GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation

26 January 2020

Jian Tang

Papers citing "GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation"

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Title
Generation of 3D Molecules in Pockets via Language Model Wei Feng L. Wang Zaiyun Lin Yanhao Zhu Han Wang ... Huting Wang Jielong Zhou Wei Peng Bo Huang Wenbiao Zhou 23 12 0 17 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 12 4 0 15 May 2023
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation Xingang Peng Jiaqi Guan Qiang Liu Jianzhu Ma DiffM 33 43 0 11 May 2023
Geometric Latent Diffusion Models for 3D Molecule Generation Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 48 133 0 02 May 2023
Molecular Design Based on Integer Programming and Splitting Data Sets by Hyperplanes Jianshen Zhu Naveed Ahmed Azam Kazuya Haraguchi Liang Zhao H. Nagamochi Tatsuya Akutsu 17 0 0 27 Apr 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 15 18 0 12 Apr 2023
Modeling and design of heterogeneous hierarchical bioinspired spider web structures using generative deep learning and additive manufacturing Wei Lu Nicolas A. Lee Markus J. Buehler AI4CE 11 1 0 11 Apr 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
A Survey on Graph Diffusion Models: Generative AI in Science for Molecule, Protein and Material Mengchun Zhang Maryam Qamar Taegoo Kang Yuna Jung Chenshuang Zhang Sung-Ho Bae Chaoning Zhang DiffM MedIm 31 44 0 04 Apr 2023
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction Jiaqi Guan Wesley Wei Qian Xingang Peng Yufeng Su Jian-wei Peng Jianzhu Ma DiffM 15 162 0 06 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 53 10 0 01 Mar 2023
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow Fangce Sun Zhihao Zhan Hongyu Guo Ming Zhang Jian Tang 16 6 0 23 Feb 2023
Instance-incremental Scene Graph Generation from Real-world Point Clouds via Normalizing Flows Chao Qi Jianqin Yin Jinghang Xu Pengxiang Ding 3DPC 31 4 0 21 Feb 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 14 8 0 16 Feb 2023
3D Molecular Generation via Virtual Dynamics Shuqi Lu Lin Yao X. Chen Hang Zheng Di He Guolin Ke DiffM 24 7 0 12 Feb 2023
Graph Generation with Diffusion Mixture Jaehyeong Jo Dongki Kim Sung Ju Hwang DiffM 24 19 0 07 Feb 2023
Rethinking Out-of-distribution (OOD) Detection: Masked Image Modeling is All You Need Jingyao Li Pengguang Chen Shaozuo Yu Zexin He Shu Liu Jiaya Jia OODD 12 42 0 06 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
Improving Graph Generation by Restricting Graph Bandwidth N. Diamant Alex Tseng Kangway V Chuang Tommaso Biancalani Gabriele Scalia 22 7 0 25 Jan 2023
A Tale of Two Latent Flows: Learning Latent Space Normalizing Flow with Short-run Langevin Flow for Approximate Inference Jianwen Xie Y. Zhu Yifei Xu Dingcheng Li Ping Li BDL DRL 12 7 0 23 Jan 2023
Domain-agnostic and Multi-level Evaluation of Generative Models G. Tadesse Jannis Born C. Cintas William Ogallo Dmitry Zubarev Matteo Manica Komminist Weldemariam ELM 19 1 0 20 Jan 2023
State of the Art and Potentialities of Graph-level Learning Zhenyu Yang Ge Zhang Jia Wu Jian Yang Quan.Z Sheng ... Charu C. Aggarwal Hao Peng Wenbin Hu Edwin R. Hancock Pietro Lio' GNN AI4CE 30 10 0 14 Jan 2023
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation Han Huang Leilei Sun Bowen Du Weifeng Lv 29 40 0 01 Jan 2023
Molecular Graph Generation by Decomposition and Reassembling Masatsugu Yamada M. Sugiyama 8 4 0 11 Dec 2022
GraphGDP: Generative Diffusion Processes for Permutation Invariant Graph Generation Han Huang Leilei Sun Bowen Du Yanjie Fu Weifeng Lv DiffM 24 42 0 04 Dec 2022
GrannGAN: Graph annotation generative adversarial networks Yoann Boget Magda Gregorova Alexandros Kalousis GAN 10 0 0 01 Dec 2022
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 20 51 0 28 Nov 2022
Revisiting Over-smoothing and Over-squashing Using Ollivier-Ricci Curvature K. Nguyen Hieu Nong T. Nguyen Nhat Ho Khuong N. Nguyen Vinh Phu Nguyen 16 61 0 28 Nov 2022
Accelerating Antimicrobial Peptide Discovery with Latent Structure Danqing Wang Zeyu Wen Fei Ye Lei Li Hao Zhou MedIm 15 2 0 28 Nov 2022
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding Haitao Lin Yufei Huang Odin Zhang Siqi Ma Meng Liu X. Li Lirong Wu Shuiwang Ji Tingjun Hou Stan Z. Li DiffM 16 60 0 21 Nov 2022
NVDiff: Graph Generation through the Diffusion of Node Vectors Xiaohui Chen Yukun Li Aonan Zhang Liping Liu DiffM 15 21 0 19 Nov 2022
Fast Graph Generation via Spectral Diffusion Tianze Luo Zhanfeng Mo Sinno Jialin Pan DiffM 13 22 0 16 Nov 2022
Toward Human-AI Co-creation to Accelerate Material Discovery Dmitry Zubarev C. Mendes E. V. Brazil Renato F. G. Cerqueira Kristin Schmidt V. Segura J. Ferreira Daniel P. Sanders 13 0 0 05 Nov 2022
Changes from Classical Statistics to Modern Statistics and Data Science Kai Zhang Shan-Yu Liu M. Xiong 21 0 0 30 Oct 2022
Modular Flows: Differential Molecular Generation Yogesh Verma Samuel Kaski Markus Heinonen Vikas K. Garg 19 14 0 12 Oct 2022
Gradient-Guided Importance Sampling for Learning Binary Energy-Based Models Meng Liu Haoran Liu Shuiwang Ji 17 5 0 11 Oct 2022
How Image Generation Helps Visible-to-Infrared Person Re-Identification? Honghu Pan Yongyong Chen Yunqing He Xin Li Zhenyu He 8 2 0 04 Oct 2022
Multi-objective Deep Data Generation with Correlated Property Control Shiyu Wang Xiaojie Guo Xuanyang Lin Bo Pan Yuanqi Du ... S. Alkhalifa K. Minbiole Bill Wuest Amarda Shehu Liang Zhao AI4CE 42 14 0 01 Oct 2022
MARS: A Motif-based Autoregressive Model for Retrosynthesis Prediction Jiahan Liu Chao-chao Yan Yang Yu Chan Lu Junzhou Huang Le Ou-Yang P. Zhao 38 13 0 27 Sep 2022
SCGG: A Deep Structure-Conditioned Graph Generative Model Faezeh Faez Negin Hashemi Dijujin M. Baghshah Hamid R. Rabiee GNN BDL 10 4 0 20 Sep 2022
Molecular Design Based on Integer Programming and Quadratic Descriptors in a Two-layered Model Jianshen Zhu Naveed Ahmed Azam Shengjuan Cao Ryota Ido Kazuya Haraguchi Liang Zhao H. Nagamochi Tatsuya Akutsu 8 3 0 13 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 41 20 0 12 Sep 2022
A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language Bing-Huang Su Dazhao Du Zhao-Qing Yang Yujie Zhou Jiangmeng Li Anyi Rao Haoran Sun Zhiwu Lu Ji-Rong Wen 42 107 0 12 Sep 2022
Diffusion Models: A Comprehensive Survey of Methods and Applications Ling Yang Zhilong Zhang Yingxia Shao Shenda Hong Runsheng Xu Yue Zhao Wentao Zhang Bin Cui Ming-Hsuan Yang DiffM MedIm 224 1,296 0 02 Sep 2022
Large-Scale Auto-Regressive Modeling Of Street Networks Michael Birsak Tom Kelly W. Para Peter Wonka GNN AI4TS 9 5 0 01 Sep 2022
String-based Molecule Generation via Multi-decoder VAE Kisoo Kwon Kuhwan Jung Jung-Geun Park Hwidong Na Jinwoo Shin DRL 27 2 0 23 Aug 2022
Improving Small Molecule Generation using Mutual Information Machine Daniel A. Reidenbach M. Livne Rajesh Ilango M. Gill Johnny Israeli 19 14 0 18 Aug 2022
Semi-Supervised Junction Tree Variational Autoencoder for Molecular Property Prediction Atia Hamidizadeh Tony Shen Martin Ester DRL 22 0 0 10 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
Graph Generative Model for Benchmarking Graph Neural Networks Minji Yoon Yue Wu John Palowitch Bryan Perozzi Ruslan Salakhutdinov 17 7 0 10 Jul 2022