Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space

25 September 2019

Papers citing "Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space"

50 / 65 papers shown

Title
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
InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization Yifan Niu Ziqi Gao Tingyang Xu Yang Liu Yatao Bian Yu Rong Junzhou Huang Jia Li 68 0 0 03 Mar 2025
MOLLM: Multi-Objective Large Language Model for Molecular Design -- Optimizing with Experts Nian Ran Yue Wang Richard Allmendinger 71 0 0 18 Feb 2025
Survey on Recent Progress of AI for Chemistry: Methods, Applications, and Opportunities Ding Hu Pengxiang Hua Zhen Huang 88 0 0 09 Feb 2025
Genetic-guided GFlowNets for Sample Efficient Molecular Optimization Hyeon-Seob Kim Minsu Kim Sanghyeok Choi Jinkyoo Park 51 3 0 31 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 75 1 0 18 Nov 2024
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design Dannong Wang Jintai Chen Zhiding Liang Tianfan Fu Xiao-Yang Liu 20 1 0 13 Sep 2024
Diagnosing and fixing common problems in Bayesian optimization for molecule design Austin Tripp José Miguel Hernández-Lobato 29 1 0 11 Jun 2024
Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation Jeff Guo Philippe Schwaller Mamba 49 7 0 27 May 2024
A Review on Fragment-based De Novo 2D Molecule Generation Sergei Voloboev VLM 29 1 0 08 May 2024
DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization Xiangxin Zhou Xiwei Cheng Yuwei Yang Yu Bao Liang Wang Quanquan Gu 34 15 0 07 Mar 2024
Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling Yuwei Yang Siqi Ouyang Xueyu Hu Mingyue Zheng Hao Zhou Lei Li 32 1 0 22 Feb 2024
Molecule Design by Latent Prompt Transformer Deqian Kong Yuhao Huang Jianwen Xie Ying Nian Wu 12 3 0 05 Oct 2023
Drug Discovery with Dynamic Goal-aware Fragments Seul Lee Seanie Lee Kenji Kawaguchi Sung Ju Hwang 17 5 0 02 Oct 2023
Will More Expressive Graph Neural Networks do Better on Generative Tasks? Xian-Quan Zou Xiangyu Zhao Pietro Lio' Yiren Zhao 15 2 0 23 Aug 2023
Molecule Design by Latent Space Energy-Based Modeling and Gradual Distribution Shifting Deqian Kong Bo Pang Tian Han Ying Nian Wu DiffM 35 7 0 09 Jun 2023
PyTrial: Machine Learning Software and Benchmark for Clinical Trial Applications Zifeng Wang B. Theodorou Tianfan Fu Cao Xiao Jimeng Sun LM&MA 22 2 0 06 Jun 2023
Materials Informatics: An Algorithmic Design Rule B. Bishnoi 11 0 0 05 May 2023
The power of motifs as inductive bias for learning molecular distributions Johanna Sommer Leon Hetzel David Ludke Fabian J. Theis Stephan Günnemann 25 5 0 04 Apr 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 60 10 0 01 Mar 2023
Domain-Agnostic Molecular Generation with Chemical Feedback Yin Fang Ningyu Zhang Zhuo Chen Lingbing Guo Xiaohui Fan Huajun Chen 33 11 0 26 Jan 2023
Molecule optimization via multi-objective evolutionary in implicit chemical space Xin Xia Yansen Su Chunhou Zheng Xiangxiang Zeng 31 1 0 17 Dec 2022
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 25 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 21 27 0 23 Nov 2022
Actively Learning Costly Reward Functions for Reinforcement Learning André Eberhard Houssam Metni G. Fahland A. Stroh Pascal Friederich OffRL 23 0 0 23 Nov 2022
Equivariant Energy-Guided SDE for Inverse Molecular Design Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 187 63 0 30 Sep 2022
Retrieval-based Controllable Molecule Generation Zichao Wang Weili Nie Zhuoran Qiao Chaowei Xiao Richard Baraniuk Anima Anandkumar 24 36 0 23 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
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
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
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo S. Hwang OODD 30 75 0 06 Jun 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
Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders Samuel Stanton Wesley J. Maddox Nate Gruver Phillip M. Maffettone E. Delaney Peyton Greenside A. Wilson BDL 31 89 0 23 Mar 2022
Molecule Generation for Drug Design: a Graph Learning Perspective Nianzu Yang Huaijin Wu Xiaoyong Pan Ye Yuan Junchi Yan 19 13 0 18 Feb 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
Genetic Algorithm for Constrained Molecular Inverse Design Yurim Lee Gydam Choi Minsug Yoon Cheongwon Kim 29 1 0 07 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
Fragment-based Sequential Translation for Molecular Optimization Benson Chen Xiang Fu Regina Barzilay Tommi Jaakkola 29 7 0 26 Oct 2021
Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design Wenhao Gao Rocío Mercado Connor W. Coley 21 57 0 12 Oct 2021
An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design Yi Zhang AI4CE 30 4 0 10 Oct 2021
Unifying Likelihood-free Inference with Black-box Optimization and Beyond Dinghuai Zhang Jie Fu Yoshua Bengio Aaron Courville 31 13 0 06 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
Molecule Generation by Principal Subgraph Mining and Assembling Xiangzhe Kong Wenbing Huang Zhixing Tan Yang Liu GNN 21 45 0 29 Jun 2021
JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design AkshatKumar Nigam R. Pollice Alán Aspuru-Guzik 29 51 0 07 Jun 2021
MARS: Markov Molecular Sampling for Multi-objective Drug Discovery Yutong Xie Chence Shi Hao Zhou Yuwei Yang Weinan Zhang Yong Yu Lei Li 24 138 0 18 Mar 2021
Golem: An algorithm for robust experiment and process optimization Matteo Aldeghi Florian Hase Riley J. Hickman Isaac Tamblyn Alán Aspuru-Guzik 25 22 0 05 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
Assigning Confidence to Molecular Property Prediction AkshatKumar Nigam R. Pollice Matthew F. D. Hurley Riley J. Hickman Matteo Aldeghi Naruki Yoshikawa Seyone Chithrananda Vincent A. Voelz Alán Aspuru-Guzik AI4CE 14 46 0 23 Feb 2021
Artificial Intelligence based Autonomous Molecular Design for Medical Therapeutic: A Perspective R. P. Joshi Neeraj Kumar 16 2 0 10 Feb 2021