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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Trillion Parameter AI Serving Infrastructure for Scientific Discovery: A Survey and Vision Nathaniel Hudson J. G. Pauloski Matt Baughman Alok V. Kamatar Mansi Sakarvadia ... Owen Price Skelly Ben Blaiszik Rick L. Stevens Kyle Chard Ian Foster MedIm 27 8 0 05 Feb 2024
Overcoming Order in Autoregressive Graph Generation Edo Cohen-Karlik Eyal Rozenberg Daniel Freedman 34 1 0 04 Feb 2024
Co-orchestration of Multiple Instruments to Uncover Structure-Property Relationships in Combinatorial Libraries B. Slautin Utkarsh Pratiush Ilia N. Ivanov Yongtao Liu Rohit K. Pant Xiaohang Zhang Ichiro Takeuchi M. Ziatdinov Sergei V. Kalinin 28 2 0 03 Feb 2024
Clustering Molecular Energy Landscapes by Adaptive Network Embedding Paula Mercurio Di Liu 11 0 0 19 Jan 2024
Simulation Based Bayesian Optimization Roi Naveiro Becky Tang 27 0 0 19 Jan 2024
Attention Based Molecule Generation via Hierarchical Variational Autoencoder Divahar Sivanesan BDL GAN 11 0 0 18 Jan 2024
Through the Dual-Prism: A Spectral Perspective on Graph Data Augmentation for Graph Classification Yutong Xia Runpeng Yu Keli Zhang Xavier Bresson Xinchao Wang Roger Zimmermann 39 4 0 18 Jan 2024
FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproduction Alexander Telepov Artem Tsypin Kuzma Khrabrov Sergey Yakukhnov Pavel Strashnov ... Egor Rumiantsev Daniel Ezhov Manvel Avetisian Olga Popova Artur Kadurin 27 4 0 18 Jan 2024
Functional Graphical Models: Structure Enables Offline Data-Driven Optimization J. Kuba Masatoshi Uehara Pieter Abbeel Sergey Levine AI4CE 23 4 0 08 Jan 2024
From Function to Distribution Modeling: A PAC-Generative Approach to Offline Optimization Qiang Zhang Ruida Zhou Yang Shen Tie Liu OffRL 41 1 0 04 Jan 2024
Accelerating Black-Box Molecular Property Optimization by Adaptively Learning Sparse Subspaces Farshud Sorourifar Thomas Banker J. Paulson 24 2 0 02 Jan 2024
Classifier-free graph diffusion for molecular property targeting Matteo Ninniri Marco Podda Davide Bacciu 40 5 0 28 Dec 2023
SANIA: Polyak-type Optimization Framework Leads to Scale Invariant Stochastic Algorithms Farshed Abdukhakimov Chulu Xiang Dmitry Kamzolov Robert Mansel Gower Martin Takáč 43 2 0 28 Dec 2023
PG-LBO: Enhancing High-Dimensional Bayesian Optimization with Pseudo-Label and Gaussian Process Guidance Taicai Chen Yue Duan Dong Li Lei Qi Yinghuan Shi Yang Gao BDL DRL 29 5 0 28 Dec 2023
Olfactory Label Prediction on Aroma-Chemical Pairs Laura Sisson Aryan Amit Barsainyan Mrityunjay Sharma Ritesh Kumar 11 0 0 26 Dec 2023
VAE for Modified 1-Hot Generative Materials Modeling, A Step Towards Inverse Material Design Khalid El-Awady 3DV 26 0 0 25 Dec 2023
De novo Drug Design using Reinforcement Learning with Multiple GPT Agents Xiuyuan Hu Guoqing Liu Yang Zhao Hao Zhang 23 20 0 21 Dec 2023
Pre-training of Molecular GNNs via Conditional Boltzmann Generator Daiki Koge N. Ono Shigehiko Kanaya AI4CE 16 0 0 20 Dec 2023
FSscore: A Machine Learning-based Synthetic Feasibility Score Leveraging Human Expertise Rebecca M. Neeser Bruno Correia Philippe Schwaller 21 1 0 20 Dec 2023
Stochastic Bayesian Optimization with Unknown Continuous Context Distribution via Kernel Density Estimation Xiaobin Huang Lei Song Ke Xue Chao Qian 34 3 0 16 Dec 2023
Holistic chemical evaluation reveals pitfalls in reaction prediction models Victor Sabanza Gil Andres M Bran Malte Franke Remi Schlama J. Luterbacher Philippe Schwaller ELM 33 1 0 14 Dec 2023
Pathway to a fully data-driven geotechnics: lessons from materials informatics Stephen Wu Yu Otake Yosuke Higo Ikumasa Yoshida AI4CE 24 4 0 01 Dec 2023
PyTorch Geometric High Order: A Unified Library for High Order Graph Neural Network Xiyuan Wang Muhan Zhang AI4CE 23 3 0 28 Nov 2023
LLamol: A Dynamic Multi-Conditional Generative Transformer for De Novo Molecular Design Niklas Dobberstein Astrid Maass J. Hamaekers 31 5 0 24 Nov 2023
nach0: Multimodal Natural and Chemical Languages Foundation Model M. Livne Z. Miftahutdinov E. Tutubalina Maksim Kuznetsov Daniil Polykovskiy ... Aastha Jhunjhunwala Anthony Costa Alex Aliper Alán Aspuru-Guzik Alex Zhavoronkov AI4CE 27 12 0 21 Nov 2023
Beyond the training set: an intuitive method for detecting distribution shift in model-based optimization Farhan N. Damani David H. Brookes Theodore Sternlieb Cameron Webster Stephen Malina Rishi Jajoo Kathy Lin Sam Sinai OffRL 27 3 0 09 Nov 2023
STRIDE: Structure-guided Generation for Inverse Design of Molecules Shehtab Zaman D. Akhiyarov Mauricio Araya-Polo Kenneth Chiu 29 1 0 06 Nov 2023
Joint Composite Latent Space Bayesian Optimization Natalie Maus Zhiyuan Jerry Lin Maximilian Balandat E. Bakshy BDL 33 2 0 03 Nov 2023
Bayesian Optimization of Function Networks with Partial Evaluations Poompol Buathong Jiayue Wan Raul Astudillo Sam Daulton Maximilian Balandat P. Frazier 26 2 0 03 Nov 2023
AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways via Contrastive Learning Mohammadamin Tavakoli Y. T. T. Chiu Alexander Shmakov Ann Marie Carlton David Van Vranken Pierre Baldi 25 2 0 02 Nov 2023
Advancing Bayesian Optimization via Learning Correlated Latent Space Seunghun Lee Jaewon Chu S. Kim Juyeon Ko Hyunwoo J. Kim BDL 49 6 0 31 Oct 2023
Efficient Subgraph GNNs by Learning Effective Selection Policies Beatrice Bevilacqua Moshe Eliasof E. Meirom Bruno Ribeiro Haggai Maron 20 13 0 30 Oct 2023
Re-evaluating Retrosynthesis Algorithms with Syntheseus Krzysztof Maziarz Austin Tripp Guoqing Liu Megan Stanley Shufang Xie Piotr Gaiñski Philipp Seidl Marwin H. S. Segler ELM 29 13 0 30 Oct 2023
Learning Invariant Molecular Representation in Latent Discrete Space Zhuang Xiang Qiang Zhang Keyan Ding Yatao Bian Xiao Wang Jingsong Lv Hongyang Chen Huajun Chen OOD 26 16 0 22 Oct 2023
Conformal Drug Property Prediction with Density Estimation under Covariate Shift Siddhartha Laghuvarapu Zhen Lin Jimeng Sun 20 4 0 18 Oct 2023
Gotta be SAFE: A New Framework for Molecular Design Emmanuel Noutahi Cristian Gabellini Michael Craig Jonathan S.C Lim Prudencio Tossou 29 16 0 16 Oct 2023
A Deep Neural Network -- Mechanistic Hybrid Model to Predict Pharmacokinetics in Rat Florian Führer Andrea Gruber Holger Diedam A. Göller Stephan Menz S. Schneckener 28 3 0 13 Oct 2023
Kernel-Elastic Autoencoder for Molecular Design Haote Li Yu Shee B. Allen F. Maschietto Victor S. Batista 21 5 0 12 Oct 2023
Transformers and Large Language Models for Chemistry and Drug Discovery Andres M Bran Philippe Schwaller LM&MA MedIm AI4CE 38 14 0 09 Oct 2023
Molecular De Novo Design through Transformer-based Reinforcement Learning Pengcheng Xu Tao Feng Tianfan Fu Siddhartha Laghuvarapu Jimeng Sun 22 1 0 09 Oct 2023
Diffusing on Two Levels and Optimizing for Multiple Properties: A Novel Approach to Generating Molecules with Desirable Properties Siyuan Guo Jihong Guan Shuigeng Zhou 38 3 0 05 Oct 2023
Molecule Design by Latent Prompt Transformer Deqian Kong Yuhao Huang Jianwen Xie Ying Nian Wu 17 3 0 05 Oct 2023
Searching for High-Value Molecules Using Reinforcement Learning and Transformers Raj Ghugare Santiago Miret Adriana Hugessen Mariano Phielipp Glen Berseth 11 16 0 04 Oct 2023
A Deep Instance Generative Framework for MILP Solvers Under Limited Data Availability Zijie Geng Xijun Li Jie Wang Xiao Li Yongdong Zhang Feng Wu 46 18 0 04 Oct 2023
SALSA: Semantically-Aware Latent Space Autoencoder Kathryn E. Kirchoff Travis Maxfield Alexander Tropsha Shawn M. Gomez 18 2 0 04 Oct 2023
De Novo Drug Design with Joint Transformers Adam Izdebski Ewelina Węglarz-Tomczak Ewa Szczurek Jakub M. Tomczak ViT 23 3 0 03 Oct 2023
MHG-GNN: Combination of Molecular Hypergraph Grammar with Graph Neural Network Akihiro Kishimoto Hiroshi Kajino Masataka Hirose Junta Fuchiwaki Indra Priyadarsini Lisa Hamada Hajime Shinohara D. Nakano Seiji Takeda AI4CE 34 4 0 28 Sep 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 25 7 0 28 Sep 2023
Understanding the Structure of QM7b and QM9 Quantum Mechanical Datasets Using Unsupervised Learning Julio J. Valdés A. Tchagang 20 2 0 25 Sep 2023
Beam Enumeration: Probabilistic Explainability For Sample Efficient Self-conditioned Molecular Design Jeff Guo P. Schwaller 32 6 0 25 Sep 2023