Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

Cometh: A continuous-time discrete-state graph diffusion model

Discrete-state denoising diffusion models led to state-of-the-art performance in graph generation, especially in the molecular domain. Recently, they have been transposed to continuous time, allowing more flexibility in the reverse process and a better trade-off between sampling efficiency and quality. Here, to leverage the benefits of both approaches, we propose Cometh, a continuous-time discrete-state graph diffusion model, integrating graph data into a continuous-time diffusion model framework. Empirically, we show that integrating continuous time leads to significant improvements across various metrics over state-of-the-art discrete-state diffusion models on a large set of molecular and non-molecular benchmark datasets.

DiGress: Discrete Denoising diffusion for graph generation

This work introduces DiGress, a discrete denoising diffusion model for generating graphs with categorical node and edge attributes. Our model defines a diffusion process that progressively edits a graph with noise (adding or removing edges, changing the categories), and a graph transformer network that learns to revert this process. With these two ingredients in place, we reduce distribution learning over graphs to a simple sequence of classification tasks. We further improve sample quality by proposing a new Markovian noise model that preserves the marginal distribution of node and edge types during diffusion, and by adding auxiliary graph-theoretic features derived from the noisy graph at each diffusion step. Finally, we propose a guidance procedure for conditioning the generation on graph-level features. Overall, DiGress achieves state-of-the-art performance on both molecular and non-molecular datasets, with up to 3x validity improvement on a dataset of planar graphs. In particular, it is the first model that scales to the large GuacaMol dataset containing 1.3M drug-like molecules without using a molecule-specific representation such as SMILES or fragments.