Stacked Predictive Sparse Coding for Classification of Distinct Regions of Tumor Histopathology.
Image-based classification of tissue histology, in terms of distinct histopathology (e.g., tumor or necrosis regions), provides a series of indices for tumor composition. Furthermore, aggregation of these indices from each whole slide image (WSI) in a large cohort can provide predictive models of clinical outcome. However, the performance of the existing techniques is hindered as a result of large technical variations (e.g., fixation, staining) and biological heterogeneities (e.g., cell type, cell state) that are always present in a large cohort. We suggest that, compared with human engineered features widely adopted in existing systems, unsupervised feature learning is more tolerant to batch effect (e.g., technical variations associated with sample preparation) and pertinent features can be learned without user intervention. This leads to a novel approach for classification of tissue histology based on unsupervised feature learning and spatial pyramid matching (SPM), which utilize sparse tissue morphometric signatures at various locations and scales. This approach has been evaluated on two distinct datasets consisting of different tumor types collected from The Cancer Genome Atlas (TCGA), and the experimental results indicate that the proposed approach is (i) extensible to different tumor types; (ii) robust in the presence of wide technical variations and biological heterogeneities; and (iii) scalable with varying training sample sizes.
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A.
Hang
H
Chang
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A.
Yin
Y
Zhou
Center for Spatial Systems Biomedicine, Oregon Health Sciences University, Portland, Oregon, U.S.A.
Paul
P
Spellman
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A.
Bahram
B
Parvin