IDEAS home Printed from https://ideas.repec.org/a/bla/biomet/v79y2023i4p3485-3496.html
   My bibliography  Save this article

Multiresolution categorical regression for interpretable cell‐type annotation

Author

Listed:
  • Aaron J. Molstad
  • Keshav Motwani

Abstract

In many categorical response regression applications, the response categories admit a multiresolution structure. That is, subsets of the response categories may naturally be combined into coarser response categories. In such applications, practitioners are often interested in estimating the resolution at which a predictor affects the response category probabilities. In this paper, we propose a method for fitting the multinomial logistic regression model in high dimensions that addresses this problem in a unified and data‐driven way. Our method allows practitioners to identify which predictors distinguish between coarse categories but not fine categories, which predictors distinguish between fine categories, and which predictors are irrelevant. For model fitting, we propose a scalable algorithm that can be applied when the coarse categories are defined by either overlapping or nonoverlapping sets of fine categories. Statistical properties of our method reveal that it can take advantage of this multiresolution structure in a way existing estimators cannot. We use our method to model cell‐type probabilities as a function of a cell's gene expression profile (i.e., cell‐type annotation). Our fitted model provides novel biological insights which may be useful for future automated and manual cell‐type annotation methodology.

Suggested Citation

  • Aaron J. Molstad & Keshav Motwani, 2023. "Multiresolution categorical regression for interpretable cell‐type annotation," Biometrics, The International Biometric Society, vol. 79(4), pages 3485-3496, December.
  • Handle: RePEc:bla:biomet:v:79:y:2023:i:4:p:3485-3496
    DOI: 10.1111/biom.13926
    as

    Download full text from publisher

    File URL: https://doi.org/10.1111/biom.13926
    Download Restriction: no

    File URL: https://libkey.io/10.1111/biom.13926?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. Nibbering, Didier & Hastie, Trevor J., 2022. "Multiclass-penalized logistic regression," Computational Statistics & Data Analysis, Elsevier, vol. 169(C).
    2. Xiaohan Yan & Jacob Bien, 2021. "Rare Feature Selection in High Dimensions," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 116(534), pages 887-900, April.
    3. Aaron J. Molstad & Adam J. Rothman, 2023. "A Likelihood-Based Approach for Multivariate Categorical Response Regression in High Dimensions," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 118(542), pages 1402-1414, April.
    4. Bianca Dumitrascu & Soledad Villar & Dustin G. Mixon & Barbara E. Engelhardt, 2021. "Optimal marker gene selection for cell type discrimination in single cell analyses," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    5. Ming Yuan & Yi Lin, 2006. "Model selection and estimation in regression with grouped variables," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 68(1), pages 49-67, February.
    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. Yi Zhao & Bingkai Wang & Chin‐Fu Liu & Andreia V. Faria & Michael I. Miller & Brian S. Caffo & Xi Luo, 2023. "Identifying brain hierarchical structures associated with Alzheimer's disease using a regularized regression method with tree predictors," Biometrics, The International Biometric Society, vol. 79(3), pages 2333-2345, September.
    2. Tutz, Gerhard & Pößnecker, Wolfgang & Uhlmann, Lorenz, 2015. "Variable selection in general multinomial logit models," Computational Statistics & Data Analysis, Elsevier, vol. 82(C), pages 207-222.
    3. Jun Yan & Jian Huang, 2012. "Model Selection for Cox Models with Time-Varying Coefficients," Biometrics, The International Biometric Society, vol. 68(2), pages 419-428, June.
    4. Ye, Ya-Fen & Shao, Yuan-Hai & Deng, Nai-Yang & Li, Chun-Na & Hua, Xiang-Yu, 2017. "Robust Lp-norm least squares support vector regression with feature selection," Applied Mathematics and Computation, Elsevier, vol. 305(C), pages 32-52.
    5. Guillaume Sagnol & Edouard Pauwels, 2019. "An unexpected connection between Bayes A-optimal designs and the group lasso," Statistical Papers, Springer, vol. 60(2), pages 565-584, April.
    6. Bakalli, Gaetan & Guerrier, Stéphane & Scaillet, Olivier, 2023. "A penalized two-pass regression to predict stock returns with time-varying risk premia," Journal of Econometrics, Elsevier, vol. 237(2).
    7. Shuichi Kawano, 2014. "Selection of tuning parameters in bridge regression models via Bayesian information criterion," Statistical Papers, Springer, vol. 55(4), pages 1207-1223, November.
    8. Peng, Heng & Lu, Ying, 2012. "Model selection in linear mixed effect models," Journal of Multivariate Analysis, Elsevier, vol. 109(C), pages 109-129.
    9. Yize Zhao & Matthias Chung & Brent A. Johnson & Carlos S. Moreno & Qi Long, 2016. "Hierarchical Feature Selection Incorporating Known and Novel Biological Information: Identifying Genomic Features Related to Prostate Cancer Recurrence," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(516), pages 1427-1439, October.
    10. G. Aneiros & P. Vieu, 2016. "Sparse nonparametric model for regression with functional covariate," Journal of Nonparametric Statistics, Taylor & Francis Journals, vol. 28(4), pages 839-859, October.
    11. Wongsa-art, Pipat & Kim, Namhyun & Xia, Yingcun & Moscone, Francesco, 2024. "Varying coefficient panel data models and methods under correlated error components: Application to disparities in mental health services in England," Regional Science and Urban Economics, Elsevier, vol. 106(C).
    12. Dong, C. & Li, S., 2021. "Specification Lasso and an Application in Financial Markets," Cambridge Working Papers in Economics 2139, Faculty of Economics, University of Cambridge.
    13. Lam, Clifford, 2008. "Estimation of large precision matrices through block penalization," LSE Research Online Documents on Economics 31543, London School of Economics and Political Science, LSE Library.
    14. Weiyang Ding & Michael K. Ng & Wenxing Zhang, 2024. "A generalized alternating direction implicit method for consensus optimization: application to distributed sparse logistic regression," Journal of Global Optimization, Springer, vol. 90(3), pages 727-753, November.
    15. Gregory Vaughan & Robert Aseltine & Kun Chen & Jun Yan, 2017. "Stagewise generalized estimating equations with grouped variables," Biometrics, The International Biometric Society, vol. 73(4), pages 1332-1342, December.
    16. Pradeep Ravikumar & John Lafferty & Han Liu & Larry Wasserman, 2009. "Sparse additive models," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 71(5), pages 1009-1030, November.
    17. Yucheng Yang & Zhong Zheng & Weinan E, 2020. "Interpretable Neural Networks for Panel Data Analysis in Economics," Papers 2010.05311, arXiv.org, revised Nov 2020.
    18. 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.
    19. Zhang, Tao & Zhang, Qingzhao & Wang, Qihua, 2014. "Model detection for functional polynomial regression," Computational Statistics & Data Analysis, Elsevier, vol. 70(C), pages 183-197.
    20. Madeleine Cule & Richard Samworth & Michael Stewart, 2010. "Maximum likelihood estimation of a multi‐dimensional log‐concave density," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(5), pages 545-607, November.

    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:79:y:2023:i:4:p:3485-3496. 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.