# SNACK: A Sequential Notation Framework for Probabilistic Graph Generation

arXiv: https://arxiv.org/abs/2610.19781 · HTML: https://mlsanity.com/paper/2610.19781/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 50 of its 70 references that are in the map.
- First posted on arXiv 14 Oct 2026.

## Builds on (most cited first, 30 of 50)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Deep contextualized word representations](https://mlsanity.com/paper/1802.05365/) (2018)
- [GLU Variants Improve Transformer](https://mlsanity.com/paper/2002.05202/) (2020)
- [Root Mean Square Layer Normalization](https://mlsanity.com/paper/1910.07467/) (2019)
- [BERT Rediscovers the Classical NLP Pipeline](https://mlsanity.com/paper/1905.05950/) (2019)
- [Improved Precision and Recall Metric for Assessing Generative Models](https://mlsanity.com/paper/1904.06991/) (2019)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [Sequence Level Training with Recurrent Neural Networks](https://mlsanity.com/paper/1511.06732/) (2015)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models](https://mlsanity.com/paper/1802.08773/) (2018)
- [Flow Network based Generative Models for Non-Iterative Diverse Candidate Generation](https://mlsanity.com/paper/2106.04399/) (2021)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation](https://mlsanity.com/paper/1806.02473/) (2018)
- [GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation](https://mlsanity.com/paper/2001.09382/) (2020)
- [On the Optimization of Deep Networks: Implicit Acceleration by Overparameterization](https://mlsanity.com/paper/1802.06509/) (2018)
- [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations](https://mlsanity.com/paper/2202.02514/) (2022)
- [Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models](https://mlsanity.com/paper/1811.12823/) (2018)
- [Permutation Invariant Graph Generation via Score-Based Generative Modeling](https://mlsanity.com/paper/2003.00638/) (2020)
- [Long Range Graph Benchmark](https://mlsanity.com/paper/2206.08164/) (2022)
- [Trajectory balance: Improved credit assignment in GFlowNets](https://mlsanity.com/paper/2201.13259/) (2022)
- [Efficient Graph Generation with Graph Recurrent Attention Networks](https://mlsanity.com/paper/1910.00760/) (2019)
- [Learning Deep Generative Models of Graphs](https://mlsanity.com/paper/1803.03324/) (2018)
- [Constrained Graph Variational Autoencoders for Molecule Design](https://mlsanity.com/paper/1805.09076/) (2018)
- [GraphDF: A Discrete Flow Model for Molecular Graph Generation](https://mlsanity.com/paper/2102.01189/) (2021)
- [Biological Sequence Design with GFlowNets](https://mlsanity.com/paper/2203.04115/) (2022)
- [GFlowNets and variational inference](https://mlsanity.com/paper/2210.00580/) (2022)
- [Multi-Objective GFlowNets](https://mlsanity.com/paper/2210.12765/) (2022)
- [Amortizing intractable inference in large language models](https://mlsanity.com/paper/2310.04363/) (2023)
- [MolecularRNN: Generating realistic molecular graphs with optimized properties](https://mlsanity.com/paper/1905.13372/) (2019)

## Abstract (arXiv)

We introduce SNACK, a string representation for probabilistic graph generation that enables sequence models to generate and model graphs with discrete node and edge features. SNACK linearizes graphs by encoding the nonzero entries of the lower-triangular adjacency matrix, establishing a bijective correspondence between valid sequences and ordered adjacency matrices. This design enables invalid logit masking to enforce structural constraints--such as chemical valence and ordering rules--guaranteeing 100% valid generated sequences. SNACK also enables principled string-based GFlowNet training by explicitly accounting for node-ordering symmetries. Across standard graph-generation tasks and molecular distribution-learning benchmarks, SNACK achieves competitive sample quality, while substantially improving the throughput of GFlowNet training relative to graph-based generation. Probing analyses further show that models trained on SNACK encode meaningful local and global graph structure despite receiving only sequential supervision. These results position SNACK as a practical framework for probabilistic graph generation with deep sequence models.