mlsanityData to 7 Oct 2026

Top-N: Equivariant set and graph generation without exchangeability

arXiv 2110.02096 ↗First posted 5 Oct 2021cs.LG stat.MLcited by 36

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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

  1. 2017Attention Is All You Needcited by 59,932
  2. 2017FiLM: Visual Reasoning with a General Conditioning Layercited by 2,286
  3. 2013Sinkhorn Distances: Lightspeed Computation of Optimal Transportation Distancescited by 2,277
  4. 2017Deep Setscited by 1,394
  5. 2018Relational inductive biases, deep learning, and graph networkscited by 1,341
  6. 2021Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gaugescited by 1,131
  7. 2017MoleculeNet: A Benchmark for Molecular Machine Learningcited by 1,037
  8. 2018Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networkscited by 878
  9. 2018Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point cloudscited by 735
  10. 2020SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networkscited by 602
  11. 2019Graph U-Netscited by 489
  12. 2019PointFlow: 3D Point Cloud Generation with Continuous Normalizing Flowscited by 487
23 more
  1. 2020Principal Neighbourhood Aggregation for Graph Netscited by 477
  2. 2018MolGAN: An implicit generative model for small molecular graphscited by 392
  3. 2018GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoderscited by 375
  4. 2018Invariant and Equivariant Graph Networkscited by 339
  5. 2018On the Generalization of Equivariance and Convolution in Neural Networks to the Action of Compact Groupscited by 296
  6. 2020PolyGen: An Autoregressive Generative Model of 3D Meshescited by 267
  7. 2020Equivariant Flows: Exact Likelihood Generative Learning for Symmetric Densitiescited by 248
  8. 2019Efficient Graph Generation with Graph Recurrent Attention Networkscited by 231
  9. 2018A General Theory of Equivariant CNNs on Homogeneous Spacescited by 223
  10. 2018Constrained Graph Variational Autoencoders for Molecule Designcited by 182
  11. 2018PointGrow: Autoregressively Learned Point Cloud Generation with Self-Attentioncited by 105
  12. 2018Multi-Objective De Novo Drug Design with Conditional Graph Generative Modelcited by 101
  13. 2021GraphEBM: Molecular Graph Generation with Energy-Based Modelscited by 85
  14. 2021SetVAE: Learning Hierarchical Composition for Generative Modeling of Set-Structured Datacited by 78
  15. 2019Deep Set Prediction Networkscited by 71
  16. 2019FSPool: Learning Set Representations with Featurewise Sort Poolingcited by 53
  17. 2020Conditional Set Generation with Transformerscited by 32
  18. 2019A Two-Step Graph Convolutional Decoder for Molecule Generationcited by 25
  19. 2020Exchangeable Neural ODE for Set Modelingcited by 19
  20. 2020Set2Graph: Learning Graphs From Setscited by 16
  21. 2021A Graph VAE and Graph Transformer Approach to Generating Molecular Graphscited by 16
  22. 2020Set Prediction without Imposing Structure as Conditional Density Estimationcited by 12
  23. 2021Generating stable molecules using imitation and reinforcement learningcited by 9

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2022: 7; 2023: 9; 2024: 10; 2025: 6; 2026: 4.

36 papers.

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  1. 2022Equivariant Diffusion for Molecule Generation in 3Dcited by 666
  2. 2022DiGress: Discrete Denoising diffusion for graph generationcited by 503
  3. 2022SPECTRE: Spectral Conditioning Helps to Overcome the Expressivity Limits of One-shot Graph Generatorscited by 96
  4. 2023MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generationcited by 96
  5. 2024Discrete-state Continuous-time Diffusion for Graph Generationcited by 73
  6. 2022A Survey on Deep Graph Generation: Methods and Applicationscited by 69
  7. 2022Diffusion Models for Graphs Benefit From Discrete State Spacescited by 69
  8. 2025Position: Graph Learning Will Lose Relevance Due To Poor Benchmarkscited by 52
  9. 2023Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generationcited by 46
  10. 2023MUDiff: Unified Diffusion for Complete Molecule Generationcited by 41
  11. 2024SemlaFlow -- Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matchingcited by 40
  12. 2026Categorical Flow Mapscited by 37
24 more
  1. 2023Trans-Dimensional Generative Modeling via Jump Diffusion Modelscited by 33
  2. 2024A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generationcited by 29
  3. 2023SwinGNN: Rethinking Permutation Invariance in Diffusion Models for Graph Generationcited by 26
  4. 2023Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3Dcited by 24
  5. 2023Symmetry Breaking and Equivariant Neural Networkscited by 24
  6. 2022Graph Neural Networks for Moleculescited by 21
  7. 2024Generative Modelling of Structurally Constrained Graphscited by 17
  8. 2025Improving Equivariant Networks with Probabilistic Symmetry Breakingcited by 15
  9. 2024Geometric Representation Condition Improves Equivariant Molecule Generationcited by 13
  10. 2023Hyperbolic Graph Diffusion Modelcited by 6
  11. 2023Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Modelcited by 4
  12. 2025Guiding Diffusion Models with Reinforcement Learning for Stable Molecule Generationcited by 4
  13. 2024A Review on Fragment-based De Novo 2D Molecule Generationcited by 3
  14. 2025Improving Rule-based Reasoning in LLMs using Neurosymbolic Representationscited by 3
  15. 2025Generating Directed Graphs with Dual Attention and Asymmetric Encodingcited by 3
  16. 2024Interpreting Equivariant Representationscited by 2
  17. 2022ReGAE: Graph autoencoder based on recursive neural networkscited by 1
  18. 2024SeaDAG: Semi-autoregressive Diffusion for Conditional Directed Acyclic Graph Generationcited by 1
  19. 2025DMol: A Highly Efficient and Chemical Motif-Preserving Molecule Generation Platformcited by 1
  20. 2024SymDiff: Equivariant Diffusion via Stochastic Symmetrisationcited by 0
  21. 2024Learning From Graph-Structured Data: Addressing Design Issues and Exploring Practical Applications in Graph Representation Learningcited by 0
  22. 2026Same Graph, Different Likelihoods: Calibration of Autoregressive Graph Generators via Permutation-Equivalent Encodingscited by 0
  23. 2026From topology learning to graph generation: A unifying perspectivecited by 0
  24. 2026GLASS: Global Latent Aggregation with Slot-based Set Decoding for Scalable All-Atom Crystal Generationcited by 0