Semantically Consistent Discrete Diffusion for 3D Biological Graph Modeling

TL;DR

This paper introduces a novel diffusion-based method for generating 3D biological graphs that maintains anatomical validity and improves downstream tasks, addressing limitations of previous approaches.

Contribution

The paper presents a new 3D biological graph generation technique using a projection operator and edge-deletion noising, enhancing realism and utility over prior methods.

Findings

Outperforms previous methods on real-world datasets

Significantly improves downstream graph labeling

Serves as an effective out-of-the-box link predictor

Abstract

3D spatial graphs play a crucial role in biological and clinical research by modeling anatomical networks such as blood vessels,neurons, and airways. However, generating 3D biological graphs while maintaining anatomical validity remains challenging, a key limitation of existing diffusion-based methods. In this work, we propose a novel 3D biological graph generation method that adheres to structural and semantic plausibility conditions. We achieve this by using a novel projection operator during sampling that stochastically fixes inconsistencies. Further, we adopt a superior edge-deletion-based noising procedure suitable for sparse biological graphs. Our method demonstrates superior performance on two real-world datasets, human circle of Willis and lung airways, compared to previous approaches. Importantly, we demonstrate that the generated samples significantly enhance downstream graph labeling performance. Furthermore, we show that our generative model is a reasonable out-of-the-box link predictior.