Work

A Topological Loss Function for Deep-Learning Based Image Segmentation Using Persistent Homology

Year: 2020

Type: article

Abstract: We introduce a method for training neural networks to perform image or volume segmentation in which prior knowledge about the topology of the segmented object can be explicitly provided and then incorporated into the training process. By using the differentiable properties of persistent homology, a concept used in topological data analysis, we can specify the desired topology of segmented objects in terms of their Betti numbers and then drive the proposed segmentations to contain the specified topological features. Importantly this process does not require any ground-truth labels, just prior knowledge of the topology of the structure being segmented. We demonstrate our approach in four experiments: one on MNIST image denoising and digit recognition, one on left ventricular myocardium segmentation from magnetic resonance imaging data from the UK Biobank, one on the ACDC public challenge dataset and one on placenta segmentation from 3-D ultrasound. We find that embedding explicit prior knowledge in neural network segmentation tasks is most beneficial when the segmentation task is especially challenging and that it can be used in either a semi-supervised or post-processing context to extract a useful training gradient from images without pixelwise labels.

Source: IEEE Transactions on Pattern Analysis and Machine Intelligence

DOI: 10.1109/tpami.2020.3013679

Authors: James R. Clough, Nicholas Byrne, Ilkay Oksuz, Veronika A. Zimmer, Julia A. Schnabel, Andrew P. King

Institutions: King's College London, Istanbul Technical University

Language: English

Topic: Topological and Geometric Data Analysis

Subfield: Computational Theory and Mathematics

Field: Computer Science

Domain: Physical Sciences

Open Access status: hybrid

Estimated APC paid: $2,045