Learning Probabilistic Structural Representation for Biomedical Image Segmentation
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Accurate segmentation of various fine-scale structures from biomedical images is a very important yet challenging problem. Existing methods use topological information as an additional training loss, but are ultimately learning a pixel-wise representation. In this paper, we propose the first deep learning method to learn a structural representation. We use discrete Morse theory and persistent homology to construct an one-parameter family of structures as the structural representation space. Furthermore, we learn a probabilistic model that can do inference tasks on such a structural representation space. We empirically demonstrate the strength of our method, i.e., generating true structures rather than pixel-maps with better topological integrity, and facilitating a human-in-the-loop annotation pipeline using the sampling of structures and structure-aware uncertainty.
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