Title
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 34 25 0 06 Oct 2022
The Vendi Score: A Diversity Evaluation Metric for Machine Learning Dan Friedman Adji Bousso Dieng EGVM 82 109 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 31 11 0 20 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 45 20 0 12 Sep 2022
Exploiting Pretrained Biochemical Language Models for Targeted Drug Design Gökçe Uludogan Elif Özkirimli K. Ülgen N. Karalı Arzucan Özgür 12 15 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 13 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 29 28 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 11 26 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 14 2 0 27 Jun 2022
LIMO: Latent Inceptionism for Targeted Molecule Generation Peter Eckmann Kunyang Sun Bo-Lu Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 41 44 0 17 Jun 2022
An Unpooling Layer for Graph Generation Yi Guo Dongmian Zou Gilad Lerman 10 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 15 23 0 01 Jun 2022
Probabilistic Transformer: Modelling Ambiguities and Distributions for RNA Folding and Molecule Design Jörg K.H. Franke Frederic Runge Frank Hutter 15 14 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 27 176 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 20 9 0 25 Apr 2022
Translation between Molecules and Natural Language Carl N. Edwards T. Lai Kevin Ros Garrett Honke Kyunghyun Cho Heng Ji 25 155 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 18 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 20 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 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 28 86 0 28 Mar 2022
Data-Efficient Graph Grammar Learning for Molecular Generation Minghao Guo Veronika Thost Beichen Li Payel Das Jie Chen Wojciech Matusik 30 36 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 31 67 0 13 Mar 2022
Score-Based Generative Models for Molecule Generation Dwaraknath Gnaneshwar Bharath Ramsundar Dhairya Gandhi Rachel C. Kurchin V. Viswanathan DiffM 22 11 0 07 Mar 2022
Autoencoding Hyperbolic Representation for Adversarial Generation Eric Qu Dongmian Zou GAN 28 4 0 30 Jan 2022
FastFlows: Flow-Based Models for Molecular Graph Generation Nathan C. Frey V. Gadepally Bharath Ramsundar 19 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 59 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 31 2 0 21 Jan 2022
Keeping it Simple: Language Models can learn Complex Molecular Distributions Daniel Flam-Shepherd Kevin Zhu A. Aspuru‐Guzik 131 142 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 34 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-Hong Wu MedIm 24 2 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 35 75 0 29 Oct 2021
An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design Yi Zhang AI4CE 28 4 0 10 Oct 2021
Deep Denerative Models for Drug Design and Response Karina Zadorozhny Lada Nuzhna AI4CE 26 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 17 26 0 26 Aug 2021
Geometric Deep Learning on Molecular Representations Kenneth Atz F. Grisoni G. Schneider AI4CE 30 286 0 26 Jul 2021
Artificial Intelligence in Drug Discovery: Applications and Techniques Jianyuan Deng Zhibo Yang Iwao Ojima Dimitris Samaras Fusheng Wang AI4TS 21 99 0 09 Jun 2021
Augmenting Molecular Deep Generative Models with Topological Data Analysis Representations Yair Schiff Vijil Chenthamarakshan Samuel C. Hoffman K. Ramamurthy Payel Das MedIm 22 9 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 22 58 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 33 10 0 04 Jun 2021
Optimizing Functionals on the Space of Probabilities with Input Convex Neural Networks David Alvarez-Melis Yair Schiff Youssef Mroueh 40 52 0 01 Jun 2021
Large-Scale Wasserstein Gradient Flows Petr Mokrov Alexander Korotin Lingxiao Li Aude Genevay Justin Solomon Evgeny Burnaev 24 71 0 01 Jun 2021
Combating small molecule aggregation with machine learning Kuan-Ting Lee An Yang Yen-Chu Lin D. Reker G. Bernardes T. Rodrigues 30 12 0 01 May 2021
Learning to design drug-like molecules in three-dimensional space using deep generative models Yibo Li Jianfeng Pei L. Lai DiffM 32 111 0 17 Apr 2021
DIG: A Turnkey Library for Diving into Graph Deep Learning Research Meng Liu Youzhi Luo Limei Wang Yaochen Xie Haonan Yuan ... Haoran Liu Cong Fu Bora Oztekin Xuan Zhang Shuiwang Ji GNN 21 118 0 23 Mar 2021
Generative Chemical Transformer: Neural Machine Learning of Molecular Geometric Structures from Chemical Language via Attention Hyunseung Kim Jonggeol Na Won Bo Lee 14 46 0 27 Feb 2021
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development Kexin Huang Tianfan Fu Wenhao Gao Yue Zhao Yusuf Roohani J. Leskovec Connor W. Coley Cao Xiao Jimeng Sun Marinka Zitnik OOD LM&MA 30 261 0 18 Feb 2021
MolGrow: A Graph Normalizing Flow for Hierarchical Molecular Generation Maksim Kuznetsov Daniil Polykovskiy 25 40 0 03 Feb 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 185 187 0 01 Feb 2021
Chemistry42: An AI-based platform for de novo molecular design Y. Ivanenkov Alexander Zhebrak Dmitry Bezrukov B. Zagribelnyy V. Aladinskiy Daniil Polykovskiy E. Putin Petrina Kamya Alex Aliper Alex Zhavoronkov 13 6 0 22 Jan 2021
Deep Graph Generators: A Survey Faezeh Faez Yassaman Ommi M. Baghshah Hamid R. Rabiee GNN AI4CE 42 57 0 31 Dec 2020