IDEAS home Printed from https://ideas.repec.org/a/bla/biomet/v77y2021i4p1397-1408.html
   My bibliography  Save this article

Histopathological imaging‐based cancer heterogeneity analysis via penalized fusion with model averaging

Author

Listed:
  • Baihua He
  • Tingyan Zhong
  • Jian Huang
  • Yanyan Liu
  • Qingzhao Zhang
  • Shuangge Ma

Abstract

Heterogeneity is a hallmark of cancer. For various cancer outcomes/phenotypes, supervised heterogeneity analysis has been conducted, leading to a deeper understanding of disease biology and customized clinical decisions. In the literature, such analysis has been oftentimes based on demographic, clinical, and omics measurements. Recent studies have shown that high‐dimensional histopathological imaging features contain valuable information on cancer outcomes. However, comparatively, heterogeneity analysis based on imaging features has been very limited. In this article, we conduct supervised cancer heterogeneity analysis using histopathological imaging features. The penalized fusion technique, which has notable advantages—such as greater flexibility—over the finite mixture modeling and other techniques, is adopted. A sparse penalization is further imposed to accommodate high dimensionality and select relevant imaging features. To improve computational feasibility and generate more reliable estimation, we employ model averaging. Computational and statistical properties of the proposed approach are carefully investigated. Simulation demonstrates its favorable performance. The analysis of The Cancer Genome Atlas (TCGA) data may provide a new way of defining/examining breast cancer heterogeneity.

Suggested Citation

  • Baihua He & Tingyan Zhong & Jian Huang & Yanyan Liu & Qingzhao Zhang & Shuangge Ma, 2021. "Histopathological imaging‐based cancer heterogeneity analysis via penalized fusion with model averaging," Biometrics, The International Biometric Society, vol. 77(4), pages 1397-1408, December.
    • Handle: RePEc:bla:biomet:v:77:y:2021:i:4:p:1397-1408
    DOI: 10.1111/biom.13357
    as

    Download full text from publisher

    File URL: https://doi.org/10.1111/biom.13357
    Download Restriction: no
    File URL: https://libkey.io/10.1111/biom.13357?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Robert Tibshirani & Michael Saunders & Saharon Rosset & Ji Zhu & Keith Knight, 2005. "Sparsity and smoothness via the fused lasso," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(1), pages 91-108, February.
    2. Hansheng Wang & Bo Li & Chenlei Leng, 2009. "Shrinkage tuning parameter selection with a diverging number of parameters," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 71(3), pages 671-683, June.
    3. Nicolas Städler & Peter Bühlmann & Sara Geer, 2010. "Rejoinder: ℓ 1 -penalization for mixture regression models," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 19(2), pages 280-285, August.
    4. Stefan Wager & Susan Athey, 2018. "Estimation and Inference of Heterogeneous Treatment Effects using Random Forests," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 113(523), pages 1228-1242, July.
    5. Xinyu Zhang & Guohua Zou & Hua Liang & Raymond J. Carroll, 2020. "Parsimonious Model Averaging With a Diverging Number of Parameters," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 115(530), pages 972-984, April.
    6. Michael S. Lawrence & Petar Stojanov & Paz Polak & Gregory V. Kryukov & Kristian Cibulskis & Andrey Sivachenko & Scott L. Carter & Chip Stewart & Craig H. Mermel & Steven A. Roberts & Adam Kiezun & Pe, 2013. "Mutational heterogeneity in cancer and the search for new cancer-associated genes," Nature, Nature, vol. 499(7457), pages 214-218, July.
    7. Nicolas Städler & Peter Bühlmann & Sara Geer, 2010. "ℓ 1 -penalization for mixture regression models," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 19(2), pages 209-256, August.
    8. Khalili, Abbas & Chen, Jiahua, 2007. "Variable Selection in Finite Mixture of Regression Models," Journal of the American Statistical Association, American Statistical Association, vol. 102, pages 1025-1038, September.
    9. Shujie Ma & Jian Huang, 2017. "A Concave Pairwise Fusion Approach to Subgroup Analysis," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 112(517), pages 410-423, January.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Sakyajit Bhattacharya & Paul McNicholas, 2014. "A LASSO-penalized BIC for mixture model selection," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 8(1), pages 45-61, March.
    2. Yang, Xinfeng & Yan, Xiaodong & Huang, Jian, 2019. "High-dimensional integrative analysis with homogeneity and sparsity recovery," Journal of Multivariate Analysis, Elsevier, vol. 174(C).
    3. Devijver, Emilie, 2017. "Joint rank and variable selection for parsimonious estimation in a high-dimensional finite mixture regression model," Journal of Multivariate Analysis, Elsevier, vol. 157(C), pages 1-13.
    4. Lu Tang & Ling Zhou & Peter X. K. Song, 2019. "Fusion learning algorithm to combine partially heterogeneous Cox models," Computational Statistics, Springer, vol. 34(1), pages 395-414, March.
    5. Mingyang Ren & Qingzhao Zhang & Sanguo Zhang & Tingyan Zhong & Jian Huang & Shuangge Ma, 2022. "Hierarchical cancer heterogeneity analysis based on histopathological imaging features," Biometrics, The International Biometric Society, vol. 78(4), pages 1579-1591, December.
    6. Ping Zeng & Yongyue Wei & Yang Zhao & Jin Liu & Liya Liu & Ruyang Zhang & Jianwei Gou & Shuiping Huang & Feng Chen, 2014. "Variable selection approach for zero-inflated count data via adaptive lasso," Journal of Applied Statistics, Taylor & Francis Journals, vol. 41(4), pages 879-894, April.
    7. Fei Wang & Lu Wang & Peter X.‐K. Song, 2016. "Fused lasso with the adaptation of parameter ordering in combining multiple studies with repeated measurements," Biometrics, The International Biometric Society, vol. 72(4), pages 1184-1193, December.
    8. Yan Li & Chun Yu & Yize Zhao & Weixin Yao & Robert H. Aseltine & Kun Chen, 2022. "Pursuing sources of heterogeneity in modeling clustered population," Biometrics, The International Biometric Society, vol. 78(2), pages 716-729, June.
    9. Shao, Lihui & Wu, Jiaqi & Zhang, Weiping & Chen, Yu, 2024. "Integrated subgroup identification from multi-source data," Computational Statistics & Data Analysis, Elsevier, vol. 193(C).
    10. Liu, Lili & Lin, Lu, 2019. "Subgroup analysis for heterogeneous additive partially linear models and its application to car sales data," Computational Statistics & Data Analysis, Elsevier, vol. 138(C), pages 239-259.
    11. Mehrabani, Ali, 2023. "Estimation and identification of latent group structures in panel data," Journal of Econometrics, Elsevier, vol. 235(2), pages 1464-1482.
    12. Ye He & Ling Zhou & Yingcun Xia & Huazhen Lin, 2023. "Center‐augmented ℓ2‐type regularization for subgroup learning," Biometrics, The International Biometric Society, vol. 79(3), pages 2157-2170, September.
    13. Hou, Zhaohan & Wang, Lei, 2024. "Heterogeneous quantile regression for longitudinal data with subgroup structures," Computational Statistics & Data Analysis, Elsevier, vol. 194(C).
    14. Lu Tang & Peter X.‐K. Song, 2021. "Poststratification fusion learning in longitudinal data analysis," Biometrics, The International Biometric Society, vol. 77(3), pages 914-928, September.
    15. Qifan Song & Guang Cheng, 2020. "Bayesian Fusion Estimation via t Shrinkage," Sankhya A: The Indian Journal of Statistics, Springer;Indian Statistical Institute, vol. 82(2), pages 353-385, August.
    16. Benjamin G. Stokell & Rajen D. Shah & Ryan J. Tibshirani, 2021. "Modelling high‐dimensional categorical data using nonconvex fusion penalties," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 83(3), pages 579-611, July.
    17. Shi, Zhentao & Huang, Jingyi, 2023. "Forward-selected panel data approach for program evaluation," Journal of Econometrics, Elsevier, vol. 234(2), pages 512-535.
    18. Lin, Fangzheng & Tang, Yanlin & Zhu, Huichen & Zhu, Zhongyi, 2022. "Spatially clustered varying coefficient model," Journal of Multivariate Analysis, Elsevier, vol. 192(C).
    19. Gerhard Tutz & Margret-Ruth Oelker, 2017. "Modelling Clustered Heterogeneity: Fixed Effects, Random Effects and Mixtures," International Statistical Review, International Statistical Institute, vol. 85(2), pages 204-227, August.
    20. Pei, Youquan & Peng, Heng & Xu, Jinfeng, 2024. "A latent class Cox model for heterogeneous time-to-event data," Journal of Econometrics, Elsevier, vol. 239(2).

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bla:biomet:v:77:y:2021:i:4:p:1397-1408. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Wiley Content Delivery (email available below). General contact details of provider: http://www.blackwellpublishing.com/journal.asp?ref=0006-341X .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.