Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation

4 October 2021

Papers citing "Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation"

47 / 47 papers shown

Title
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks Xinyu Wang Jinbo Bi Minghu Song CLL 54 0 0 01 May 2025
Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation Taojie Kuang Qianli Ma Athanasios V. Vasilakos Yu Wang Qiang Cheng Zhixiang Ren 42 0 0 11 Mar 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation Mohit Pandey G. Subbaraj Artem Cherkasov Martin Ester Emmanuel Bengio AI4CE 57 1 0 08 Mar 2025
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows Xiangxin Zhou Yi Xiao Haowei Lin Xinheng He Jiaqi Guan Yang Wang Qiang Liu F. I. S. Kevin Zhou Liang Wang Jianzhu Ma AI4CE 47 0 0 06 Mar 2025
Dynamic Search for Inference-Time Alignment in Diffusion Models Xiner Li Masatoshi Uehara Xingyu Su Gabriele Scalia Tommaso Biancalani Aviv Regev Sergey Levine Shuiwang Ji 42 0 0 03 Mar 2025
Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces Nianze Tao OOD OODD BDL 95 0 0 16 Dec 2024
Molecule Generation with Fragment Retrieval Augmentation Seul Lee Karsten Kreis Srimukh Prasad Veccham Meng Liu Danny Reidenbach Saee Paliwal Arash Vahdat Weili Nie VLM 63 1 0 18 Nov 2024
Text-Guided Multi-Property Molecular Optimization with a Diffusion Language Model Yida Xiong Kun Li Weiwei Liu Jia Wu Bo Du Shirui Pan Wenbin Hu 15 0 0 17 Oct 2024
Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding Xiner Li Yulai Zhao Chenyu Wang Gabriele Scalia Gökçen Eraslan Surag Nair Tommaso Biancalani Aviv Regev Sergey Levine Masatoshi Uehara 47 22 0 15 Aug 2024
Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation Jeff Guo Philippe Schwaller Mamba 32 2 0 27 May 2024
Regressor-free Molecule Generation to Support Drug Response Prediction Kun Li Xiuwen Gong Shirui Pan Jia Wu Bo Du Wenbin Hu 16 1 0 23 May 2024
MAGE: Model-Level Graph Neural Networks Explanations via Motif-based Graph Generation Zhaoning Yu Hongyang Gao 37 3 0 21 May 2024
A Review on Fragment-based De Novo 2D Molecule Generation Sergei Voloboev VLM 27 1 0 08 May 2024
Diffusion-Driven Domain Adaptation for Generating 3D Molecules Haokai Hong Wanyu Lin Kay Chen Tan DiffM 29 2 0 01 Apr 2024
Mol-AIR: Molecular Reinforcement Learning with Adaptive Intrinsic Rewards for Goal-directed Molecular Generation Jinyeong Park Jaegyoon Ahn Jonghwan Choi Jibum Kim 20 1 0 29 Mar 2024
Graph Diffusion Policy Optimization Yijing Liu Chao Du Tianyu Pang Chongxuan Li Wei Chen Min-Bin Lin 16 7 0 26 Feb 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 14 4 0 18 Jan 2024
Empirical Evidence for the Fragment level Understanding on Drug Molecular Structure of LLMs Xiuyuan Hu Guoqing Liu Yang Zhao Hao Zhang 10 0 0 15 Jan 2024
De novo Drug Design using Reinforcement Learning with Multiple GPT Agents Xiuyuan Hu Guoqing Liu Yang Zhao Hao Zhang 13 19 0 21 Dec 2023
Docking-based generative approaches in the search for new drug candidates Tomasz Danel Jan Leski Sabina Podlewska Igor T. Podolak 11 22 0 22 Nov 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 16 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
Drug Discovery with Dynamic Goal-aware Fragments Seul Lee Seanie Lee Kenji Kawaguchi Sung Ju Hwang 13 5 0 02 Oct 2023
MatSciML: A Broad, Multi-Task Benchmark for Solid-State Materials Modeling Kin Long Kelvin Lee Carmelo Gonzales Marcel Nassar Matthew Spellings Mikhail Galkin Santiago Miret 14 15 0 12 Sep 2023
Graph Generation with $K^2$ -trees Yunhui Jang Dongwoo Kim Sungsoo Ahn 24 3 0 30 May 2023
MAGNet: Motif-Agnostic Generation of Molecules from Shapes Leon Hetzel Johanna Sommer Bastian Alexander Rieck Fabian J. Theis Stephan Günnemann 16 4 0 30 May 2023
MotifRetro: Exploring the Combinability-Consistency Trade-offs in retrosynthesis via Dynamic Motif Editing Zhangyang Gao Xingran Chen Cheng Tan Stan Z. Li 6 1 0 20 May 2023
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D Bo Qiang Yuxuan Song Minkai Xu Jingjing Gong B. Gao Hao Zhou Weiying Ma Yanyan Lan DiffM 38 5 0 05 May 2023
Are VAEs Bad at Reconstructing Molecular Graphs? Hagen Muenkler Hubert Misztela Michał Pikusa Marwin H. S. Segler Nadine Schneider Krzysztof Maziarz DRL 17 2 0 04 May 2023
The power of motifs as inductive bias for learning molecular distributions Johanna Sommer Leon Hetzel David Ludke Fabian J. Theis Stephan Günnemann 17 4 0 04 Apr 2023
Utilizing Reinforcement Learning for de novo Drug Design Hampus Gummesson Svensson C. Tyrchan O. Engkvist M. Chehreghani 17 17 0 30 Mar 2023
Deep Learning Methods for Small Molecule Drug Discovery: A Survey Wenhao Hu Yingying Liu Xuanyu Chen Wenhao Chai Hangyue Chen Hongwei Wang Gaoang Wang 42 10 0 01 Mar 2023
De Novo Molecular Generation via Connection-aware Motif Mining Zijie Geng Shufang Xie Yingce Xia Lijun Wu Tao Qin Jie Wang Yongdong Zhang Feng Wu Tie-Yan Liu 8 32 0 02 Feb 2023
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 7 51 0 28 Nov 2022
Group SELFIES: A Robust Fragment-Based Molecular String Representation Austin H. Cheng Andy Cai Santiago Miret Gustavo Malkomes Mariano Phielipp Alán Aspuru-Guzik 11 27 0 23 Nov 2022
Accurate, reliable and interpretable solubility prediction of druglike molecules with attention pooling and Bayesian learning Seongok Ryu Sumin Lee 6 5 0 29 Sep 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo S. Hwang OODD 17 72 0 06 Jun 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 19 75 0 28 Mar 2022
Molecule Generation for Drug Design: a Graph Learning Perspective Nianzu Yang Huaijin Wu Xiaoyong Pan Ye Yuan Junchi Yan 14 13 0 18 Feb 2022
Knowledge-informed Molecular Learning: A Survey on Paradigm Transfer Yin Fang Zhuo Chen Xiaohui Fan Qiang Zhang 32 3 0 17 Feb 2022
Learning to Discover Medicines T. Nguyen Thin Nguyen T. Tran 16 1 0 14 Feb 2022
Molecule Generation by Principal Subgraph Mining and Assembling Xiangzhe Kong Wenbing Huang Zhixing Tan Yang Liu GNN 8 21 0 29 Jun 2021
We Should at Least Be Able to Design Molecules That Dock Well Tobiasz Ciepliński Tomasz Danel Sabina Podlewska Stanislaw Jastrzebski 10 29 0 20 Jun 2020
Soft Actor-Critic for Discrete Action Settings Petros Christodoulou OffRL 101 292 0 16 Oct 2019
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 181 878 0 07 Jun 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 208 1,205 0 12 Feb 2018
Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning Y. Gal Zoubin Ghahramani UQCV BDL 245 9,042 0 06 Jun 2015