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Structured Sparse Principal Components Analysis With the TV-Elastic Net Penalty
NeuroSpin, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France.
Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.ORCID iD: 0000-0001-7119-7646
Energy Transition Institute: VeDeCoM, 78 000 Versailles, France.
NeuroSpin, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France.
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2018 (English)In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 37, no 2, p. 396-407Article in journal (Refereed) Published
Abstract [en]

Principal component analysis (PCA) is an exploratory tool widely used in data analysis to uncover the dominant patterns of variability within a population. Despite its ability to represent a data set in a low-dimensional space, PCA’s interpretability remains limited. Indeed, the components produced by PCA are often noisy or exhibit no visually meaningful patterns. Furthermore, the fact that the components are usually non-sparse may also impede interpretation, unless arbitrary thresholding is applied. However, in neuroimaging, it is essential to uncover clinically interpretable phenotypic markers that would account for the main variability in the brain images of a population. Recently, some alternatives to the standard PCA approach, such as sparse PCA (SPCA), have been proposed, their aim being to limit the density of the components. Nonetheless, sparsity alone does not entirely solve the interpretability problem in neuroimaging, since it may yield scattered andunstable components. We hypothesized that the incorporation of prior information regarding the structure of the data may lead to improved relevance and interpretability of brain patterns. We therefore present a simple extension of the popular PCA framework that adds structured sparsity penalties on the loading vectors in order to identify the few stable regions in the brain images that capture most of the variability. Such structured sparsity can be obtained by combining, e.g., l1 and total variation (TV) penalties, where the TV regularization encodes information on the underlying structure of the data. This paper presents the structured SPCA (denoted SPCA-TV) optimization framework and its resolution. We demonstrate SPCA-TV’s effectiveness and versatility on three different data sets. It can be applied to any kind of structured data, such as, e.g., N-dimensional array images or meshes of cortical surfaces. The gains of SPCA-TV over unstructured approaches (such as SPCA and ElasticNet PCA) or structured approach (such as GraphNet PCA) are significant, since SPCA-TV reveals the variability within a data set in the form of intelligible brain patterns that are easier to interpret and more stable across different samples.

Place, publisher, year, edition, pages
IEEE, 2018. Vol. 37, no 2, p. 396-407
Keywords [en]
MRI, unsupervised machine learning, PCA, total variation
National Category
Computer and Information Sciences
Research subject
Computerized Image Analysis
Identifiers
URN: urn:nbn:se:umu:diva-145277DOI: 10.1109/TMI.2017.2749140ISI: 000424467000006PubMedID: 28880163OAI: oai:DiVA.org:umu-145277DiVA, id: diva2:1185830
Available from: 2018-02-26 Created: 2018-02-26 Last updated: 2018-06-09Bibliographically approved

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Löfstedt, Tommy

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