Joint and individual analysis of breast cancer histologic images and genomic covariates

Iain Carmichael; Benjamin C. Calhoun; Katherine A. Hoadley; Melissa A. Troester; Joseph Geradts; Heather D. Couture; Linnea Olsson; Charles M. Perou; Marc Niethammer; Jan Hannig; J. S. Marron

arXiv · 1912.00434

Joint and individual analysis of breast cancer histologic images and genomic covariates

Iain Carmichael·Benjamin C. Calhoun·Katherine A. Hoadley·Melissa A. Troester·Joseph Geradts·Heather D. Couture·Linnea Olsson·Charles M. Perou·Marc Niethammer·Jan Hannig·J. S. Marron

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Abstract

A key challenge in modern data analysis is understanding connections between complex and differing modalities of data. For example, two of the main approaches to the study of breast cancer are histopathology (analyzing visual characteristics of tumors) and genetics. While histopathology is the gold standard for diagnostics and there have been many recent breakthroughs in genetics, there is little overlap between these two fields. We aim to bridge this gap by developing methods based on Angle-based Joint and Individual Variation Explained (AJIVE) to directly explore similarities and differences between these two modalities. Our approach exploits Convolutional Neural Networks (CNNs) as a powerful, automatic method for image feature extraction to address some of the challenges presented by statistical analysis of histopathology image data. CNNs raise issues of interpretability that we address by developing novel methods to explore visual modes of variation captured by statistical algorithms (e.g. PCA or AJIVE) applied to CNN features. Our results provide many interpretable connections and contrasts between histopathology and genetics.

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Iain Carmichael, Benjamin C. Calhoun, Katherine A. Hoadley, Melissa A. Troester, Joseph Geradts, Heather D. Couture, Linnea Olsson, Charles M. Perou, Marc Niethammer, Jan Hannig, J. S. Marron. 2019-12-01. Joint and individual analysis of breast cancer histologic images and genomic covariates. https://arxiv.org/abs/1912.00434

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