Top-N: Equivariant set and graph generation without exchangeability
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Abstract (arXiv)
This work addresses one-shot set and graph generation, and, more specifically, the parametrization of probabilistic decoders that map a vector-shaped prior to a distribution over sets or graphs. Sets and graphs are most commonly generated by first sampling points i.i.d. from a normal distribution, and then processing these points along with the prior vector using Transformer layers or Graph Neural Networks. This architecture is designed to generate exchangeable distributions, i.e., all permutations of the generated outputs are equally likely. We however show that it only optimizes a proxy to the evidence lower bound, which makes it hard to train. We then study equivariance in generative settings and show that non-exchangeable methods can still achieve permutation equivariance. Using this result, we introduce Top-n creation, a differentiable generation mechanism that uses the latent vector to select the most relevant points from a trainable reference set. Top-n can replace i.i.d. generation in any Variational Autoencoder or Generative Adversarial Network. Experimentally, our method outperforms i.i.d. generation by 15% at SetMNIST reconstruction, by 33% at object detection on CLEVR, generates sets that are 74% closer to the true distribution on a synthetic molecule-like dataset, and generates more valid molecules on QM9.
Key facts. Cited by 36 papers in the map (data through 7 Oct 2026). Builds on 35 of its 55 references that are in the map. First posted on arXiv 5 Oct 2021.
Builds on
35 of 55 references.
References · 35
- 2017Attention Is All You Needcited by 59,932
- 2017FiLM: Visual Reasoning with a General Conditioning Layercited by 2,286
- 2013Sinkhorn Distances: Lightspeed Computation of Optimal Transportation Distancescited by 2,277
- 2017Deep Setscited by 1,394
- 2018Relational inductive biases, deep learning, and graph networkscited by 1,341
- 2021Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gaugescited by 1,131
- 2017MoleculeNet: A Benchmark for Molecular Machine Learningcited by 1,037
- 2018Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networkscited by 878
- 2018Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point cloudscited by 735
- 2020SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networkscited by 602
- 2019Graph U-Netscited by 489
- 2019PointFlow: 3D Point Cloud Generation with Continuous Normalizing Flowscited by 487
23 more
- 2020Principal Neighbourhood Aggregation for Graph Netscited by 477
- 2018MolGAN: An implicit generative model for small molecular graphscited by 392
- 2018GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoderscited by 375
- 2018Invariant and Equivariant Graph Networkscited by 339
- 2018On the Generalization of Equivariance and Convolution in Neural Networks to the Action of Compact Groupscited by 296
- 2020PolyGen: An Autoregressive Generative Model of 3D Meshescited by 267
- 2020Equivariant Flows: Exact Likelihood Generative Learning for Symmetric Densitiescited by 248
- 2019Efficient Graph Generation with Graph Recurrent Attention Networkscited by 231
- 2018A General Theory of Equivariant CNNs on Homogeneous Spacescited by 223
- 2018Constrained Graph Variational Autoencoders for Molecule Designcited by 182
- 2018PointGrow: Autoregressively Learned Point Cloud Generation with Self-Attentioncited by 105
- 2018Multi-Objective De Novo Drug Design with Conditional Graph Generative Modelcited by 101
- 2021GraphEBM: Molecular Graph Generation with Energy-Based Modelscited by 85
- 2021SetVAE: Learning Hierarchical Composition for Generative Modeling of Set-Structured Datacited by 78
- 2019Deep Set Prediction Networkscited by 71
- 2019FSPool: Learning Set Representations with Featurewise Sort Poolingcited by 53
- 2020Conditional Set Generation with Transformerscited by 32
- 2019A Two-Step Graph Convolutional Decoder for Molecule Generationcited by 25
- 2020Exchangeable Neural ODE for Set Modelingcited by 19
- 2020Set2Graph: Learning Graphs From Setscited by 16
- 2021A Graph VAE and Graph Transformer Approach to Generating Molecular Graphscited by 16
- 2020Set Prediction without Imposing Structure as Conditional Density Estimationcited by 12
- 2021Generating stable molecules using imitation and reinforcement learningcited by 9
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Citing papers per year: 2022: 7; 2023: 9; 2024: 10; 2025: 6; 2026: 4.
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- 2022Equivariant Diffusion for Molecule Generation in 3Dcited by 666
- 2022DiGress: Discrete Denoising diffusion for graph generationcited by 503
- 2022SPECTRE: Spectral Conditioning Helps to Overcome the Expressivity Limits of One-shot Graph Generatorscited by 96
- 2023MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generationcited by 96
- 2024Discrete-state Continuous-time Diffusion for Graph Generationcited by 73
- 2022A Survey on Deep Graph Generation: Methods and Applicationscited by 69
- 2022Diffusion Models for Graphs Benefit From Discrete State Spacescited by 69
- 2025Position: Graph Learning Will Lose Relevance Due To Poor Benchmarkscited by 52
- 2023Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generationcited by 46
- 2023MUDiff: Unified Diffusion for Complete Molecule Generationcited by 41
- 2024SemlaFlow -- Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matchingcited by 40
- 2026Categorical Flow Mapscited by 37
24 more
- 2023Trans-Dimensional Generative Modeling via Jump Diffusion Modelscited by 33
- 2024A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generationcited by 29
- 2023SwinGNN: Rethinking Permutation Invariance in Diffusion Models for Graph Generationcited by 26
- 2023Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3Dcited by 24
- 2023Symmetry Breaking and Equivariant Neural Networkscited by 24
- 2022Graph Neural Networks for Moleculescited by 21
- 2024Generative Modelling of Structurally Constrained Graphscited by 17
- 2025Improving Equivariant Networks with Probabilistic Symmetry Breakingcited by 15
- 2024Geometric Representation Condition Improves Equivariant Molecule Generationcited by 13
- 2023Hyperbolic Graph Diffusion Modelcited by 6
- 2023Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Modelcited by 4
- 2025Guiding Diffusion Models with Reinforcement Learning for Stable Molecule Generationcited by 4
- 2024A Review on Fragment-based De Novo 2D Molecule Generationcited by 3
- 2025Improving Rule-based Reasoning in LLMs using Neurosymbolic Representationscited by 3
- 2025Generating Directed Graphs with Dual Attention and Asymmetric Encodingcited by 3
- 2024Interpreting Equivariant Representationscited by 2
- 2022ReGAE: Graph autoencoder based on recursive neural networkscited by 1
- 2024SeaDAG: Semi-autoregressive Diffusion for Conditional Directed Acyclic Graph Generationcited by 1
- 2025DMol: A Highly Efficient and Chemical Motif-Preserving Molecule Generation Platformcited by 1
- 2024SymDiff: Equivariant Diffusion via Stochastic Symmetrisationcited by 0
- 2024Learning From Graph-Structured Data: Addressing Design Issues and Exploring Practical Applications in Graph Representation Learningcited by 0
- 2026Same Graph, Different Likelihoods: Calibration of Autoregressive Graph Generators via Permutation-Equivalent Encodingscited by 0
- 2026From topology learning to graph generation: A unifying perspectivecited by 0
- 2026GLASS: Global Latent Aggregation with Slot-based Set Decoding for Scalable All-Atom Crystal Generationcited by 0
- 2026GLASS: Global Latent Aggregation with Slot-based Set Decoding for Scalable All-Atom Crystal Generation29 Sep 2026
- 2026From topology learning to graph generation: A unifying perspective2 Sep 2026
- 2026Same Graph, Different Likelihoods: Calibration of Autoregressive Graph Generators via Permutation-Equivalent Encodings7 Apr 2026
- 2026Categorical Flow Maps12 Feb 2026
- 2025Guiding Diffusion Models with Reinforcement Learning for Stable Molecule Generation22 Aug 2025
- 2025Generating Directed Graphs with Dual Attention and Asymmetric Encoding19 Jun 2025
- 2025DMol: A Highly Efficient and Chemical Motif-Preserving Molecule Generation Platform8 Apr 2025
- 2025Improving Equivariant Networks with Probabilistic Symmetry Breaking27 Mar 2025
- 2025Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks20 Feb 2025
- 2025Improving Rule-based Reasoning in LLMs using Neurosymbolic Representations31 Jan 2025
- 2024Learning From Graph-Structured Data: Addressing Design Issues and Exploring Practical Applications in Graph Representation Learning9 Nov 2024
- 2024SeaDAG: Semi-autoregressive Diffusion for Conditional Directed Acyclic Graph Generation21 Oct 2024
24 more
- 2024SymDiff: Equivariant Diffusion via Stochastic Symmetrisation8 Oct 2024
- 2024Geometric Representation Condition Improves Equivariant Molecule Generation4 Oct 2024
- 2024Generative Modelling of Structurally Constrained Graphs25 Jun 2024
- 2024SemlaFlow -- Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matching11 Jun 2024
- 2024Discrete-state Continuous-time Diffusion for Graph Generation19 May 2024
- 2024A Review on Fragment-based De Novo 2D Molecule Generation8 May 2024
- 2024A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation13 Feb 2024
- 2024Interpreting Equivariant Representations23 Jan 2024
- 2023Symmetry Breaking and Equivariant Neural Networks14 Dec 2023
- 2023SwinGNN: Rethinking Permutation Invariance in Diffusion Models for Graph Generation4 Jul 2023
- 2023Hyperbolic Graph Diffusion Model13 Jun 2023
- 2023Trans-Dimensional Generative Modeling via Jump Diffusion Models25 May 2023
- 2023Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D5 May 2023
- 2023MUDiff: Unified Diffusion for Complete Molecule Generation28 Apr 2023
- 2023Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Model13 Mar 2023
- 2023MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation17 Feb 2023
- 2023Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation1 Jan 2023
- 2022Diffusion Models for Graphs Benefit From Discrete State Spaces4 Oct 2022
- 2022DiGress: Discrete Denoising diffusion for graph generation29 Sep 2022
- 2022Graph Neural Networks for Molecules12 Sep 2022
- 2022SPECTRE: Spectral Conditioning Helps to Overcome the Expressivity Limits of One-shot Graph Generators4 Apr 2022
- 2022Equivariant Diffusion for Molecule Generation in 3D31 Mar 2022
- 2022A Survey on Deep Graph Generation: Methods and Applications13 Mar 2022
- 2022ReGAE: Graph autoencoder based on recursive neural networks28 Jan 2022
- 2022Equivariant Diffusion for Molecule Generation in 3Dcited by 666
- 2022DiGress: Discrete Denoising diffusion for graph generationcited by 503
- 2023MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generationcited by 96
- 2024Discrete-state Continuous-time Diffusion for Graph Generationcited by 73
- 2022Diffusion Models for Graphs Benefit From Discrete State Spacescited by 69
- 2026Categorical Flow Mapscited by 37
- 2023Trans-Dimensional Generative Modeling via Jump Diffusion Modelscited by 33
- 2023SwinGNN: Rethinking Permutation Invariance in Diffusion Models for Graph Generationcited by 26
- 2023Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3Dcited by 24
- 2024Generative Modelling of Structurally Constrained Graphscited by 17
- 2023Hyperbolic Graph Diffusion Modelcited by 6
- 2025Guiding Diffusion Models with Reinforcement Learning for Stable Molecule Generationcited by 4
12 most cited of 15 All 15 (JSON)
- 2026Categorical Flow Maps12 Feb 2026
- 2025Guiding Diffusion Models with Reinforcement Learning for Stable Molecule Generation22 Aug 2025
- 2025DMol: A Highly Efficient and Chemical Motif-Preserving Molecule Generation Platform8 Apr 2025
- 2024SeaDAG: Semi-autoregressive Diffusion for Conditional Directed Acyclic Graph Generation21 Oct 2024
- 2024SymDiff: Equivariant Diffusion via Stochastic Symmetrisation8 Oct 2024
- 2024Generative Modelling of Structurally Constrained Graphs25 Jun 2024
- 2024Discrete-state Continuous-time Diffusion for Graph Generation19 May 2024
- 2023SwinGNN: Rethinking Permutation Invariance in Diffusion Models for Graph Generation4 Jul 2023
- 2023Hyperbolic Graph Diffusion Model13 Jun 2023
- 2023Trans-Dimensional Generative Modeling via Jump Diffusion Models25 May 2023
- 2023Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D5 May 2023
- 2023MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation17 Feb 2023
12 newest of 15 All 15 (JSON)
- 2022SPECTRE: Spectral Conditioning Helps to Overcome the Expressivity Limits of One-shot Graph Generatorscited by 96
- 2022A Survey on Deep Graph Generation: Methods and Applicationscited by 69
- 2025Position: Graph Learning Will Lose Relevance Due To Poor Benchmarkscited by 52
- 2023Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generationcited by 46
- 2023MUDiff: Unified Diffusion for Complete Molecule Generationcited by 41
- 2024SemlaFlow -- Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matchingcited by 40
- 2024A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generationcited by 29
- 2023Symmetry Breaking and Equivariant Neural Networkscited by 24
- 2022Graph Neural Networks for Moleculescited by 21
- 2025Improving Equivariant Networks with Probabilistic Symmetry Breakingcited by 15
- 2024Geometric Representation Condition Improves Equivariant Molecule Generationcited by 13
- 2023Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Modelcited by 4
12 most cited of 20 All 20 (JSON)
- 2026GLASS: Global Latent Aggregation with Slot-based Set Decoding for Scalable All-Atom Crystal Generation29 Sep 2026
- 2026From topology learning to graph generation: A unifying perspective2 Sep 2026
- 2026Same Graph, Different Likelihoods: Calibration of Autoregressive Graph Generators via Permutation-Equivalent Encodings7 Apr 2026
- 2025Generating Directed Graphs with Dual Attention and Asymmetric Encoding19 Jun 2025
- 2025Improving Equivariant Networks with Probabilistic Symmetry Breaking27 Mar 2025
- 2025Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks20 Feb 2025
- 2024Learning From Graph-Structured Data: Addressing Design Issues and Exploring Practical Applications in Graph Representation Learning9 Nov 2024
- 2024Geometric Representation Condition Improves Equivariant Molecule Generation4 Oct 2024
- 2024SemlaFlow -- Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matching11 Jun 2024
- 2024A Review on Fragment-based De Novo 2D Molecule Generation8 May 2024
- 2024A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation13 Feb 2024
- 2024Interpreting Equivariant Representations23 Jan 2024
12 newest of 20 All 20 (JSON)