mlsanityData to 7 Oct 2026

Syntax-Directed Variational Autoencoder for Structured Data

arXiv 1802.08786 ↗First posted 24 Feb 2018cs.LG cs.CLcited by 103

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Abstract (arXiv)

Deep generative models have been enjoying success in modeling continuous data. However it remains challenging to capture the representations for discrete structures with formal grammars and semantics, e.g., computer programs and molecular structures. How to generate both syntactically and semantically correct data still remains largely an open problem. Inspired by the theory of compiler where the syntax and semantics check is done via syntax-directed translation (SDT), we propose a novel syntax-directed variational autoencoder (SD-VAE) by introducing stochastic lazy attributes. This approach converts the offline SDT check into on-the-fly generated guidance for constraining the decoder. Comparing to the state-of-the-art methods, our approach enforces constraints on the output space so that the output will be not only syntactically valid, but also semantically reasonable. We evaluate the proposed model with applications in programming language and molecules, including reconstruction and program/molecule optimization. The results demonstrate the effectiveness in incorporating syntactic and semantic constraints in discrete generative models, which is significantly better than current state-of-the-art approaches.

Key facts. Cited by 103 papers in the map (data through 7 Oct 2026). First posted on arXiv 24 Feb 2018.

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Citing papers per year: 2021: 24; 2022: 30; 2023: 18; 2024: 17; 2025: 9; 2026: 5.

103 papers.

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  1. 2023A Comprehensive Survey of AI-Generated Content (AIGC): A History of Generative AI from GAN to ChatGPTcited by 221
  2. 2022Graph neural networks for materials science and chemistrycited by 181
  3. 2021GraphDF: A Discrete Flow Model for Molecular Graph Generationcited by 177
  4. 2022A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Languagecited by 129
  5. 2022Generating 3D Molecules for Target Protein Bindingcited by 104
  6. 2023Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspectivecited by 91
  7. 2021GraphEBM: Molecular Graph Generation with Energy-Based Modelscited by 85
  8. 2022Local Latent Space Bayesian Optimization over Structured Inputscited by 78
  9. 2022Equivariant Energy-Guided SDE for Inverse Molecular Designcited by 72
  10. 2022A Survey on Deep Graph Generation: Methods and Applicationscited by 69
  11. 2021Keeping it Simple: Language Models can learn Complex Molecular Distributionscited by 68
  12. 2022MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Designcited by 66
38 more
  1. 2022MDM: Molecular Diffusion Model for 3D Molecule Generationcited by 58
  2. 2023Grammar Prompting for Domain-Specific Language Generation with Large Language Modelscited by 58
  3. 2021Differentiable Scaffolding Tree for Molecular Optimizationcited by 53
  4. 2024Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generationcited by 53
  5. 2021Improving black-box optimization in VAE latent space using decoder uncertaintycited by 51
  6. 2023Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generationcited by 46
  7. 2021Combining Latent Space and Structured Kernels for Bayesian Optimization over Combinatorial Spacescited by 45
  8. 2022LIMO: Latent Inceptionism for Targeted Molecule Generationcited by 40
  9. 2022Towards Data-and Knowledge-Driven Artificial Intelligence: A Survey on Neuro-Symbolic Computingcited by 34
  10. 20223DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Designcited by 33
  11. 2021JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Designcited by 31
  12. 2024A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generationcited by 29
  13. 2021Artificial Intelligence in Drug Discovery: Applications and Techniquescited by 28
  14. 2021Scalable deeper graph neural networks for high-performance materials property predictioncited by 26
  15. 2022Data-Efficient Graph Grammar Learning for Molecular Generationcited by 26
  16. 2023Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3Dcited by 24
  17. 2021MolGrow: A Graph Normalizing Flow for Hierarchical Molecular Generationcited by 22
  18. 2025FlowMol3: Flow Matching for 3D De Novo Small-Molecule Generationcited by 20
  19. 2023Advancing Bayesian Optimization via Learning Correlated Latent Spacecited by 18
  20. 2022GLSO: Grammar-guided Latent Space Optimization for Sample-efficient Robot Design Automationcited by 16
  21. 2022Interpretable Molecular Graph Generation via Monotonic Constraintscited by 15
  22. 2025LLM/Agent-as-Data-Analyst: A Surveycited by 15
  23. 2021Neural Program Generation Modulo Static Analysiscited by 13
  24. 2023Efficient Generator of Mathematical Expressions for Symbolic Regressioncited by 13
  25. 2022Modular Flows: Differential Molecular Generationcited by 11
  26. 2024GP-MoLFormer: A Foundation Model For Molecular Generationcited by 11
  27. 2024Inversion-based Latent Bayesian Optimizationcited by 11
  28. 2021Polygrammar: Grammar for Digital Polymer Representation and Generationcited by 8
  29. 2022Conditional β-VAE for De Novo Molecular Generationcited by 8
  30. 2022Probabilistic Generative Transformer Language models for Generative Design of Moleculescited by 8
  31. 2023Molecule Design by Latent Prompt Transformercited by 8
  32. 2021A generative model for molecule generation based on chemical reaction treescited by 6
  33. 2021Augmenting Molecular Deep Generative Models with Topological Data Analysis Representationscited by 6
  34. 2021Learning Space Partitions for Path Planningcited by 6
  35. 2022Graph Machine Learning for Design of High-Octane Fuelscited by 6
  36. 2023Knowledge-augmented Graph Machine Learning for Drug Discovery: A Surveycited by 6
  37. 2023Graph-Induced Syntactic-Semantic Spaces in Transformer-Based Variational AutoEncoderscited by 6
  38. 2024GraphXForm: Graph transformer for computer-aided molecular designcited by 6

50 most cited of 103 All 103 (JSON)