GuacaMol: Benchmarking Models for De Novo Molecular Design

22 November 2018

Papers citing "GuacaMol: Benchmarking Models for De Novo Molecular Design"

50 / 69 papers shown

Title
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks Xinyu Wang Jinbo Bi Minghu Song CLL 62 0 0 01 May 2025
Latent Bayesian Optimization via Autoregressive Normalizing Flows Seunghun Lee Jinyoung Park Jaewon Chu Minseo Yoon H. Kim BDL 30 1 0 21 Apr 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation Mohit Pandey G. Subbaraj Artem Cherkasov Martin Ester Emmanuel Bengio AI4CE 79 1 0 08 Mar 2025
A Survey of Graph Transformers: Architectures, Theories and Applications Chaohao Yuan Kangfei Zhao Ercan Engin Kuruoglu Liang Wang Tingyang Xu Wenbing Huang Deli Zhao Hong Cheng Yu Rong 55 4 0 23 Feb 2025
Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization N. Maus Kyurae Kim Yimeng Zeng Haydn Jones Fangping Wan Marcelo Der Torossian Torres Cesar de la Fuente-Nunez J. Gardner 80 0 0 31 Jan 2025
Federated Discrete Denoising Diffusion Model for Molecular Generation with OpenFL Kevin Ta Patrick Foley Mattson Thieme Abhishek Pandey Prashant Shah 68 0 0 21 Jan 2025
The Jungle of Generative Drug Discovery: Traps, Treasures, and Ways Out Rıza Özçelik F. Grisoni 46 0 0 24 Dec 2024
Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces Nianze Tao OOD OODD BDL 100 0 0 16 Dec 2024
GraphXForm: Graph transformer for computer-aided molecular design Jonathan Pirnay Jan G. Rittig Alexander B. Wolf Martin Grohe Jakob Burger Alexander Mitsos D. G. Grimm AI4CE 51 1 0 03 Nov 2024
A Bayesian Flow Network Framework for Chemistry Tasks Nianze Tao Minori Abe BDL 29 2 0 28 Jul 2024
Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Trees Alexia Jolicoeur-Martineau A. Baratin Kisoo Kwon Boris Knyazev Yan Zhang 36 1 0 12 Jul 2024
Active learning for affinity prediction of antibodies Alexandra Gessner Sebastian W. Ober Owen Vickery Dino Oglic Talip Uçar AI4CE 24 4 0 11 Jun 2024
Cometh: A continuous-time discrete-state graph diffusion model Antoine Siraudin Fragkiskos D. Malliaros Christopher Morris 36 3 0 10 Jun 2024
A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences Miguel González Duque Richard Michael Simon Bartels Yevgen Zainchkovskyy Søren Hauberg Wouter Boomsma 42 4 0 07 Jun 2024
Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate? Kangyu Zheng Yingzhou Lu Zaixi Zhang Zhongwei Wan Yao Ma Marinka Zitnik Tianfan Fu ELM 32 6 0 04 Jun 2024
Discrete-state Continuous-time Diffusion for Graph Generation Zhe Xu Ruizhong Qiu Yuzhong Chen Huiyuan Chen Xiran Fan Menghai Pan Zhichen Zeng Mahashweta Das Hanghang Tong 37 8 0 19 May 2024
GP-MoLFormer: A Foundation Model For Molecular Generation Jerret Ross Brian M. Belgodere Samuel C. Hoffman Vijil Chenthamarakshan Youssef Mroueh Payel Das Payel Das 36 5 0 04 Apr 2024
Genetic algorithms are strong baselines for molecule generation Austin Tripp José Miguel Hernández-Lobato 32 16 0 13 Oct 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 20 7 0 28 Sep 2023
Reinforcement Learning for Generative AI: A Survey Yuanjiang Cao Quan.Z Sheng Julian McAuley Lina Yao SyDa 46 10 0 28 Aug 2023
Models Matter: The Impact of Single-Step Retrosynthesis on Synthesis Planning Paula Torren-Peraire Alan Kai Hassen S. Genheden Jonas Verhoeven Djork-Arné Clevert Mike Preuss Igor V. Tetko 18 10 0 10 Aug 2023
ChiENN: Embracing Molecular Chirality with Graph Neural Networks Piotr Gaiñski Michał Koziarski Jacek Tabor Marek Śmieja GNN 32 3 0 05 Jul 2023
High-Dimensional Bayesian Optimization via Semi-Supervised Learning with Optimized Unlabeled Data Sampling Y. Yin Yu Wang Gang Xu 24 4 0 04 May 2023
SELFormer: Molecular Representation Learning via SELFIES Language Models Atakan Yüksel Erva Ulusoy Atabey Ünlü Tunca Dogan 25 55 0 10 Apr 2023
A supplemental investigation of non-linearity in quantum generative models with respect to simulatability and optimization Kaitlin Gili Rohan S. Kumar Mykolas Sveistrys C. Ballance 32 3 0 01 Feb 2023
Retrosynthetic Planning with Dual Value Networks Guoqing Liu Di Xue Shufang Xie Yingce Xia Austin Tripp Krzysztof Maziarz Marwin H. S. Segler Tao Qin Zongzhang Zhang Tie-Yan Liu OffRL 13 12 0 31 Jan 2023
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 25 51 0 28 Nov 2022
An Empirical Evaluation of Zeroth-Order Optimization Methods on AI-driven Molecule Optimization Elvin Lo Pin-Yu Chen 24 0 0 27 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 32 11 0 22 Oct 2022
PEMP: Leveraging Physics Properties to Enhance Molecular Property Prediction Yuancheng Sun Yimeng Chen Weizhi Ma Wenhao Huang Kang Liu Zhiming Ma Wei-Ying Ma Yanyan Lan 20 7 0 18 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
Probabilistic Generative Transformer Language models for Generative Design of Molecules Lai Wei Nihang Fu Yuqi Song Qian Wang Jianjun Hu AI4CE 31 11 0 20 Sep 2022
A biologically-inspired multi-modal evaluation of molecular generative machine learning E. Vinogradova Abay Artykbayev Alisher Amanatay Mukhamejan Karatayev Maxim Mametkulov ... K. Pats Rustam Zhumagambetov Ferdinand Molnár Vsevolod A. Peshkov S. Fazli ELM 13 0 0 20 Aug 2022
Improving Small Molecule Generation using Mutual Information Machine Daniel A. Reidenbach M. Livne Rajesh Ilango M. Gill Johnny Israeli 23 14 0 18 Aug 2022
Chemical transformer compression for accelerating both training and inference of molecular modeling Yi Yu K. Börjesson 19 0 0 16 May 2022
3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design Yinan Huang Xing Peng Jianzhu Ma Muhan Zhang BDL 30 47 0 15 May 2022
Conditional $β$ -VAE for De Novo Molecular Generation Ryan J. Richards A. Groener BDL DRL 22 10 0 01 May 2022
SELFIES and the future of molecular string representations Mario Krenn Qianxiang Ai Senja Barthel Nessa Carson Angelo Frei ... Andrew Wang Andrew D. White A. Young Rose Yu A. Aspuru‐Guzik 32 147 0 31 Mar 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 31 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 31 67 0 13 Mar 2022
Biases in In Silico Evaluation of Molecular Optimization Methods and Bias-Reduced Evaluation Methodology Hiroshi Kajino Kohei Miyaguchi Takayuki Osogami 59 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 51 69 0 28 Jan 2022
A molecular generative model with genetic algorithm and tree search for cancer samples Sejin Park Hyunju Lee 21 1 0 16 Dec 2021
AugLiChem: Data Augmentation Library of Chemical Structures for Machine Learning Rishikesh Magar Yuyang Wang Cooper Lorsung Chen Liang Hariharan Ramasubramanian Peiyuan Li A. Farimani 26 27 0 30 Nov 2021
Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations Keir Adams L. Pattanaik Connor W. Coley 21 32 0 08 Oct 2021
Differentiable Scaffolding Tree for Molecular Optimization Tianfan Fu Wenhao Gao Cao Xiao Jacob Yasonik Connor W. Coley Jimeng Sun 25 75 0 22 Sep 2021
Geometric Deep Learning on Molecular Representations Kenneth Atz F. Grisoni G. Schneider AI4CE 30 287 0 26 Jul 2021
Improving black-box optimization in VAE latent space using decoder uncertainty Pascal Notin José Miguel Hernández-Lobato Y. Gal 24 61 0 30 Jun 2021
Molecule Generation by Principal Subgraph Mining and Assembling Xiangzhe Kong Wenbing Huang Zhixing Tan Yang Liu GNN 21 45 0 29 Jun 2021
Graph Context Encoder: Graph Feature Inpainting for Graph Generation and Self-supervised Pretraining Oriel Frigo Rémy Brossard David Dehaene 37 1 0 18 Jun 2021