arXiv:2606.08258v2 Announce Type: replace Abstract: Understanding and comparing structures in scalar fields is a central challenge in scientific visualization, with applications ranging from feature analysis to temporal and structural comparison. The Morse-Smale (MS) complex provides a natural representation by decomposing a scalar field into regions induced by gradient flow. However, existing approaches typically rely on graph-based representations, matching critical points without explicitly establishing correspondences between regions. In this work, we represent the MS complex as a hypergraph, where critical points form nodes and regions define hyperedges. We introduce MS-COOT, a co-optimal transport distance that jointly computes correspondences between critical points and regions. This formulation enables explicit region-to-region matching within a distance-based framework, allowing identification of region-level events such as splitting and merging. We instantiate this framework with domain-specific components, including a hypernetwork function encoding relationships between critical points and regions, persistence-based probability measures, and a sample cost term that incorporates critical point attributes. We evaluate MS-COOT on datasets spanning 2D simulations, 3D surface meshes, and volumetric data. Our results show that MS-COOT provides distinct characterization of certain region-level structural changes compared to graph-based distances, achieves competitive accuracy in shape classification, and improves classification of simulation parameter settings in a 3D ensemble.