Graph Generation with $k^2$-Trees

Abstract

Generating graphs from a target distribution is a significant challenge across many domains, including drug discovery and social network analysis. In this work, we introduce a novel graph generation method leveraging $K^2$ representation, originally designed for lossless graph compression. The $K^2$ representation enables compact generation while concurrently capturing an inherent hierarchical structure of a graph. In addition, we make contributions by (1) presenting a sequential $K^2$ representation that incorporates pruning, flattening, and tokenization processes and (2) introducing a Transformer-based architecture designed to generate the sequence by incorporating a specialized tree positional encoding scheme. Finally, we extensively evaluate our algorithm on four general and two molecular graph datasets to confirm its superiority for graph generation.