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JOINT AND INDIVIDUAL ANALYSIS OF BREAST CANCER HISTOLOGIC IMAGES AND GENOMIC COVARIATES.

Publication ,  Journal Article
Carmichael, I; Calhoun, BC; Hoadley, KA; Troester, MA; Geradts, J; Couture, HD; Olsson, L; Perou, CM; Niethammer, M; Hannig, J; Marron, JS
Published in: Ann Appl Stat
December 2021

The two main approaches in the study of breast cancer are histopathology (analyzing visual characteristics of tumors) and genomics. While both histopathology and genomics are fundamental to cancer research, the connections between these fields have been relatively superficial. We bridge this gap by investigating the Carolina Breast Cancer Study through the development of an integrative, exploratory analysis framework. Our analysis gives insights - some known, some novel - that are engaging to both pathologists and geneticists. Our analysis framework is based on Angle-based Joint and Individual Variation Explained (AJIVE) for statistical data integration and exploits Convolutional Neural Networks (CNNs) as a powerful, automatic method for image feature extraction. CNNs raise interpretability issues 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.

Duke Scholars

Published In

Ann Appl Stat

DOI

ISSN

1932-6157

Publication Date

December 2021

Volume

15

Issue

4

Start / End Page

1697 / 1722

Location

United States

Related Subject Headings

  • Statistics & Probability
  • 4905 Statistics
  • 1403 Econometrics
  • 0104 Statistics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Carmichael, I., Calhoun, B. C., Hoadley, K. A., Troester, M. A., Geradts, J., Couture, H. D., … Marron, J. S. (2021). JOINT AND INDIVIDUAL ANALYSIS OF BREAST CANCER HISTOLOGIC IMAGES AND GENOMIC COVARIATES. Ann Appl Stat, 15(4), 1697–1722. https://doi.org/10.1214/20-aoas1433
Carmichael, Iain, Benjamin C. Calhoun, Katherine A. Hoadley, Melissa A. Troester, Joseph Geradts, Heather D. Couture, Linnea Olsson, et al. “JOINT AND INDIVIDUAL ANALYSIS OF BREAST CANCER HISTOLOGIC IMAGES AND GENOMIC COVARIATES.Ann Appl Stat 15, no. 4 (December 2021): 1697–1722. https://doi.org/10.1214/20-aoas1433.
Carmichael I, Calhoun BC, Hoadley KA, Troester MA, Geradts J, Couture HD, et al. JOINT AND INDIVIDUAL ANALYSIS OF BREAST CANCER HISTOLOGIC IMAGES AND GENOMIC COVARIATES. Ann Appl Stat. 2021 Dec;15(4):1697–722.
Carmichael, Iain, et al. “JOINT AND INDIVIDUAL ANALYSIS OF BREAST CANCER HISTOLOGIC IMAGES AND GENOMIC COVARIATES.Ann Appl Stat, vol. 15, no. 4, Dec. 2021, pp. 1697–722. Pubmed, doi:10.1214/20-aoas1433.
Carmichael I, Calhoun BC, Hoadley KA, Troester MA, Geradts J, Couture HD, Olsson L, Perou CM, Niethammer M, Hannig J, Marron JS. JOINT AND INDIVIDUAL ANALYSIS OF BREAST CANCER HISTOLOGIC IMAGES AND GENOMIC COVARIATES. Ann Appl Stat. 2021 Dec;15(4):1697–1722.

Published In

Ann Appl Stat

DOI

ISSN

1932-6157

Publication Date

December 2021

Volume

15

Issue

4

Start / End Page

1697 / 1722

Location

United States

Related Subject Headings

  • Statistics & Probability
  • 4905 Statistics
  • 1403 Econometrics
  • 0104 Statistics