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Life sciences · Preprint
arXiv · September 28, 2026
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Embedding structured objects into Euclidean spaces has enabled a wide range of successful machine learning applications. Such objects include words, documents, image patches, time series, and graph nodes. In contrast, embedding entire graphs remains a challenging problem. Existing methods either sustain the original order of the graph nodes or match the output nodes to the input ones, both of which create scalability issues. In this work, we propose a graph representation as a cloud of hyperballs, which allows us to define a specific, typically unique, node ordering. Based on this representation, we propose GeoGAE, an autoencoder, in which the Transformer encoder translates a hyperball cloud into a graph-level embedding, and the Transformer decoder translates the graph-level embedding back into the graph. This formulation enables the model to capture both the global graph structure and local relational patterns. We evaluate our method on multiple graph datasets, spanning various domains. The results demonstrate effectiveness of our method in encoding and reconstructing graphs from their embeddings.