paper
arXiv cs.LG
October 28th, 2026 at 4:00 AM

SNACK: A Sequential Notation Framework for Probabilistic Graph Generation

arXiv:2610.19781v3 Announce Type: replace-cross Abstract: We introduce SNACK, a string representation for probabilistic graph generation that enables language models to generate 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, thereby guaranteeing 100% valid generated sequences while sticking to standard language modeling for effective training. 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.

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Canonical link: https://arxiv.org/abs/2610.19781