hongsong Feng Rui Wang C. Zhan Guo-Wei Wei 21 0 0 13 Jun 2023
Happy People -- Image Synthesis as Black-Box Optimization Problem in the Discrete Latent Space of Deep Generative Models Steffen Jung Jan Christian Schwedhelm C. Schillings M. Keuper 36 1 0 11 Jun 2023
Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective Jiatong Li Yunqing Liu Wenqi Fan Xiao Wei Hui Liu Jiliang Tang Qing Li 28 84 0 11 Jun 2023
Adaptive Batch Sizes for Active Learning A Probabilistic Numerics Approach Masaki Adachi Satoshi Hayakawa Martin Jørgensen Xingchen Wan Vu Nguyen Harald Oberhauser Michael A. Osborne 28 5 0 09 Jun 2023
Expectation-Complete Graph Representations with Homomorphisms Pascal Welke Maximilian Thiessen Fabian Jogl Thomas Gärtner 18 6 0 09 Jun 2023
Molecule Design by Latent Space Energy-Based Modeling and Gradual Distribution Shifting Deqian Kong Bo Pang Tian Han Ying Nian Wu DiffM 41 7 0 09 Jun 2023
Gradient-Informed Quality Diversity for the Illumination of Discrete Spaces Raphael Boige Guillaume Richard Jérémie Donà Thomas Pierrot Antoine Cully 22 5 0 08 Jun 2023
CIN++: Enhancing Topological Message Passing Lorenzo Giusti Teodora Reu Francesco Ceccarelli Cristian Bodnar Pietro Lio GNN 34 7 0 06 Jun 2023
InstructZero: Efficient Instruction Optimization for Black-Box Large Language Models Lichang Chen Jiuhai Chen Tom Goldstein Heng-Chiao Huang Dinesh Manocha 19 42 0 05 Jun 2023
LIC-GAN: Language Information Conditioned Graph Generative GAN Model Robert Lo Arnhav Datar Abishek Sridhar GAN 22 2 0 02 Jun 2023
Balancing Exploration and Exploitation: Disentangled $β$ -CVAE in De Novo Drug Design Guang Jun Nicholas Ang Deanne Chin Bingquan Shen 28 0 0 02 Jun 2023
Symmetric Replay Training: Enhancing Sample Efficiency in Deep Reinforcement Learning for Combinatorial Optimization Hyeon-Seob Kim Minsu Kim Sungsoo Ahn Jinkyoo Park OffRL 39 7 0 02 Jun 2023
Protein Design with Guided Discrete Diffusion Nate Gruver Samuel Stanton Nathan C. Frey Tim G. J. Rudner I. Hotzel J. Lafrance-Vanasse A. Rajpal Kyunghyun Cho A. Wilson DiffM 42 101 0 31 May 2023
Relaxing the Additivity Constraints in Decentralized No-Regret High-Dimensional Bayesian Optimization Anthony Bardou Patrick Thiran Thomas Begin 16 4 0 31 May 2023
MAGNet: Motif-Agnostic Generation of Molecules from Shapes Leon Hetzel Johanna Sommer Bastian Alexander Rieck Fabian J. Theis Stephan Günnemann 35 6 0 30 May 2023
IDToolkit: A Toolkit for Benchmarking and Developing Inverse Design Algorithms in Nanophotonics Jia-Qi Yang Yucheng Xu Jianwei Shen Ke-Bin Fan De-Chuan Zhan Yang Yang 32 1 0 30 May 2023
Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration Haitao Lin Yufei Huang Haotian Zhang Lirong Wu Siyuan Li Zhiyuan Chen Stan Z. Li DiffM 19 23 0 30 May 2023
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining Shengchao Liu Weitao Du Zhiming Ma Hongyu Guo Jian Tang 26 30 0 28 May 2023
Vecchia Gaussian Process Ensembles on Internal Representations of Deep Neural Networks Felix Jimenez Matthias Katzfuss BDL UQCV 64 1 0 26 May 2023
Pair-Variational Autoencoders (PairVAE) for Linking and Cross-Reconstruction of Characterization Data from Complementary Structural Characterization Techniques Shizhao Lu A. Jayaraman 28 9 0 25 May 2023
Inverse Protein Folding Using Deep Bayesian Optimization Natalie Maus Yimeng Zeng Daniel A. Anderson Phillip M. Maffettone Aaron C. Solomon Peyton Greenside Osbert Bastani Jacob R. Gardner 28 2 0 25 May 2023
The Behavior and Convergence of Local Bayesian Optimization Kaiwen Wu Kyurae Kim Roman Garnett Jacob R. Gardner 45 9 0 24 May 2023
Learning Relevant Contextual Variables Within Bayesian Optimization Julien Martinelli Ayush Bharti A. Tiihonen S. T. John Louis Filstroff Sabina J. Sloman Patrick Rinke Samuel Kaski 48 0 0 23 May 2023
Robust Model-Based Optimization for Challenging Fitness Landscapes Saba Ghaffari Ehsan Saleh A. Schwing Yu-xiong Wang Martin D. Burke Saurabh Sinha 27 1 0 23 May 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 33 34 0 22 May 2023
RGCVAE: Relational Graph Conditioned Variational Autoencoder for Molecule Design Davide Rigoni Nicoló Navarin A. Sperduti BDL 28 1 0 19 May 2023