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
Heterophily-informed Message Passing Haishan Wang Arno Solin Vikas K. Garg 27 0 0 28 Apr 2025
DMol: A Schedule-Driven Diffusion Model for Highly Efficient and Versatile Molecule Generation Peizhi Niu Yu-Hsiang Wang Vishal Rana Chetan Rupakheti Abhishek Pandey O. Milenkovic 26 0 0 08 Apr 2025
Make Autoregressive Great Again: Diffusion-Free Graph Generation with Next-Scale Prediction Samuel Belkadi Steve Hong Marian Chen DiffM 45 0 0 30 Mar 2025
Critical Iterative Denoising: A Discrete Generative Model Applied to Graphs Yoann Boget Alexandros Kalousis DiffM 56 0 0 27 Mar 2025
Graphical Transformation Models Matthias Herp Johannes Brachem Michael Altenbuchinger Thomas Kneib 36 0 0 22 Mar 2025
Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Sihang Li Kenji Kawaguchi Tat-Seng Chua X. Wang MedIm 59 0 0 19 Mar 2025
A Reinforcement Learning-Driven Transformer GAN for Molecular Generation Chen Li Huidong Tang Ye Zhu Yoshihiro Yamanishi AI4CE 38 0 0 17 Mar 2025
Probabilistic Graph Circuits: Deep Generative Models for Tractable Probabilistic Inference over Graphs Milan Papez Martin Rektoris Václav Smídl Tomás Pevný TPM 78 0 0 15 Mar 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation Mohit Pandey G. Subbaraj Artem Cherkasov Martin Ester Emmanuel Bengio AI4CE 66 1 0 08 Mar 2025
Backdoor Attacks on Discrete Graph Diffusion Models Jiawen Wang Samin Karim Yuan Hong Binghui Wang DiffM 63 0 0 08 Mar 2025
InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization Yifan Niu Ziqi Gao Tingyang Xu Yang Liu Yatao Bian Yu Rong Junzhou Huang Jia Li 68 0 0 03 Mar 2025
Auto-encoding Molecules: Graph-Matching Capabilities Matter Magnus Cunow Gerrit Großmann GNN 32 0 0 01 Mar 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 100 3 0 18 Feb 2025
Towards Efficient Molecular Property Optimization with Graph Energy Based Models Luca Miglior Lorenzo Simone Marco Podda Davide Bacciu AI4CE 64 0 0 17 Feb 2025
HOG-Diff: Higher-Order Guided Diffusion for Graph Generation Yiming Huang Tolga Birdal DiffM 76 0 0 06 Feb 2025
On the Probability of Necessity and Sufficiency of Explaining Graph Neural Networks: A Lower Bound Optimization Approach Ruichu Cai Yuxuan Zhu Xuexin Chen Yuan Fang Min-man Wu Jie Qiao Z. Hao 46 7 0 31 Dec 2024
MING: A Functional Approach to Learning Molecular Generative Models Van Khoa Nguyen Maciej Falkiewicz Giangiacomo Mercatali Alexandros Kalousis DiffM AI4CE 21 0 0 16 Oct 2024
CRUcialG: Reconstruct Integrated Attack Scenario Graphs by Cyber Threat Intelligence Reports Wenrui Cheng Tiantian Zhu Tieming Chen Qixuan Yuan J. Ying Hongmei Li Chunlin Xiong Mingda Li Mingqi Lv Yan Chen 20 1 0 15 Oct 2024
NetDiff: Deep Graph Denoising Diffusion for Ad Hoc Network Topology Generation Félix Marcoccia C. Adjih P. Mühlethaler DiffM 16 0 0 09 Oct 2024
Text-guided Diffusion Model for 3D Molecule Generation Yanchen Luo Junfeng Fang Sihang Li Zhiyuan Liu Jiancan Wu An Zhang Wenjie Du Xiang Wang 29 6 0 04 Oct 2024
How Discrete and Continuous Diffusion Meet: Comprehensive Analysis of Discrete Diffusion Models via a Stochastic Integral Framework Yinuo Ren Haoxuan Chen Grant M. Rotskoff Lexing Ying 33 3 0 04 Oct 2024
G2T-LLM: Graph-to-Tree Text Encoding for Molecule Generation with Fine-Tuned Large Language Models Zhaoning Yu Xiangyang Xu Hongyang Gao 28 2 0 03 Oct 2024
When Molecular GAN Meets Byte-Pair Encoding Huidong Tang Chen Li Yasuhiko Morimoto 19 0 0 29 Sep 2024
Mitigating Exposure Bias in Score-Based Generation of Molecular Conformations Sijia Wang Chen Wang Zhenhao Zhao Jiqiang Zhang Weiran Cai 21 0 0 21 Sep 2024
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design Dannong Wang Jintai Chen Zhiding Liang Tianfan Fu Xiao-Yang Liu 18 0 0 13 Sep 2024
On the design space between molecular mechanics and machine learning force fields Yuanqing Wang Kenichiro Takaba Michael S. Chen Marcus Wieder Yuzhi Xu ... Kyunghyun Cho Joe G. Greener Peter K. Eastman Stefano Martiniani M. Tuckerman AI4CE 37 4 0 03 Sep 2024
IFH: a Diffusion Framework for Flexible Design of Graph Generative Models Samuel Cognolato A. Sperduti Luciano Serafini DiffM 31 0 0 23 Aug 2024
GraphSPNs: Sum-Product Networks Benefit From Canonical Orderings Milan Papež Martin Rektoris Václav Šmídl Tomáš Pevný TPM 47 0 0 18 Aug 2024
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much? Rafał Karczewski Samuel Kaski Markus Heinonen Vikas K. Garg 33 0 0 12 Aug 2024
Cycle-Configuration: A Novel Graph-theoretic Descriptor Set for Molecular Inference Bowen Song Jianshen Zhu Naveed Ahmed Azam Kazuya Haraguchi Liang Zhao Tatsuya Akutsu 19 0 0 09 Aug 2024
Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Trees Alexia Jolicoeur-Martineau A. Baratin Kisoo Kwon Boris Knyazev Yan Zhang 36 1 0 12 Jul 2024
Leveraging Latent Evolutionary Optimization for Targeted Molecule Generation Siddartha Reddy N Sai Prakash MV V. Varun Vishal Vaddina Saisubramaniam Gopalakrishnan 51 0 0 02 Jul 2024
Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization Siyi Gu Minkai Xu Alexander Powers Weili Nie Tomas Geffner Karsten Kreis J. Leskovec Arash Vahdat Stefano Ermon 43 7 0 01 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 11 0 23 Jun 2024
AntibodyFlow: Normalizing Flow Model for Designing Antibody Complementarity-Determining Regions Bohao Xu Y Samuel Wang Wenyu Chen Shimin Shan OOD 16 0 0 19 Jun 2024
Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space Mohamed Amine Ketata Nicholas Gao Johanna Sommer Tom Wollschlager Stephan Günnemann DiffM 36 1 0 15 Jun 2024
Advancing Graph Generation through Beta Diffusion Yilin He Xinyang Liu Bo Chen Mingyuan Zhou DiffM 24 0 0 13 Jun 2024
Cometh: A continuous-time discrete-state graph diffusion model Antoine Siraudin Fragkiskos D. Malliaros Christopher Morris 29 3 0 10 Jun 2024
Variational Flow Matching for Graph Generation Floor Eijkelboom Grigory Bartosh C. A. Naesseth Max Welling Jan Willem van de Meent 31 10 0 07 Jun 2024
$Diffusion Models in $\textit{De Novo}$ Drug Design$ Diffusion Models in $\textit{De Novo}$ Drug Design Amira Alakhdar Barnabás Póczos Newell Washburn MedIm 34 13 0 07 Jun 2024
Improving global awareness of linkset predictions using Cross-Attentive Modulation tokens Félix Marcoccia C. Adjih P. Mühlethaler 36 0 0 28 May 2024
Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation Jeff Guo Philippe Schwaller Mamba 42 7 0 27 May 2024
Particle physics DL-simulation with control over generated data properties Karol Rogoziñski Jan Dubiñski Przemyslaw Rokita Kamil Deja AI4CE 21 2 0 22 May 2024
Towards Graph Contrastive Learning: A Survey and Beyond Wei Ju Yifan Wang Yifang Qin Zhengyan Mao Zhiping Xiao ... Dongjie Wang Qingqing Long Siyu Yi Xiao Luo Ming Zhang 47 12 0 20 May 2024
A Review on Fragment-based De Novo 2D Molecule Generation Sergei Voloboev VLM 29 1 0 08 May 2024
Generated Contents Enrichment Mahdi Naseri Jiayan Qiu Zhou Wang 29 0 0 06 May 2024
Data-Efficient Molecular Generation with Hierarchical Textual Inversion Seojin Kim Jaehyun Nam Sihyun Yu Younghoon Shin Jinwoo Shin 23 2 0 05 May 2024
SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints M. Cretu Charles Harris Julien Roy Emmanuel Bengio Pietro Lió Bruno Correia Julien Roy Emmanuel Bengio Pietro Liò 32 1 0 02 May 2024
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes BDL DiffM 44 11 0 30 Apr 2024
AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design Xinze Li Penglei Wang Tianfan Fu Wenhao Gao Chengtao Li Leilei Shi Junhong Liu 33 2 0 02 Apr 2024