HSG-12M: A Large-Scale Benchmark of Spatial Multigraphs from the Energy Spectra of Non-Hermitian Crystals

AI is transforming scientific research by revealing new ways to understand complex physical systems, but its impact remains constrained by the lack of large, high-quality domain-specific datasets. A rich, largely untapped resource lies in non-Hermitian quantum physics, where the energy spectra of crystals form intricate geometries on the complex plane—termed as $\textit{Hamiltonian spectral graphs}$. Despite their significance as fingerprints for electronic behavior, their systematic study has been intractable due to the reliance on manual extraction. To unlock this potential, we introduce $\textbf{Poly2Graph}$ (https://github.com/sarinstein-yan/Poly2Graph): a high-performance, open-source pipeline that automates the mapping of 1-D crystal Hamiltonians to spectral graphs. Using this tool, we present $\textbf{HSG-12M}$ (https://github.com/sarinstein-yan/HSG-12M): a dataset containing 11.6 million static and 5.1 million dynamic Hamiltonian spectral graphs across 1401 characteristic-polynomial classes, distilled from 177 TB of spectral potential data. Crucially, HSG-12M is the first large-scale dataset of $\textit{spatial multigraphs}$—graphs embedded in a metric space where multiple geometrically distinct trajectories between two nodes are retained as separate edges. This simultaneously addresses a critical gap, as existing graph benchmarks overwhelmingly assume simple, non-spatial edges, discarding vital geometric information. Benchmarks with popular GNNs expose new challenges in learning spatial multi-edges at scale. Beyond its practical utility, we show that spectral graphs serve as universal topological fingerprints of polynomials, vectors, and matrices, forging a new algebra-to-graph link. HSG-12M lays the groundwork for data-driven scientific discovery in condensed matter physics, new opportunities in geometry-aware graph learning and beyond.