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GraphDF: A Discrete Flow Model for Molecular Graph Generation
v1v2 (latest)

GraphDF: A Discrete Flow Model for Molecular Graph Generation

International Conference on Machine Learning (ICML), 2021
1 February 2021
Youzhi Luo
Keqiang Yan
Shuiwang Ji
    DRL
ArXiv (abs)PDFHTML

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

50 / 139 papers shown
Graph VQ-Transformer (GVT): Fast and Accurate Molecular Generation via High-Fidelity Discrete Latents
Graph VQ-Transformer (GVT): Fast and Accurate Molecular Generation via High-Fidelity Discrete Latents
Haozhuo Zheng
Cheng Wang
Yang Liu
60
0
0
02 Dec 2025
PISA: Prioritized Invariant Subgraph Aggregation
PISA: Prioritized Invariant Subgraph Aggregation
Ali Ghasemi
F. Wani
Maria Sofia Bucarelli
Fabrizio Silvestri
OOD
126
0
0
27 Nov 2025
BadGraph: A Backdoor Attack Against Latent Diffusion Model for Text-Guided Graph Generation
BadGraph: A Backdoor Attack Against Latent Diffusion Model for Text-Guided Graph Generation
Liang Ye
Shengqin Chen
Jiazhu Dai
DiffM
141
0
0
23 Oct 2025
Towards Unsupervised Open-Set Graph Domain Adaptation via Dual Reprogramming
Towards Unsupervised Open-Set Graph Domain Adaptation via Dual Reprogramming
Zhen Zhang
Bingsheng He
OOD
161
0
0
21 Oct 2025
Controllable Graph Generation with Diffusion Models via Inference-Time Tree Search Guidance
Controllable Graph Generation with Diffusion Models via Inference-Time Tree Search Guidance
Jiachi Zhao
Zehong Wang
Yamei Liao
Chuxu Zhang
Yanfang Ye
151
0
0
12 Oct 2025
Hierarchical Bayesian Flow Networks for Molecular Graph Generation
Hierarchical Bayesian Flow Networks for Molecular Graph Generation
Yida Xiong
Jiameng Chen
Kun Li
Hongzhi Zhang
Xiantao Cai
Wenbin Hu
186
0
0
11 Oct 2025
Toward a Unified Geometry Understanding: Riemannian Diffusion Framework for Graph Generation and Prediction
Toward a Unified Geometry Understanding: Riemannian Diffusion Framework for Graph Generation and Prediction
Y. Gao
Xingcheng Fu
Qingyun Sun
Jianxin Li
Xianxian Li
DiffM
204
0
0
06 Oct 2025
Graph Generation with Spectral Geodesic Flow Matching
Graph Generation with Spectral Geodesic Flow Matching
Xikun Huang
Tianyu Ruan
Chihao Zhang
Shihua Zhang
167
0
0
02 Oct 2025
How to Make Large Language Models Generate 100% Valid Molecules?
How to Make Large Language Models Generate 100% Valid Molecules?
Wen Tao
Jing Tang
Alvin Chan
Bryan Hooi
Baolong Bi
Nanyun Peng
Yuansheng Liu
Yiwei Wang
93
2
0
27 Sep 2025
Cognitive Structure Generation: From Educational Priors to Policy Optimization
Cognitive Structure Generation: From Educational Priors to Policy Optimization
Hengnian Gu
Zhifu Chen
Yuxin Chen
Jin Peng Zhou
Dongdai Zhou
DiffM
152
0
0
18 Aug 2025
IBEX: Information-Bottleneck-EXplored Coarse-to-Fine Molecular Generation under Limited Data
IBEX: Information-Bottleneck-EXplored Coarse-to-Fine Molecular Generation under Limited Data
Dong Xu
Zhangfan Yang
Jenna Xinyi Yao
Shuangbao Song
Zexuan Zhu
Junkai Ji
131
0
0
14 Aug 2025
Sparse Probabilistic Graph Circuits
Sparse Probabilistic Graph Circuits
Martin Rektoris
Milan Papez
Václav Smídl
Tomás Pevný
TPM
221
0
0
11 Aug 2025
MolSnap: Snap-Fast Molecular Generation with Latent Variational Mean Flow
MolSnap: Snap-Fast Molecular Generation with Latent Variational Mean Flow
Md Atik Ahamed
Qiang Ye
Q. Cheng
BDL
132
1
0
07 Aug 2025
Beyond Interactions: Node-Level Graph Generation for Knowledge-Free Augmentation in Recommender Systems
Beyond Interactions: Node-Level Graph Generation for Knowledge-Free Augmentation in Recommender Systems
Zhaoyan Wang
Hyunjun Ahn
In-Young Ko
140
0
0
28 Jul 2025
Controlled Generation with Equivariant Variational Flow Matching
Controlled Generation with Equivariant Variational Flow Matching
Floor Eijkelboom
Heiko Zimmermann
Sharvaree P. Vadgama
Erik J. Bekkers
Max Welling
C. A. Naesseth
Jan-Willem van de Meent
BDL
313
4
0
23 Jun 2025
Generating Directed Graphs with Dual Attention and Asymmetric Encoding
Generating Directed Graphs with Dual Attention and Asymmetric Encoding
Alba Carballo-Castro
Manuel Madeira
Yiming Qin
D. Thanou
Pascal Frossard
342
0
0
19 Jun 2025
GGBall: Graph Generative Model on Poincaré Ball
GGBall: Graph Generative Model on Poincaré Ball
Tianci Bu
Chuanrui Wang
Hao Ma
Haoren Zheng
Xin Lu
Tailin Wu
222
0
0
08 Jun 2025
Materials Generation in the Era of Artificial Intelligence: A Comprehensive Survey
Materials Generation in the Era of Artificial Intelligence: A Comprehensive Survey
Zhixun Li
Bin Cao
Rui Jiao
Shu Wu
Ding Wang
...
Sihan Yang
Yu Rong
Liang Wang
Tong-yi Zhang
Jeffrey Xu Yu
3DVAI4CE
344
7
0
22 May 2025
Learning Flexible Forward Trajectories for Masked Molecular Diffusion
Learning Flexible Forward Trajectories for Masked Molecular Diffusion
Hyunjin Seo
Taewon Kim
Sihyun Yu
SungSoo Ahn
DiffMAI4CE
599
0
0
22 May 2025
Unveiling and Steering Connectome Organization with Interpretable Latent Variables
Unveiling and Steering Connectome Organization with Interpretable Latent Variables
Yubin Li
Xingyu Liu
Guozhang Chen
382
0
0
19 May 2025
Heterophily-informed Message Passing
Heterophily-informed Message Passing
Haishan Wang
Arno Solin
Vikas Garg
399
0
0
28 Apr 2025
DMol: A Highly Efficient and Chemical Motif-Preserving Molecule Generation Platform
DMol: A Highly Efficient and Chemical Motif-Preserving Molecule Generation Platform
Peizhi Niu
Yu-Hsiang Wang
Vishal Rana
Chetan Rupakheti
Abhishek Pandey
O. Milenkovic
675
1
0
08 Apr 2025
Diffusion-Free Graph Generation with Next-Scale Prediction
Diffusion-Free Graph Generation with Next-Scale Prediction
Samuel Belkadi
Steve Hong
Marian Chen
M. Cretu
Charles Harris
Pietro Liò
DiffM
264
0
0
30 Mar 2025
Simple and Critical Iterative Denoising: A Recasting of Discrete Diffusion in Graph Generation
Simple and Critical Iterative Denoising: A Recasting of Discrete Diffusion in Graph Generation
Yoann Boget
DiffM
393
0
0
27 Mar 2025
Graph Generative Models Evaluation with Masked Autoencoder
Graph Generative Models Evaluation with Masked AutoencoderPacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), 2025
Chengen Wang
Murat Kantarcioglu
249
0
0
17 Mar 2025
Probabilistic Graph Circuits: Deep Generative Models for Tractable Probabilistic Inference over Graphs
Probabilistic Graph Circuits: Deep Generative Models for Tractable Probabilistic Inference over GraphsConference on Uncertainty in Artificial Intelligence (UAI), 2025
Milan Papez
Martin Rektoris
Václav Smídl
Tomás Pevný
TPM
359
1
0
15 Mar 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation
Mohit Pandey
G. Subbaraj
Artem Cherkasov
Martin Ester
Emmanuel Bengio
AI4CE
515
4
0
08 Mar 2025
Backdoor Attacks on Discrete Graph Diffusion Models
Jiawen Wang
Samin Karim
Yuan Hong
Binghui Wang
DiffM
473
1
0
08 Mar 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule GenerationInternational Conference on Learning Representations (ICLR), 2025
Zhiyuan Liu
Yanchen Luo
Han Huang
Enzhi Zhang
Changhao Nai
Cunchun Li
Yaorui Shi
Xiang Wang
Kenji Kawaguchi
Tat-Seng Chua
489
17
0
18 Feb 2025
Towards Efficient Molecular Property Optimization with Graph Energy Based Models
Towards Efficient Molecular Property Optimization with Graph Energy Based Models
Luca Miglior
Lorenzo Simone
Marco Podda
Davide Bacciu
AI4CE
209
1
0
17 Feb 2025
HOG-Diff: Higher-Order Guided Diffusion for Graph Generation
HOG-Diff: Higher-Order Guided Diffusion for Graph Generation
Yiming Huang
Tolga Birdal
DiffM
408
4
0
06 Feb 2025
Graph Generative Pre-trained Transformer
Graph Generative Pre-trained Transformer
Xiaohui Chen
Yinkai Wang
Jiaxing He
Yuanqi Du
S. Hassoun
Xiaolin Xu
Tianpeng Liu
452
8
0
02 Jan 2025
TreeFormer: Single-view Plant Skeleton Estimation via Tree-constrained
  Graph Generation
TreeFormer: Single-view Plant Skeleton Estimation via Tree-constrained Graph GenerationIEEE Workshop/Winter Conference on Applications of Computer Vision (WACV), 2024
Xinpeng Liu
Hiroaki Santo
Yosuke Toda
Fumio Okura
340
2
0
25 Nov 2024
Hybrid Generative AI for De Novo Design of Co-Crystals with Enhanced
  Tabletability
Hybrid Generative AI for De Novo Design of Co-Crystals with Enhanced TabletabilityNeural Information Processing Systems (NeurIPS), 2024
Nina Gubina
Andrei Dmitrenko
Gleb Solovev
Lyubov Yamshchikova
Oleg Petrov
Ivan Lebedev
N. Serov
Grigorii Kirgizov
Nikolay Nikitin
Vladimir Vinogradov
157
1
0
22 Oct 2024
MING: A Functional Approach to Learning Molecular Generative Models
MING: A Functional Approach to Learning Molecular Generative ModelsInternational Conference on Artificial Intelligence and Statistics (AISTATS), 2024
Van Khoa Nguyen
Maciej Falkiewicz
Giangiacomo Mercatali
Alexandros Kalousis
DiffMAI4CE
202
0
0
16 Oct 2024
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning
Peter Eckmann
D. Wu
G. Heinzelmann
Michael K. Gilson
Rose Yu
AI4CE
301
0
0
15 Oct 2024
Text-guided Diffusion Model for 3D Molecule Generation
Text-guided Diffusion Model for 3D Molecule Generation
Yanchen Luo
Cunchun Li
Changhao Nai
Zhiyuan Liu
Jiancan Wu
An Zhang
Wenjie Du
Xiang Wang
222
10
0
04 Oct 2024
G2T-LLM: Graph-to-Tree Text Encoding for Molecule Generation with
  Fine-Tuned Large Language Models
G2T-LLM: Graph-to-Tree Text Encoding for Molecule Generation with Fine-Tuned Large Language Models
Zhaoning Yu
Xiangyang Xu
Hongyang Gao
192
3
0
03 Oct 2024
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design
Dannong Wang
Jintai Chen
Zhiding Liang
Tianfan Fu
Xiao-Yang Liu
223
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0
13 Sep 2024
IFH: a Diffusion Framework for Flexible Design of Graph Generative
  Models
IFH: a Diffusion Framework for Flexible Design of Graph Generative ModelsEuropean Conference on Artificial Intelligence (ECAI), 2024
Samuel Cognolato
A. Sperduti
Luciano Serafini
DiffM
204
0
0
23 Aug 2024
GraphSPNs: Sum-Product Networks Benefit From Canonical Orderings
GraphSPNs: Sum-Product Networks Benefit From Canonical Orderings
Milan Papež
Martin Rektoris
Václav Šmídl
Tomáš Pevný
TPM
357
2
0
18 Aug 2024
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much?
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much?International Conference on Artificial Intelligence and Statistics (AISTATS), 2024
Rafał Karczewski
Samuel Kaski
Markus Heinonen
Vikas Garg
327
0
0
12 Aug 2024
Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Trees
Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Trees
Alexia Jolicoeur-Martineau
A. Baratin
Kisoo Kwon
Boris Knyazev
Yan Zhang
328
3
0
12 Jul 2024
Generative Model for Small Molecules with Latent Space RL Fine-Tuning to
  Protein Targets
Generative Model for Small Molecules with Latent Space RL Fine-Tuning to Protein Targets
Ulrich A. Mbou Sob
Qiulin Li
Miguel Arbesú
Oliver E. Bent
Andries P. Smit
Arnu Pretorius
246
1
0
02 Jul 2024
Leveraging Latent Evolutionary Optimization for Targeted Molecule
  Generation
Leveraging Latent Evolutionary Optimization for Targeted Molecule Generation
Siddartha Reddy N
Sai Prakash MV
V. Varun
Vishal Vaddina
Saisubramaniam Gopalakrishnan
225
2
0
02 Jul 2024
Generative Modelling of Structurally Constrained Graphs
Generative Modelling of Structurally Constrained Graphs
Manuel Madeira
Clément Vignac
D. Thanou
Pascal Frossard
DiffM
212
9
0
25 Jun 2024
Advancing Graph Generation through Beta Diffusion
Advancing Graph Generation through Beta Diffusion
Yilin He
Xinyang Liu
Bo Chen
Mingyuan Zhou
DiffM
202
3
0
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Large Generative Graph Models
Large Generative Graph Models
Yu Wang
Ryan Rossi
Namyong Park
Huiyuan Chen
Nesreen K. Ahmed
Puja Trivedi
Franck Dernoncourt
Danai Koutra
Hanyu Wang
AI4CE
302
6
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07 Jun 2024
Diffusion Models in $\textit{De Novo}$ Drug Design
Diffusion Models in De Novo\textit{De Novo}De Novo Drug DesignJournal of Chemical Information and Modeling (JCIM), 2024
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199
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Variational Flow Matching for Graph Generation
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Floor Eijkelboom
Grigory Bartosh
C. A. Naesseth
Max Welling
Jan-Willem van de Meent
449
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123
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