Cell Anomaly Localisation using Structured Uncertainty Prediction NetworksDownload PDF

Published: 28 Feb 2022, Last Modified: 16 May 2023MIDL 2022Readers: Everyone
Keywords: Generative models, variational autoencoders, out-of-distribution detection, structured uncertainty
Abstract: This paper proposes an unsupervised approach to anomaly detection in bright-field or fluorescence cell microscopy, where our goal is to localise malaria parasites. This is achieved by building a generative model (a variational autoencoder) that describes healthy cell images, where we additionally model the structure of the predicted image uncertainty, rather than assuming pixelwise independence in the likelihood function. This provides a “whitened” residual representation, where the anticipated structured mistakes by the generative model are reduced, but distinctive structures that did not occur in the training distribution, e.g. parasites are highlighted. We employ the recently published Structured Uncertainty Prediction Networks approach to enable tractable learning of the uncertainty structure. Here, the residual covariance matrix is efficiently approximated using a sparse Cholesky parameterisation. We demonstrate that our proposed approach is more effective for detecting real and synthetic structured image perturbations compared to diagonal Gaussian likelihoods.
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Paper Type: methodological development
Primary Subject Area: Unsupervised Learning and Representation Learning
Secondary Subject Area: Uncertainty Estimation
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Code And Data: The repository will be made public once the dataset is uploaded and some cleanup is finished at https://github.com/boykovdn/unsupervised_cells_supn (a few weeks' time).
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