GraphDF: A Discrete Flow Model for Molecular Graph Generation

1 February 2021

Papers citing "GraphDF: A Discrete Flow Model for Molecular Graph Generation"

50 / 122 papers shown

Title
Data-centric Graph Learning: A Survey Jixi Liu Deyu Bo Cheng Yang Haoran Dai Qi Zhang Yixin Xiao Yufei Peng Chuan Shi GNN 27 19 0 08 Oct 2023
Diffusing on Two Levels and Optimizing for Multiple Properties: A Novel Approach to Generating Molecules with Desirable Properties Siyuan Guo Jihong Guan Shuigeng Zhou 30 3 0 05 Oct 2023
Molecule Design by Latent Prompt Transformer Deqian Kong Yuhao Huang Jianwen Xie Ying Nian Wu 10 3 0 05 Oct 2023
Drug Discovery with Dynamic Goal-aware Fragments Seul Lee Seanie Lee Kenji Kawaguchi Sung Ju Hwang 15 5 0 02 Oct 2023
Target-aware Variational Auto-encoders for Ligand Generation with Multimodal Protein Representation Learning Haoxiang Luo Gang Sun 32 2 0 02 Aug 2023
Autoregressive Diffusion Model for Graph Generation Lingkai Kong Jiaming Cui Haotian Sun Yuchen Zhuang B. Prakash Chao Zhang DiffM 26 65 0 17 Jul 2023
Towards Symmetry-Aware Generation of Periodic Materials Youzhi Luo Chengkai Liu Shuiwang Ji DiffM 24 21 0 06 Jul 2023
SwinGNN: Rethinking Permutation Invariance in Diffusion Models for Graph Generation Qi Yan Zhen-Long Liang Yang Song Renjie Liao Lele Wang DiffM 50 18 0 04 Jul 2023
DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins Lei Huang Zheng Yuan Huihui Yan Rong Sheng Linjing Liu ... Nanjun Chen Fei Huang Songfang Huang Ka-Chun Wong Yaoyun Zhang 16 0 0 24 Jun 2023
Discrete Graph Auto-Encoder Yoann Boget Magda Gregorova Alexandros Kalousis 13 4 0 13 Jun 2023
Hyperbolic Graph Diffusion Model Lingfeng Wen Xuan Tang Mingjie Ouyang Xiangxiang Shen Jian Yang Daxin Zhu Mingsong Chen Xian Wei 31 2 0 13 Jun 2023
Efficient Approximations of Complete Interatomic Potentials for Crystal Property Prediction Yu-Ching Lin Keqiang Yan Youzhi Luo Yi Liu Xiaoning Qian Shuiwang Ji 66 33 0 12 Jun 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
Graph Generation with $K^2$ -trees Yunhui Jang Dongwoo Kim Sungsoo Ahn 32 2 0 30 May 2023
MAGNet: Motif-Agnostic Generation of Molecules from Shapes Leon Hetzel Johanna Sommer Bastian Alexander Rieck Fabian J. Theis Stephan Günnemann 18 6 0 30 May 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 24 16 0 21 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 18 5 0 15 May 2023
A Latent Diffusion Model for Protein Structure Generation Cong Fu Keqiang Yan Limei Wang Wing Yee Au Michael McThrow Tao Komikado Koji Maruhashi Kanji Uchino Xiaoning Qian Shuiwang Ji DiffM 18 31 0 06 May 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
A Comprehensive Survey on Deep Graph Representation Learning Wei Ju Zheng Fang Yiyang Gu Zequn Liu Qingqing Long ... Jingyang Yuan Yusheng Zhao Yifan Wang Xiao Luo Ming Zhang GNN AI4TS 31 141 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
FairGen: Towards Fair Graph Generation Lecheng Zheng Dawei Zhou Hanghang Tong Jiejun Xu Yada Zhu Jingrui He 22 7 0 30 Mar 2023
Instance-incremental Scene Graph Generation from Real-world Point Clouds via Normalizing Flows Chao Qi Jianqin Yin Jinghang Xu Pengxiang Ding 3DPC 33 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 22 8 0 16 Feb 2023
Graph Generation with Diffusion Mixture Jaehyeong Jo Dongki Kim Sung Ju Hwang DiffM 24 19 0 07 Feb 2023
Generative Diffusion Models on Graphs: Methods and Applications C. Liu Wenqi Fan Yunqing Liu Jiatong Li Hang Li Hui Liu Jiliang Tang Qing Li MedIm DiffM 32 58 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
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation Han Huang Leilei Sun Bowen Du Weifeng Lv 40 40 0 01 Jan 2023
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
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 22 51 0 28 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
Modular Flows: Differential Molecular Generation Yogesh Verma Samuel Kaski Markus Heinonen Vikas K. Garg 29 14 0 12 Oct 2022
Gradient-Guided Importance Sampling for Learning Binary Energy-Based Models Meng Liu Haoran Liu Shuiwang Ji 24 5 0 11 Oct 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
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 43 13 0 27 Sep 2022
Periodic Graph Transformers for Crystal Material Property Prediction Keqiang Yan Yi Liu Yu-Ching Lin Shuiwang Ji AI4TS 88 84 0 23 Sep 2022
SCGG: A Deep Structure-Conditioned Graph Generative Model Faezeh Faez Negin Hashemi Dijujin M. Baghshah Hamid R. Rabiee GNN BDL 15 4 0 20 Sep 2022
MDM: Molecular Diffusion Model for 3D Molecule Generation Lei Huang Hengtong Zhang Tingyang Xu Ka-Chun Wong DiffM 18 81 0 13 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 45 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 44 107 0 12 Sep 2022
Distributional Drift Adaptation with Temporal Conditional Variational Autoencoder for Multivariate Time Series Forecasting Hui He Qi Zhang Kun Yi Kaize Shi ZhenDong Niu Longbin Cao TTA AI4TS 16 4 0 01 Sep 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
Graph Generative Model for Benchmarking Graph Neural Networks Minji Yoon Yue Wu John Palowitch Bryan Perozzi Ruslan Salakhutdinov 17 7 0 10 Jul 2022
FlowX: Towards Explainable Graph Neural Networks via Message Flows Shurui Gui Hao Yuan Jie Wang Qicheng Lao Kang Li Shuiwang Ji 32 11 0 26 Jun 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
ResNorm: Tackling Long-tailed Degree Distribution Issue in Graph Neural Networks via Normalization Langzhang Liang Zenglin Xu Zixing Song Irwin King Yuan Qi Jieping Ye 32 21 0 16 Jun 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo S. Hwang OODD 28 75 0 06 Jun 2022