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
Diffusion-Driven Domain Adaptation for Generating 3D Molecules Haokai Hong Wanyu Lin Kay Chen Tan DiffM 37 2 0 01 Apr 2024
Molecular Generative Adversarial Network with Multi-Property Optimization Huidong Tang Chen Li Sayaka Kamei Yoshihiro Yamanishi Yasuhiko Morimoto 22 0 0 29 Mar 2024
GLAD: Improving Latent Graph Generative Modeling with Simple Quantization Van Khoa Nguyen Yoann Boget Frantzeska Lavda Alexandros Kalousis 29 2 0 25 Mar 2024
Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks Yuxuan Song Jingjing Gong Yanru Qu Hao Zhou Mingyue Zheng Jingjing Liu Wei-Ying Ma 28 10 0 17 Mar 2024
GraphRCG: Self-Conditioned Graph Generation Song Wang Zhen Tan Xinyu Zhao Tianlong Chen Huan Liu Jundong Li 36 0 0 02 Mar 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
Continual Learning on Graphs: A Survey Zonggui Tian Duanhao Zhang Hong-Ning Dai 32 5 0 09 Feb 2024
Pard: Permutation-Invariant Autoregressive Diffusion for Graph Generation Lingxiao Zhao Xueying Ding L. Akoglu DiffM 21 8 0 06 Feb 2024
A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer Zhangyang Gao Daize Dong Cheng Tan Jun-Xiong Xia Bozhen Hu Stan Z. Li 41 6 0 04 Feb 2024
Overcoming Order in Autoregressive Graph Generation Edo Cohen-Karlik Eyal Rozenberg Daniel Freedman 30 1 0 04 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 20 0 0 28 Jan 2024
Unsupervised Learning of Graph from Recipes Aissatou Diallo Antonis Bikakis Luke Dickens Anthony Hunter Rob Miller SSL 12 0 0 22 Jan 2024
Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry Zeyu Wang Tianyi Jiang Jinhuan Wang Qi Xuan AI4CE 16 7 0 07 Jan 2024
Natural Adversarial Patch Generation Method Based on Latent Diffusion Model Xianyi Chen Fazhan Liu Dong Jiang Kai Yan AAML DiffM 14 1 0 27 Dec 2023
Diffusion-Driven Generative Framework for Molecular Conformation Prediction Bobin Yang Jie Deng Zhenghan Chen Ruoxue Wu DiffM 21 0 0 22 Dec 2023
Vector Field Oriented Diffusion Model for Crystal Material Generation Astrid Klipfel Yael Fregier A. Sayede Zied Bouraoui DiffM 19 4 0 20 Dec 2023
Equivariant Flow Matching with Hybrid Probability Transport Yuxuan Song Jingjing Gong Minkai Xu Ziyao Cao Yanyan Lan Stefano Ermon Hao Zhou Wei-Ying Ma DiffM 10 44 0 12 Dec 2023
A Simple and Scalable Representation for Graph Generation Yunhui Jang Seul Lee Sungsoo Ahn 11 4 0 04 Dec 2023
Distributed Reinforcement Learning for Molecular Design: Antioxidant case Huanyi Qin D. Akhiyarov Sophie Loehle Kenneth Chiu Mauricio Araya-Polo 15 0 0 03 Dec 2023
Optimizing ZX-Diagrams with Deep Reinforcement Learning Maximilian Nägele Florian Marquardt AI4CE 20 9 0 30 Nov 2023
GlycoNMR: Dataset and benchmarks for NMR chemical shift prediction of carbohydrates with graph neural networks Zizhang Chen R. P. Badman Lachele Foley Robert Woods Pengyu Hong 25 0 0 28 Nov 2023
BrainNetDiff: Generative AI Empowers Brain Network Generation via Multimodal Diffusion Model Yongcheng Zong Shuqiang Wang MedIm DiffM 17 0 0 09 Nov 2023
CDGraph: Dual Conditional Social Graph Synthesizing via Diffusion Model Jui-Yi Tsai Ya-Wen Teng Ho Chiok Yew De-Nian Yang Lydia Y. Chen DiffM 15 1 0 03 Nov 2023
ARTree: A Deep Autoregressive Model for Phylogenetic Inference Tianyu Xie Cheng Zhang 20 4 0 14 Oct 2023
Genetic algorithms are strong baselines for molecule generation Austin Tripp José Miguel Hernández-Lobato 30 16 0 13 Oct 2023
Crystal-GFN: sampling crystals with desirable properties and constraints Mila AI4Science Alex Hernandez-Garcia Alexandre Duval Alexandra Volokhova Yoshua Bengio Divya Sharma P. Carrier Yasmine Benabed Michal Koziarski Victor Schmidt 141 18 0 07 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 24 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
Will More Expressive Graph Neural Networks do Better on Generative Tasks? Xian-Quan Zou Xiangyu Zhao Pietro Lio' Yiren Zhao 10 2 0 23 Aug 2023
Leveraging Side Information for Ligand Conformation Generation using Diffusion-Based Approaches Nhat-Khang Ngô Truong Son-Hy Yuan Yao DiffM 22 0 0 02 Aug 2023
Disentangling Node Attributes from Graph Topology for Improved Generalizability in Link Prediction Ayan Chatterjee Robin G. Walters G. Menichetti Tina Eliassi-Rad AI4CE 19 1 0 17 Jul 2023
Autoregressive Diffusion Model for Graph Generation Lingkai Kong Jiaming Cui Haotian Sun Yuchen Zhuang B. Prakash Chao Zhang DiffM 18 65 0 17 Jul 2023
Towards Symmetry-Aware Generation of Periodic Materials Youzhi Luo Chengkai Liu Shuiwang Ji DiffM 16 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 46 18 0 04 Jul 2023
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation Danny Reidenbach Aditi S. Krishnapriyan 22 7 0 26 Jun 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 11 0 0 24 Jun 2023
Advancing Biomedicine with Graph Representation Learning: Recent Progress, Challenges, and Future Directions Fang Li Yi Nian Zenan Sun Cui Tao LM&MA OOD AI4TS AI4CE 25 5 0 18 Jun 2023
Discrete Graph Auto-Encoder Yoann Boget Magda Gregorova Alexandros Kalousis 8 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 27 7 0 09 Jun 2023
Explanation Graph Generation via Generative Pre-training over Synthetic Graphs H. Cui Sha Li Yu Zhang Qi Shi 11 1 0 01 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
Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration Haitao Lin Yufei Huang Haotian Zhang Lirong Wu Siyuan Li Zhiyuan Chen Stan Z. Li DiffM 14 23 0 30 May 2023
GC-Flow: A Graph-Based Flow Network for Effective Clustering Tianchun Wang F. Mirzazadeh X. Zhang Jing Chen BDL 37 6 0 26 May 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 6 16 0 21 May 2023
RGCVAE: Relational Graph Conditioned Variational Autoencoder for Molecule Design Davide Rigoni Nicoló Navarin A. Sperduti BDL 12 1 0 19 May 2023