title: Stacked Predictive Sparse Decomposition for Classification of Histology Sections.
abstract: Image-based classification of histology sections, in terms of distinct components (e.g., tumor, stroma, normal), provides a series of indices for histology composition (e.g., the percentage of each distinct components in histology sections), and enables the study of nuclear properties within each component. Furthermore, the study of these indices, constructed from each whole slide image in a large cohort, has the potential to provide predictive models of clinical outcome. For example, correlations can be established between the constructed indices and the patients' survival information at cohort level, which is a fundamental step towards personalized medicine. However, performance of the existing techniques is hindered as a result of large technical variations (e.g., variations of color/textures in tissue images due to non-standard experimental protocols) and biological heterogeneities (e.g., cell type, cell state) that are always present in a large cohort. We propose a system that automatically learns a series of dictionary elements for representing the underlying spatial distribution using stacked predictive sparse decomposition. The learned representation is then fed into the spatial pyramid matching framework with a linear support vector machine classifier. The system has been evaluated for classification of distinct histological components for two cohorts of tumor types. Throughput has been increased by using of graphical processing unit (GPU), and evaluation indicates a superior performance results, compared with previous research.
authors.affiliation: Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
authors.forename: Hang
authors.initials: H
authors.lastname: Chang
authors.affiliation: Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
authors.forename: Yin
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Center for Comparative Medicine, UC Davis, Davis, CA, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Borowsky
authors.affiliation: ECE Department, University of Delaware, Newark, DE, USA.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Barner
authors.affiliation: Center for Spatial Systems Biomedicine, Oregon Health Sciences University, Portland, ON, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Spellman
authors.affiliation: Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
authors.forename: Bahram
authors.initials: B
authors.lastname: Parvin
keywords: Classification; Sparse coding; Tissue histology; Unsupervised feature learning