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Life sciences · Preprint
arXiv · September 29, 2026
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Topological structures such as simplicial complexes, hypergraphs, and cell complexes extend standard graph models by modeling higher-order relationships. These structures appear in many modern datasets and require specialized methods for generating meaningful embeddings. In this paper, we introduce TopoEmbedX, a unified framework for embedding a wide range of topological domains into Euclidean spaces. The package brings together several existing topological embedding algorithms---DeepCell, Cell2Vec, CellDiff2Vec, HOLE, and HOGLEE---and introduces five new algorithms: ComplexNetMF, ComplexRep, ComplexRandNE, ComplexWalklets, and ComplexHeat. These algorithms extend well-known graph embedding techniques to higher-order settings using the augmented Hasse graph of a topological domain. TopoEmbedX provides a clear, consistent, and easy-to-use framework for topological representation learning. Experiments show that the embeddings generated by TopoEmbedX support tasks such as classification and regression across multidimensional data.