Differentiable Scaffolding Tree for Molecular Optimization

22 September 2021

Wenhao Gao

Jimeng Sun

Papers citing "Differentiable Scaffolding Tree for Molecular Optimization"

47 / 47 papers shown

Title
GraphPINE: Graph Importance Propagation for Interpretable Drug Response Prediction Yoshitaka Inoue Tianfan Fu Augustin Luna 26 0 0 07 Apr 2025
Offline Model-Based Optimization: Comprehensive Review Minsu Kim Jiayao Gu Ye Yuan Taeyoung Yun Z. Liu Yoshua Bengio Can Chen OffRL 65 2 0 21 Mar 2025
MOLLM: Multi-Objective Large Language Model for Molecular Design -- Optimizing with Experts Nian Ran Yue Wang Richard Allmendinger 62 0 0 18 Feb 2025
Survey on Recent Progress of AI for Chemistry: Methods, Applications, and Opportunities Ding Hu Pengxiang Hua Zhen Huang 77 0 0 09 Feb 2025
DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaboration Sizhe Liu Y. Lu Siyu Chen Xiyang Hu Jieyu Zhao Tianfan Fu Yue Zhao LLMAG 79 6 0 24 Nov 2024
Generative Artificial Intelligence for Navigating Synthesizable Chemical Space Wenhao Gao Shitong Luo Connor W. Coley 24 5 0 04 Oct 2024
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design Dannong Wang Jintai Chen Zhiding Liang Tianfan Fu Xiao-Yang Liu 18 1 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 36 0 0 23 Aug 2024
DrugCLIP: Contrastive Drug-Disease Interaction For Drug Repurposing Yingzhou Lu Yaojun Hu Chenhao Li VLM 27 9 0 02 Jul 2024
Efficient Evolutionary Search Over Chemical Space with Large Language Models Haorui Wang Marta Skreta C. Ser Wenhao Gao Lingkai Kong ... Yanqiao Zhu Yuanqi Du Alán Aspuru-Guzik Kirill Neklyudov Chao Zhang 37 12 0 23 Jun 2024
drGAT: Attention-Guided Gene Assessment of Drug Response Utilizing a Drug-Cell-Gene Heterogeneous Network Yoshitaka Inoue Hunmin Lee Tianfan Fu Augustin Luna 30 6 0 14 May 2024
Data-Efficient Molecular Generation with Hierarchical Textual Inversion Seojin Kim Jaehyun Nam Sihyun Yu Younghoon Shin Jinwoo Shin 31 2 0 05 May 2024
Language Interaction Network for Clinical Trial Approval Estimation Chufan Gao Tianfan Fu Jimeng Sun 24 1 0 26 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 42 27 0 01 Apr 2024
3M-Diffusion: Latent Multi-Modal Diffusion for Text-Guided Generation of Molecular Graphs Huaisheng Zhu Teng Xiao V. Honavar DiffM 32 5 0 11 Mar 2024
Learning on Multimodal Graphs: A Survey Ciyuan Peng Jiayuan He Feng Xia 30 6 0 07 Feb 2024
Uncertainty Quantification on Clinical Trial Outcome Prediction Tianyi Chen Yingzhou Lu Nan Hao Capucine Van Rechem Jintai Chen Tianfan Fu 23 21 0 07 Jan 2024
Molecular De Novo Design through Transformer-based Reinforcement Learning Pengcheng Xu Tao Feng Tianfan Fu Siddhartha Laghuvarapu Jimeng Sun 14 1 0 09 Oct 2023
Molecule Design by Latent Prompt Transformer Deqian Kong Yuhao Huang Jianwen Xie Ying Nian Wu 10 3 0 05 Oct 2023
Beam Enumeration: Probabilistic Explainability For Sample Efficient Self-conditioned Molecular Design Jeff Guo P. Schwaller 24 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 13 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 33 7 0 09 Jun 2023
A Review on Knowledge Graphs for Healthcare: Resources, Applications, and Promises Hejie Cui Jiaying Lu Shiyu Wang Shiyu Wang Wenjing Ma ... Fei Wang Carl Yang Mengdi Huai Fei Wang Carl Yang 36 12 0 07 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
GNN-Ensemble: Towards Random Decision Graph Neural Networks Wenqi Wei Mu Qiao D. Jadav AAML AI4CE 28 3 0 20 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 58 10 0 01 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 31 140 0 08 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 24 32 0 08 Feb 2023
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 22 51 0 28 Nov 2022
State-specific protein-ligand complex structure prediction with a multi-scale deep generative model Zhuoran Qiao Weili Nie Arash Vahdat Thomas F. Miller Anima Anandkumar DiffM 31 84 0 30 Sep 2022
Multimodal learning with graphs Yasha Ektefaie George Dasoulas Ayush Noori Maha Farhat Marinka Zitnik 51 82 0 07 Sep 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
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 25 86 0 28 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
Disentangled Spatiotemporal Graph Generative Models Yuanqi Du Xiaojie Guo Hengning Cao Yanfang Ye Liang Zhao 21 20 0 28 Feb 2022
Interpretable Molecular Graph Generation via Monotonic Constraints Yuanqi Du Xiaojie Guo Amarda Shehu Liang Zhao 60 19 0 28 Feb 2022
Regression Transformer: Concurrent sequence regression and generation for molecular language modeling Jannis Born Matteo Manica 13 91 0 01 Feb 2022
HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space Zhiyuan Chen Xiaomin Fang Zixu Hua Yueyang Huang Fan Wang Hua-Hong Wu MedIm 22 2 0 30 Nov 2021
Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design Wenhao Gao Rocío Mercado Connor W. Coley 19 57 0 12 Oct 2021
A Survey on Graph Structure Learning: Progress and Opportunities Yanqiao Zhu Weizhi Xu Jinghao Zhang Yuanqi Du Jieyu Zhang Qiang Liu Carl Yang Shu Wu GNN AI4CE 18 98 0 04 Mar 2021
HINT: Hierarchical Interaction Network for Trial Outcome Prediction Leveraging Web Data Tianfan Fu Kexin Huang Cao Xiao Lucas Glass Jimeng Sun 18 59 0 08 Feb 2021
MIMOSA: Multi-constraint Molecule Sampling for Molecule Optimization Tianfan Fu Cao Xiao Xinhao Li Lucas Glass Jimeng Sun 14 75 0 05 Oct 2020
Bitcoin Transaction Forecasting with Deep Network Representation Learning Wenqi Wei Qi Zhang Ling Liu AI4TS 23 20 0 15 Jul 2020
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 200 885 0 07 Jun 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 224 1,337 0 12 Feb 2018
Determinantal point processes for machine learning Alex Kulesza B. Taskar 160 1,122 0 25 Jul 2012