Title
Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Model Yiran Zhou Liangren Zhang Yuheng Ding Ningfeng Liu Song Song L. Zhang Bowei Huang Zhenming Liu AI4CE 103 12 0 13 Mar 2023
Domain-Agnostic Molecular Generation with Chemical Feedback Yin Fang Ningyu Zhang Zhuo Chen Lingbing Guo Xiaohui Fan Huajun Chen 241 17 0 26 Jan 2023
Domain-agnostic and Multi-level Evaluation of Generative Models G. Tadesse Jannis Born C. Cintas William Ogallo Dmitry Zubarev Matteo Manica Komminist Weldemariam ELM 80 2 0 20 Jan 2023
Improving Molecule Properties Through 2-Stage VAE Chenghui Zhou Barnabás Póczós DRL 98 1 0 06 Dec 2022
Group SELFIES: A Robust Fragment-Based Molecular String Representation Austin H. Cheng Andy Cai Santiago Miret Gustavo Malkomes Mariano Phielipp Alán Aspuru-Guzik 119 32 0 23 Nov 2022
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding Haitao Lin Yufei Huang Odin Zhang Siqi Ma Meng Liu X. Li Lirong Wu Shuiwang Ji Tingjun Hou Stan Z. Li DiffM 193 75 0 21 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 91 2 0 15 Nov 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 112 12 0 22 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 80 5 0 19 Oct 2022
A Transformer-based Generative Model for De Novo Molecular Design Wenlu Wang Ye Wang Honggang Zhao Simone Sciabola 72 0 0 17 Oct 2022
Modular Flows: Differential Molecular Generation Yogesh Verma Samuel Kaski Markus Heinonen Vikas Garg 154 15 0 12 Oct 2022
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 125 29 0 06 Oct 2022
The Vendi Score: A Diversity Evaluation Metric for Machine Learning Dan Friedman Adji Bousso Dieng EGVM 249 144 0 05 Oct 2022
Probabilistic Generative Transformer Language models for Generative Design of Molecules Lai Wei Nihang Fu Yuqi Song Qian Wang Jianjun Hu AI4CE 125 13 0 20 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 229 36 0 12 Sep 2022
Exploiting Pretrained Biochemical Language Models for Targeted Drug Design Gökçe Uludogan Elif Özkirimli K. Ülgen N. Karalı Arzucan Özgür 75 18 0 02 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 72 0 0 20 Aug 2022
Controllable Data Generation by Deep Learning: A Review Shiyu Wang Yuanqi Du Xiaojie Guo Bo Pan Zhaohui Qin Liang Zhao 155 32 0 19 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 133 31 0 08 Jul 2022
Materials Transformers Language Models for Generative Materials Design: a benchmark study Nihang Fu Lai Wei Yuqi Song Qinyang Li Rui Xin Sadman Sadeed Omee Rongzhi Dong Edirisuriya M Dilanga Siriwardane Jianjun Hu 98 2 0 27 Jun 2022
LIMO: Latent Inceptionism for Targeted Molecule Generation Peter Eckmann Kunyang Sun Bo Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 140 52 0 17 Jun 2022
An Unpooling Layer for Graph Generation Yi Guo Dongmian Zou Gilad Lerman 91 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 122 29 0 01 Jun 2022
Probabilistic Transformer: Modelling Ambiguities and Distributions for RNA Folding and Molecule Design Jörg Franke Frederic Runge Frank Hutter 114 16 0 27 May 2022
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets Xingang Peng Shitong Luo Jiaqi Guan Qi Xie Jian-wei Peng Jianzhu Ma 168 211 0 15 May 2022
Crystal Transformer: Self-learning neural language model for Generative and Tinkering Design of Materials Lai Wei Qinyang Li Yuqi Song Stanislav Stefanov Edirisuriya M Dilanga Siriwardane Fanglin Chen Jianjun Hu AI4CE 88 9 0 25 Apr 2022
Translation between Molecules and Natural Language Carl Edwards T. Lai Kevin Ros Garrett Honke Kyunghyun Cho Heng Ji 184 190 0 25 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 95 0 0 19 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 81 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 118 177 0 31 Mar 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 251 93 0 28 Mar 2022
Data-Efficient Graph Grammar Learning for Molecular Generation Minghao Guo Veronika Thost Beichen Li Payel Das Jie Chen Wojciech Matusik 114 37 0 15 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 172 80 0 13 Mar 2022
Score-Based Generative Models for Molecule Generation Dwaraknath Gnaneshwar Bharath Ramsundar Dhairya Gandhi Rachel C. Kurchin V. Viswanathan DiffM 60 13 0 07 Mar 2022
Autoencoding Hyperbolic Representation for Adversarial Generation Eric Qu Dongmian Zou GAN 142 6 0 30 Jan 2022
FastFlows: Flow-Based Models for Molecular Graph Generation Nathan C. Frey V. Gadepally Bharath Ramsundar 76 12 0 28 Jan 2022
Biases in In Silico Evaluation of Molecular Optimization Methods and Bias-Reduced Evaluation Methodology Hiroshi Kajino Kohei Miyaguchi Takayuki Osogami 127 1 0 28 Jan 2022
Reinforcement Learning for Personalized Drug Discovery and Design for Complex Diseases: A Systems Pharmacology Perspective Ryan K. Tan Yang Liu Lei Xie 102 2 0 21 Jan 2022
Keeping it Simple: Language Models can learn Complex Molecular Distributions Daniel Flam-Shepherd Kevin Zhu A. Aspuru‐Guzik 286 156 0 06 Dec 2021
Sample-Efficient Generation of Novel Photo-acid Generator Molecules using a Deep Generative Model Samuel C. Hoffman Vijil Chenthamarakshan Dmitry Zubarev Daniel P. Sanders Payel Das 97 5 0 02 Dec 2021
HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space Zhiyuan Chen Xiaomin Fang Zixu Hua Yueyang Huang Fan Wang Hua Wu MedIm 111 3 0 30 Nov 2021
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design Miguel García-Ortegón G. Simm Austin Tripp José Miguel Hernández-Lobato A. Bender S. Bacallado 138 87 0 29 Oct 2021
An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design Yi Zhang AI4CE 106 6 0 10 Oct 2021
Deep Denerative Models for Drug Design and Response Karina Zadorozhny Lada Nuzhna AI4CE 63 1 0 14 Sep 2021
Hybrid quantum-classical machine learning for generative chemistry and drug design A. I. Gircha A. S. Boev K. Avchaciov P. Fedichev A. Fedorov AI4CE BDL 96 35 0 26 Aug 2021
Geometric Deep Learning on Molecular Representations Kenneth Atz F. Grisoni G. Schneider AI4CE 192 333 0 26 Jul 2021
Artificial Intelligence in Drug Discovery: Applications and Techniques Jianyuan Deng Zhibo Yang Iwao Ojima Dimitris Samaras Fusheng Wang AI4TS 193 126 0 09 Jun 2021
Augmenting Molecular Deep Generative Models with Topological Data Analysis Representations Yair Schiff Vijil Chenthamarakshan Samuel C. Hoffman Karthikeyan N. Ramamurthy Payel Das MedIm 123 10 0 08 Jun 2021
High-Dimensional Bayesian Optimisation with Variational Autoencoders and Deep Metric Learning Antoine Grosnit Rasul Tutunov A. Maraval Ryan-Rhys Griffiths Alexander I. Cowen-Rivers ... Wenlong Lyu Zhitang Chen Jun Wang Jan Peters Haitham Bou-Ammar BDL DRL 151 65 0 07 Jun 2021
Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery Yulun Wu Mikaela Cashman Nicholas Choma E. Prates V. G. M. Vergara ... M. Head Rick L. Stevens Peter Nugent Daniel A. Jacobson James B. Brown GNN 224 10 0 04 Jun 2021