Masahiro Negishi

Masahiro Negishi, Aron Walsh

There has been rapid progress in generative artificial intelligence (AI) models for inorganic crystal design, which can efficiently generate large numbers of candidate compounds after being trained on databases of known crystals. However, it remains unclear whether they genuinely expand the accessible materials search space beyond conventional strategies such as elemental substitution within known structure types. We address this question by developing a workflow to assess whether AI-generated crystals are duplicates of training structures, reproducible by elemental substitution, or unmatched by either criterion. Applying this workflow to representative generative models reveals that 81-92% of chemically valid and metastable generated crystals are either training duplicates or substitution-derived structures. This tendency is particularly strong in high-symmetry crystal systems, even though many possible structural prototypes remain unexplored. Further analysis of the underlying structural fingerprints shows that low-symmetry structures beyond duplication or substitution can be interpreted as interpolation in training-data-rich regions, while high-symmetry duplicates appear to result from memorisation in training-sparse regions. Our findings highlight a limitation in the current generation of models that exhibit a bias towards known structural prototypes in the high symmetry regions, but enable wider exploration of the low-symmetry structural space.

Masahiro Negishi, Thomas Gärtner, Pascal Welke

We investigate the distance function learned by message passing neural networks (MPNNs) in specific tasks, aiming to capture the functional distance between prediction targets that MPNNs implicitly learn. This contrasts with previous work, which links MPNN distances on arbitrary tasks to structural distances on graphs that ignore task-specific information. To address this gap, we distill the distance between MPNN embeddings into an interpretable graph distance. Our method uses optimal transport on the Weisfeiler Leman Labeling Tree (WILT), where the edge weights reveal subgraphs that strongly influence the distance between embeddings. This approach generalizes two well-known graph kernels and can be computed in linear time. Through extensive experiments, we demonstrate that MPNNs define the relative position of embeddings by focusing on a small set of subgraphs that are known to be functionally important in the domain.