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
Graph-based Molecular Representation Learning Zhichun Guo Kehan Guo B. Nan Yijun Tian Roshni G. Iyer ... Olaf Wiest Xiangliang Zhang Wei Wang Chuxu Zhang Nitesh V. Chawla AI4CE 22 60 0 08 Jul 2022
Accelerating Material Design with the Generative Toolkit for Scientific Discovery Matteo Manica Jannis Born Joris Cadow Dimitrios Christofidellis A. Dave ... Lauren N. McHugh Alexy Khrabrov Payel Das Seiji Takeda John Smith 19 26 0 08 Jul 2022
Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching Shengchao Liu Hongyu Guo Jian Tang 23 77 0 27 Jun 2022
LIMO: Latent Inceptionism for Targeted Molecule Generation Peter Eckmann Kunyang Sun Bo-Lu Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 43 44 0 17 Jun 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo Sung Ju Hwang OODD 30 75 0 06 Jun 2022
An Unpooling Layer for Graph Generation Yi Guo Dongmian Zou Gilad Lerman 16 2 0 04 Jun 2022
High-Order Pooling for Graph Neural Networks with Tensor Decomposition Chenqing Hua Guillaume Rabusseau Jian Tang 72 25 0 24 May 2022
3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design Yinan Huang Xing Peng Jianzhu Ma Muhan Zhang BDL 30 47 0 15 May 2022
Bandits for Structure Perturbation-based Black-box Attacks to Graph Neural Networks with Theoretical Guarantees Binghui Wang Youqin Li Pan Zhou AAML 26 13 0 07 May 2022
Conditional $β$ -VAE for De Novo Molecular Generation Ryan J. Richards A. Groener BDL DRL 24 10 0 01 May 2022
Generating 3D Molecules for Target Protein Binding Meng Liu Youzhi Luo Kanji Uchino Koji Maruhashi Shuiwang Ji 16 112 0 19 Apr 2022
Explanation Graph Generation via Pre-trained Language Models: An Empirical Study with Contrastive Learning Swarnadeep Saha Prateek Yadav Joey Tianyi Zhou 11 9 0 11 Apr 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 31 86 0 28 Mar 2022
Gransformer: Transformer-based Graph Generation Ahmad Khajenezhad Seyed Ali Osia Mahmood Karimian H. Beigy 22 2 0 25 Mar 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 67 178 0 20 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
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation Minkai Xu Lantao Yu Yang Song Chence Shi Stefano Ermon Jian Tang BDL DiffM 24 496 0 06 Mar 2022
Multi-Objective Latent Space Optimization of Generative Molecular Design Models Naﬁz Abeer Nathan M. Urban Ryan Weil Francis J. Alexander Byung-Jun Yoon 23 15 0 01 Mar 2022
Disentangled Spatiotemporal Graph Generative Models Yuanqi Du Xiaojie Guo Hengning Cao Yanfang Ye Liang Zhao 28 21 0 28 Feb 2022
Molecule Generation for Drug Design: a Graph Learning Perspective Nianzu Yang Huaijin Wu Xiaoyong Pan Ye Yuan Junchi Yan 19 13 0 18 Feb 2022
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery Zhaocheng Zhu Chence Shi Zuobai Zhang Shengchao Liu Minghao Xu ... Chang Ma Runcheng Liu Louis-Pascal Xhonneux Meng Qu Jian Tang OOD VLM MedIm 14 70 0 16 Feb 2022
Learning to Discover Medicines T. Nguyen Thin Nguyen T. Tran 32 1 0 14 Feb 2022
Target-aware Molecular Graph Generation Cheng Tan Zhangyang Gao Stan Z. Li 21 25 0 10 Feb 2022
Learning to Predict Graphs with Fused Gromov-Wasserstein Barycenters Luc Brogat-Motte Rémi Flamary Céline Brouard Juho Rousu Florence dÁlché-Buc 25 19 0 08 Feb 2022
A Variational Edge Partition Model for Supervised Graph Representation Learning Yingying He Chaojie Wang Hao Zhang Bo Chen Mingyuan Zhou 19 5 0 07 Feb 2022
Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations Jaehyeong Jo Seul Lee Sung Ju Hwang DiffM 22 210 0 05 Feb 2022
Direct Molecular Conformation Generation Jinhua Zhu Yingce Xia Chang-Shu Liu Lijun Wu Shufang Xie ... Tao Qin Wen-gang Zhou Houqiang Li Haiguang Liu Tie-Yan Liu 26 41 0 03 Feb 2022
Regression Transformer: Concurrent sequence regression and generation for molecular language modeling Jannis Born Matteo Manica 13 91 0 01 Feb 2022
Autoencoding Hyperbolic Representation for Adversarial Generation Eric Qu Dongmian Zou GAN 36 4 0 30 Jan 2022
FastFlows: Flow-Based Models for Molecular Graph Generation Nathan C. Frey V. Gadepally Bharath Ramsundar 19 12 0 28 Jan 2022
Bringing Your Own View: Graph Contrastive Learning without Prefabricated Data Augmentations Yuning You Tianlong Chen Zhangyang Wang Yang Shen SSL 24 61 0 04 Jan 2022
Permutation Equivariant Generative Adversarial Networks for Graphs Yoann Boget Magda Gregorova Alexandros Kalousis GAN 11 0 0 07 Dec 2021
HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space Zhiyuan Chen Xiaomin Fang Zixu Hua Yueyang Huang Fan Wang Hua-Hong Wu MedIm 27 2 0 30 Nov 2021
Deep Molecular Representation Learning via Fusing Physical and Chemical Information Shuwen Yang Ziyao Li Guojie Song Lingsheng Cai AI4CE 38 28 0 28 Nov 2021
Network representation learning: A macro and micro view Xueyi Liu Jie Tang GNN AI4TS 17 23 0 21 Nov 2021
Combining Latent Space and Structured Kernels for Bayesian Optimization over Combinatorial Spaces Aryan Deshwal J. Doppa BDL 30 42 0 01 Nov 2021
Fragment-based Sequential Translation for Molecular Optimization Benson Chen Xiang Fu Regina Barzilay Tommi Jaakkola 29 7 0 26 Oct 2021
CausalAF: Causal Autoregressive Flow for Safety-Critical Driving Scenario Generation Wenhao Ding Hao-ming Lin Bo-wen Li Ding Zhao 24 28 0 26 Oct 2021
Molecular Graph Generation via Geometric Scattering Dhananjay Bhaskar Jackson D. Grady Michal Perlmutter Smita Krishnaswamy GNN 26 6 0 12 Oct 2021
Crystal Diffusion Variational Autoencoder for Periodic Material Generation Tian Xie Xiang Fu O. Ganea Regina Barzilay Tommi Jaakkola DiffM BDL 212 232 0 12 Oct 2021
An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design Yi Zhang AI4CE 32 4 0 10 Oct 2021
Weakly Supervised Concept Map Generation through Task-Guided Graph Translation Jiaying Lu Xiangjue Dong Carl Yang 32 3 0 08 Oct 2021
Unifying Likelihood-free Inference with Black-box Optimization and Beyond Dinghuai Zhang Jie Fu Yoshua Bengio Aaron Courville 31 13 0 06 Oct 2021
Simulated annealing for optimization of graphs and sequences Xianggen Liu Pengyong Li Fandong Meng Hao Zhou Huasong Zhong Jie Zhou Lili Mou Sen Song 49 19 0 01 Oct 2021
Differentiable Scaffolding Tree for Molecular Optimization Tianfan Fu Wenhao Gao Cao Xiao Jacob Yasonik Connor W. Coley Jimeng Sun 25 75 0 22 Sep 2021
A Method for Inferring Polymers Based on Linear Regression and Integer Programming Ryota Ido Shengjuan Cao Jianshen Zhu Naveed Ahmed Azam Kazuya Haraguchi Liang Zhao H. Nagamochi Tatsuya Akutsu 24 6 0 24 Aug 2021
C5T5: Controllable Generation of Organic Molecules with Transformers D. Rothchild Alex Tamkin Julie H. Yu Ujval Misra Joseph E. Gonzalez 46 29 0 23 Aug 2021
Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search Naveed Ahmed Azam Jianshen Zhu Kazuya Haraguchi Liang Zhao H. Nagamochi Tatsuya Akutsu 22 5 0 23 Aug 2021
X-GGM: Graph Generative Modeling for Out-of-Distribution Generalization in Visual Question Answering Jingjing Jiang Zi-yi Liu Yifan Liu Zhixiong Nan N. Zheng OOD 28 19 0 24 Jul 2021
An Inverse QSAR Method Based on Linear Regression and Integer Programming Jianshen Zhu Naveed Ahmed Azam Kazuya Haraguchi Liang Zhao H. Nagamochi Tatsuya Akutsu 23 1 0 06 Jul 2021