Spectral symmetry fingerprints in equivariant representations

Molecular representations are essential for the evaluation of molecular similarity and the development of structure-property relationships. Despite the known importance of 3D structure to determine chemical and physical properties, the most widely used molecular fingerprints encode only two-dimensional connectivity. Such representations fail to distinguish similar but distinct stereoisomers and conformers. Alternative 3D methods are typically defined pairwise, making their application to large chemical spaces prohibitive, while deep learning embeddings are expressive but uninterpretable and limited by their training data diversity. Here, we introduce novel physics-inspired molecular fingerprints based on principles from spectral graph theory. We represent molecules as a complete graph in 3D space, with edge weights encoding heuristic physical interactions. Eigenvalue decomposition of the resulting graph Laplacian matrix results in a computationally efficient fixed-length chemical fingerprint that encodes 3D structure while obeying necessary physical symmetries of permutation and E(3) invariance. Spectral fingerprints differentiate between unique molecular structures with identical 2D connectivity, overcoming a limitation of 2D descriptors, while maintaining the low computational cost needed for efficient screening of vast chemical spaces. We evaluate our fingerprints with community detection algorithms and observe strong performance against representative baselines across datasets from organic, inorganic, biological, reticular, and reaction chemistry. Nearest-neighbor property estimation and applicability domain analyses reveal the utility of our molecular representation in machine learning and cheminformatics. We anticipate that spectral fingerprints will serve as generalizable, interpretable, and efficient measures of chemical similarity that incorporate 3D information at minimal cost.

Symmetry is everywhere in nature and society. Geometric deep learning exploits symmetries in data to improve the performance and efficiency of deep learning systems. In this paper, we extend geometric deep learning to utilize richer symmetry structures. Specifically, we develop order-equivariant neural networks (OENN), which generalize standard graph message passing and sheaf neural networks via the theory of equivariant bundles over face posets (face categories). We (i) characterize all linear order-equivariant maps, (ii) build OENN layers, and (iii) prove universal approximation theorems (UATs) for continuous order-equivariant maps, which are new results even when restricted to sheaf neural networks (for which no UAT was known before). We illustrate the framework on graph and sheaf models. Our results can also be seen as extending the known UAT for graph neural networks to a more general setting that subsumes sheaf neural networks as well. In addition, we show that OENN can be extended further to CENN, Category-Equivariant Neural Network, which gives the general form of equivariant neural networks as well as of equivariant universal approximation theorems, allowing us to leverage categorical symmetry in data (e.g., non-invertible symmetries on multiple objects with compositional relations on those symmetries).

Continuous symmetries are fundamental to many scientific and learning problems, yet they are often unknown a priori. Existing symmetry discovery approaches typically search directly in the space of transformation generators or rely on learned augmentation schemes. We propose a fundamentally different perspective based on spectral structure. We introduce a framework for discovering continuous one-parameter subgroups using the Generalized Fourier Transform (GFT). Our central observation is that invariance to a subgroup induces structured sparsity in the spectral decomposition of a function across irreducible representations. Instead of optimizing over generators, we detect symmetries by identifying this induced sparsity pattern in the spectral domain. We develop symmetry detection procedures on maximal tori, where the GFT reduces to multi-dimensional Fourier analysis through their irreducible representations. Across structured tasks, including the double pendulum and top quark tagging, we demonstrate that spectral sparsity reliably reveals one-parameter symmetries. These results position spectral analysis as a principled and interpretable alternative to generator-based symmetry discovery.