Papers citing 'MIMOSA: Multi-constraint Molecule Sampling for Molecule Optimization'

Title
Large Language Models for Controllable Multi-property Multi-objective Molecule Optimization Vishal Dey Xiao Hu Xia Ning 138 3 0 29 May 2025
MolEditRL: Structure-Preserving Molecular Editing via Discrete Diffusion and Reinforcement Learning Yuanxin Zhuang Dazhong Shen Ying Sun 158 1 0 26 May 2025
GraphPINE: Graph Importance Propagation for Interpretable Drug Response Prediction Yoshitaka Inoue Tianfan Fu Augustin Luna 145 0 0 07 Apr 2025
InversionGNN: A Dual Path Network for Multi-Property Molecular OptimizationInternational Conference on Learning Representations (ICLR), 2025 Yifan Niu Ziqi Gao Qifeng Bai Yang Liu Yatao Bian Yu Rong Junzhou Huang Jia Li 264 1 0 03 Mar 2025
DrugImproverGPT: A Large Language Model for Drug Optimization with Fine-Tuning via Structured Policy Optimization Xuefeng Liu Songhao Jiang Siyu Chen Zhuoran Yang Yuxin Chen Ian Foster Rick L. Stevens LM&MA OffRL 266 4 0 11 Feb 2025
Text-guided multi-property molecular optimization with a diffusion language modelInformation Fusion (Inf. Fusion), 2024 Yida Xiong Kun Li Jiameng Chen Hongzhi Zhang Di Lin Shirui Pan Wenbin Hu 308 8 0 17 Oct 2024
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design Dannong Wang Jintai Chen Zhiding Liang Tianfan Fu Xiao-Yang Liu 174 5 0 13 Sep 2024
DrugAgent: Multi-Agent Large Language Model-Based Reasoning for Drug-Target Interaction Prediction Yoshitaka Inoue Tianci Song Tianfan Fu Augustin Luna Tianfan Fu LLMAG 343 8 0 23 Aug 2024
DrugCLIP: Contrastive Drug-Disease Interaction For Drug Repurposing Yingzhou Lu Yaojun Hu Chenhao Li VLM 189 10 0 02 Jul 2024
TrialBench: Multi-Modal Artificial Intelligence-Ready Clinical Trial Datasets Jintai Chen Yaojun Hu Mingchen Cai Yingzhou Lu Yue Wang ... Yuqiang Li Lucas Glass Tianfan Fu Marinka Zitnik Tianfan Fu 374 19 0 30 Jun 2024
Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate? Kangyu Zheng Yingzhou Lu Zaixi Zhang Zhongwei Wan Yao Ma Marinka Zitnik Tianfan Fu ELM 179 10 0 04 Jun 2024
AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design Xinze Li Penglei Wang Tianfan Fu Wenhao Gao Chengtao Li Leilei Shi Junhong Liu 201 5 0 02 Apr 2024
TWIN-GPT: Digital Twins for Clinical Trials via Large Language Model Yue Wang Tianfan Fu Yinlong Xu Zihan Ma Hongxia Xu Yingzhou Lu Bang Du Hong-Yan Gao Jian Wu LM&MA 254 58 0 01 Apr 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 241 3 0 22 Feb 2024
Uncertainty Quantification on Clinical Trial Outcome Prediction Tianyi Chen Yingzhou Lu Nan Hao Capucine Van Rechem Jintai Chen Tianfan Fu 286 28 0 07 Jan 2024
Lo-Hi: Practical ML Drug Discovery BenchmarkNeural Information Processing Systems (NeurIPS), 2023 Simon Steshin VLM 141 12 0 10 Oct 2023
Molecular De Novo Design through Transformer-based Reinforcement Learning Pengcheng Xu Tao Feng Tianfan Fu Siddhartha Laghuvarapu Jimeng Sun 492 3 0 09 Oct 2023
Beam Enumeration: Probabilistic Explainability For Sample Efficient Self-conditioned Molecular DesignInternational Conference on Learning Representations (ICLR), 2023 Jeff Guo P. Schwaller 237 8 0 25 Sep 2023
Will More Expressive Graph Neural Networks do Better on Generative Tasks?LOG IN (LOG IN), 2023 Xian-Quan Zou Xiangyu Zhao Pietro Lio Yiren Zhao 132 3 0 23 Aug 2023
Molecule Design by Latent Space Energy-Based Modeling and Gradual Distribution ShiftingConference on Uncertainty in Artificial Intelligence (UAI), 2023 Deqian Kong Bo Pang Tian Han Ying Nian Wu DiffM 178 6 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 244 3 0 06 Jun 2023
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3DInternational Conference on Machine Learning (ICML), 2023 Yiran Zhou Yuxuan Song Minkai Xu Jingjing Gong B. Gao Hao Zhou Weiying Ma Yanyan Lan DiffM 243 26 0 05 May 2023
GNN-Ensemble: Towards Random Decision Graph Neural NetworksBigData Congress [Services Society] (BSS), 2023 Wenqi Wei Mu Qiao D. Jadav AAML AI4CE 142 9 0 20 Mar 2023
Machine Learning for Synthetic Data Generation: A Review Ying-Cheng Lu Minjie Shen Huazheng Wang Xiao Wang Capucine Van Rechem Tianfan Fu Wenqi Wei SyDa 889 224 0 08 Feb 2023
Molecule optimization via multi-objective evolutionary in implicit chemical space Xin Xia Yansen Su Chunhou Zheng Xiangxiang Zeng 167 1 0 17 Dec 2022
Reinforced Genetic Algorithm for Structure-based Drug DesignNeural Information Processing Systems (NeurIPS), 2022 Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 185 64 0 28 Nov 2022
Computer-Aided Multi-Objective Optimization in Small Molecule DiscoveryPatterns (Patterns), 2022 Jenna C. Fromer Connor W. Coley 202 88 0 13 Oct 2022
Controllable Data Generation by Deep Learning: A ReviewACM Computing Surveys (ACM CSUR), 2022 Shiyu Wang Yuanqi Du Xiaojie Guo Bo Pan Zhaohui Qin Bo Pan 581 38 0 19 Jul 2022
ADBench: Anomaly Detection BenchmarkNeural Information Processing Systems (NeurIPS), 2022 Songqiao Han Xiyang Hu Hailiang Huang Mingqi Jiang Yue Zhao OOD 311 375 0 19 Jun 2022
PyGOD: A Python Library for Graph Outlier DetectionJournal of machine learning research (JMLR), 2022 Kay Liu Yingtong Dou Xueying Ding Xiyang Hu Ruitong Zhang Hao Peng Kai Shu Philip S. Yu AI4TS 231 69 0 26 Apr 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 410 95 0 28 Mar 2022
Accelerating Bayesian Optimization for Biological Sequence Design with Denoising AutoencodersInternational Conference on Machine Learning (ICML), 2022 Samuel Stanton Wesley J. Maddox Nate Gruver Phillip M. Maffettone E. Delaney Peyton Greenside A. Wilson BDL 202 122 0 23 Mar 2022
Accelerating Stochastic Probabilistic Inference Minta Liu Suliang Bu 126 0 0 15 Mar 2022
Disentangled Spatiotemporal Graph Generative ModelsAAAI Conference on Artificial Intelligence (AAAI), 2022 Yuanqi Du Xiaojie Guo Hengning Cao Yanfang Ye Bo Pan 223 23 0 28 Feb 2022
Interpretable Molecular Graph Generation via Monotonic ConstraintsSDM (SDM), 2022 Yuanqi Du Xiaojie Guo Amarda Shehu Bo Pan 194 23 0 28 Feb 2022
Molecule Generation for Drug Design: a Graph Learning PerspectiveFundamental Research (FR), 2022 Nianzu Yang Huaijin Wu Xiaoyong Pan Ye Yuan Junchi Yan 320 29 0 18 Feb 2022
Splitting numerical integration for matrix completion Qianqian Song 166 0 0 14 Feb 2022
ECOD: Unsupervised Outlier Detection Using Empirical Cumulative Distribution FunctionsIEEE Transactions on Knowledge and Data Engineering (TKDE), 2022 Zheng Li Yue Zhao Xiyang Hu N. Botta C. Ionescu George H. Chen 400 384 0 02 Jan 2022
Approximate Inference via Clustering Qianqian Song 166 0 0 28 Nov 2021
Differentiable Scaffolding Tree for Molecular Optimization Tianfan Fu Wenhao Gao Cao Xiao Jacob Yasonik Connor W. Coley Jimeng Sun 193 85 0 22 Sep 2021
Realistic molecule optimization on a learned graph manifold Rémy Brossard Oriel Frigo David Dehaene 108 0 0 03 Jun 2021
HINT: Hierarchical Interaction Network for Trial Outcome Prediction Leveraging Web DataPatterns (Patterns), 2021 Tianfan Fu Kexin Huang Cao Xiao Lucas Glass Jimeng Sun 269 77 0 08 Feb 2021
Bitcoin Transaction Forecasting with Deep Network Representation LearningIEEE Transactions on Emerging Topics in Computing (IEEE TETC), 2020 Wenqi Wei Qi Zhang Ling Liu AI4TS 196 24 0 15 Jul 2020