MARS: Markov Molecular Sampling for Multi-objective Drug Discovery

18 March 2021

Yong Yu

Lei Li

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Papers citing "MARS: Markov Molecular Sampling for Multi-objective Drug Discovery"

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Title
LLM-Augmented Chemical Synthesis and Design Decision Programs Haorui Wang Jeff Guo Lingkai Kong R. Ramprasad Philippe Schwaller Yuanqi Du Chao Zhang 21 0 0 11 May 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation Mohit Pandey G. Subbaraj Artem Cherkasov Martin Ester Emmanuel Bengio AI4CE 66 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 50 0 0 06 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
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 100 3 0 18 Feb 2025
MOLLM: Multi-Objective Large Language Model for Molecular Design -- Optimizing with Experts Nian Ran Yue Wang Richard Allmendinger 58 0 0 18 Feb 2025
Neural Flow Samplers with Shortcut Models Wuhao Chen Zijing Ou Yingzhen Li 77 0 0 11 Feb 2025
Molecule Generation with Fragment Retrieval Augmentation Seul Lee Karsten Kreis Srimukh Prasad Veccham Meng Liu Danny Reidenbach Saee Paliwal Arash Vahdat Weili Nie VLM 68 1 0 18 Nov 2024
Online Mirror Descent for Tchebycheff Scalarization in Multi-Objective Optimization Meitong Liu Xiaoyuan Zhang Chulin Xie Kate Donahue Han Zhao 13 1 0 29 Oct 2024
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 40 0 0 15 Oct 2024
Mitigating Exposure Bias in Score-Based Generation of Molecular Conformations Sijia Wang Chen Wang Zhenhao Zhao Jiqiang Zhang Weiran Cai 21 0 0 21 Sep 2024
Decomposed Direct Preference Optimization for Structure-Based Drug Design Xiwei Cheng Xiangxin Zhou Yuwei Yang Yu Bao Quanquan Gu 38 3 0 19 Jul 2024
Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Trees Alexia Jolicoeur-Martineau A. Baratin Kisoo Kwon Boris Knyazev Yan Zhang 33 1 0 12 Jul 2024
Leveraging Latent Evolutionary Optimization for Targeted Molecule Generation Siddartha Reddy N Sai Prakash MV V. Varun Vishal Vaddina Saisubramaniam Gopalakrishnan 49 0 0 02 Jul 2024
Global Human-guided Counterfactual Explanations for Molecular Properties via Reinforcement Learning Danqing Wang Antonis Antoniades Kha-Dinh Luong Edwin Zhang Mert Kosan Jiachen Li Ambuj Singh William Yang Wang Lei Li AI4CE 18 0 0 19 Jun 2024
Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning of Variational Autoencoders Naﬁz Abeer Sanket R. Jantre Nathan M. Urban Byung-Jun Yoon 36 0 0 31 May 2024
Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation Jeff Guo Philippe Schwaller Mamba 42 7 0 27 May 2024
A Review on Fragment-based De Novo 2D Molecule Generation Sergei Voloboev VLM 29 1 0 08 May 2024
Dynamic Backtracking in GFlowNets: Enhancing Decision Steps with Reward-Dependent Adjustment Mechanisms Shuai Guo Jielei Chu Lei Zhu Zhaoyu Li Tianrui Li AI4CE 29 2 0 08 Apr 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 31 5 0 04 Apr 2024
Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model Peng Zhou Jianmin Wang Chunyan Li Zixu Wang Yiping Liu ... Xibao Cai Houtim Lai Wei Liu Longyue Wang Xiangxiang Zeng 11 0 0 20 Mar 2024
DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization Xiangxin Zhou Xiwei Cheng Yuwei Yang Yu Bao Liang Wang Quanquan Gu 29 14 0 07 Mar 2024
Smooth Tchebycheff Scalarization for Multi-Objective Optimization Xi Lin Xiao-Yan Zhang Zhiyuan Yang Fei Liu Zhenkun Wang Qingfu Zhang 30 16 0 29 Feb 2024
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design Jiaqi Guan Xiangxin Zhou Yuwei Yang Yu Bao Jian-wei Peng Jianzhu Ma Qiang Liu Liang Wang Quanquan Gu 20 66 0 26 Feb 2024
Graph Diffusion Policy Optimization Yijing Liu Chao Du Tianyu Pang Chongxuan Li Wei Chen Min-Bin Lin 24 7 0 26 Feb 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
MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in Practical Generative Modeling Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 29 4 0 16 Feb 2024
Evolution Guided Generative Flow Networks Zarif Ikram Ling Pan Dianbo Liu 81 1 0 03 Feb 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
Advancing Bayesian Optimization via Learning Correlated Latent Space Seunghun Lee Jaewon Chu S. Kim Juyeon Ko Hyunwoo J. Kim BDL 31 5 0 31 Oct 2023
Learning to Scale Logits for Temperature-Conditional GFlowNets Minsu Kim Joohwan Ko Taeyoung Yun Dinghuai Zhang Ling Pan W. Kim Jinkyoo Park Emmanuel Bengio Yoshua Bengio AI4CE 25 21 0 04 Oct 2023
Local Search GFlowNets Minsu Kim Taeyoung Yun Emmanuel Bengio Dinghuai Zhang Yoshua Bengio Sungsoo Ahn Jinkyoo Park 24 33 0 04 Oct 2023
Drug Discovery with Dynamic Goal-aware Fragments Seul Lee Seanie Lee Kenji Kawaguchi Sung Ju Hwang 15 5 0 02 Oct 2023
Order-Preserving GFlowNets Yihang Chen Lukas Mauch 25 9 0 30 Sep 2023
Compositional Sculpting of Iterative Generative Processes Yixuan Wang Sebastiaan De Peuter Mingtong Zhang Vikas K. Garg Samuel Kaski Tommi Jaakkola DiffM 22 15 0 28 Sep 2023
Beam Enumeration: Probabilistic Explainability For Sample Efficient Self-conditioned Molecular Design Jeff Guo P. Schwaller 19 6 0 25 Sep 2023
Will More Expressive Graph Neural Networks do Better on Generative Tasks? Xian-Quan Zou Xiangyu Zhao Pietro Lio' Yiren Zhao 8 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 25 7 0 09 Jun 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 25 34 0 22 May 2023
MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation Yiheng Zhu Zhenqiu Ouyang Ben Liao Jialun Wu YiXuan Wu Chang-Yu Hsieh Tingjun Hou Jian Wu AI4CE 10 4 0 15 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 18 0 05 May 2023
Structure-Aware Group Discrimination with Adaptive-View Graph Encoder: A Fast Graph Contrastive Learning Framework Zhenshuo Zhang Yun Zhu Haizhou Shi Siliang Tang 16 1 0 09 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 50 10 0 01 Mar 2023
Stochastic Generative Flow Networks L. Pan Dinghuai Zhang Moksh Jain Longbo Huang Yoshua Bengio BDL 36 30 0 19 Feb 2023
Distributional GFlowNets with Quantile Flows Dinghuai Zhang L. Pan Ricky T. Q. Chen Aaron Courville Yoshua Bengio 22 25 0 11 Feb 2023
Sample-efficient Multi-objective Molecular Optimization with GFlowNets Yiheng Zhu Jialun Wu Chaowen Hu Jiahuan Yan Chang-Yu Hsieh Tingjun Hou Jian Wu 17 30 0 08 Feb 2023
GFlowNets for AI-Driven Scientific Discovery Moksh Jain T. Deleu Jason S. Hartford Cheng-Hao Liu Alex Hernandez-Garcia Yoshua Bengio AI4CE 21 44 0 01 Feb 2023
Domain-Agnostic Molecular Generation with Chemical Feedback Yin Fang Ningyu Zhang Zhuo Chen Lingbing Guo Xiaohui Fan Huajun Chen 28 11 0 26 Jan 2023
Molecule optimization via multi-objective evolutionary in implicit chemical space Xin Xia Yansen Su Chunhou Zheng Xiangxiang Zeng 21 1 0 17 Dec 2022
Scaffold-Based Multi-Objective Drug Candidate Optimization Agustin Kruel Andrew D. McNaughton Neeraj Kumar 25 1 0 15 Dec 2022