IDEAS home Printed from https://ideas.repec.org/a/spr/advdac/v16y2022i2d10.1007_s11634-021-00465-4.html
   My bibliography  Save this article

Robust logistic zero-sum regression for microbiome compositional data

Author

Listed:
  • G. S. Monti

    (University of Milano-Bicocca)

  • P. Filzmoser

    (Vienna University of Technology)

Abstract

We introduce the Robust Logistic Zero-Sum Regression (RobLZS) estimator, which can be used for a two-class problem with high-dimensional compositional covariates. Since the log-contrast model is employed, the estimator is able to do feature selection among the compositional parts. The proposed method attains robustness by minimizing a trimmed sum of deviances. A comparison of the performance of the RobLZS estimator with a non-robust counterpart and with other sparse logistic regression estimators is conducted via Monte Carlo simulation studies. Two microbiome data applications are considered to investigate the stability of the estimators to the presence of outliers. Robust Logistic Zero-Sum Regression is available as an R package that can be downloaded at https://github.com/giannamonti/RobZS .

Suggested Citation

  • G. S. Monti & P. Filzmoser, 2022. "Robust logistic zero-sum regression for microbiome compositional data," 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. 16(2), pages 301-324, June.
    • Handle: RePEc:spr:advdac:v:16:y:2022:i:2:d:10.1007_s11634-021-00465-4
    DOI: 10.1007/s11634-021-00465-4
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s11634-021-00465-4
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1007/s11634-021-00465-4?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Junjie Qin & Ruiqiang Li & Jeroen Raes & Manimozhiyan Arumugam & Kristoffer Solvsten Burgdorf & Chaysavanh Manichanh & Trine Nielsen & Nicolas Pons & Florence Levenez & Takuji Yamada & Daniel R. Mende, 2010. "A human gut microbial gene catalogue established by metagenomic sequencing," Nature, Nature, vol. 464(7285), pages 59-65, March.
    2. N. Neykov & P. Filzmoser & P. Neytchev, 2014. "Erratum to: Ultrahigh dimensional variable selection through the penalized maximum trimmed likelihood estimator," Statistical Papers, Springer, vol. 55(3), pages 917-918, August.
    3. Croux, Christophe & Haesbroeck, Gentiane, 2003. "Implementing the Bianco and Yohai estimator for logistic regression," Computational Statistics & Data Analysis, Elsevier, vol. 44(1-2), pages 273-295, October.
    4. Sun, Hongwei & Cui, Yuehua & Gao, Qian & Wang, Tong, 2020. "Trimmed LASSO regression estimator for binary response data," Statistics & Probability Letters, Elsevier, vol. 159(C).
    5. Stephen Bates & Robert Tibshirani, 2019. "Log‐ratio lasso: Scalable, sparse estimation for log‐ratio models," Biometrics, The International Biometric Society, vol. 75(2), pages 613-624, June.
    6. Friedman, Jerome H. & Hastie, Trevor & Tibshirani, Rob, 2010. "Regularization Paths for Generalized Linear Models via Coordinate Descent," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 33(i01).
    7. Mei Dong & Longhai Li & Man Chen & Anthony Kusalik & Wei Xu, 2020. "Predictive analysis methods for human microbiome data with application to Parkinson’s disease," PLOS ONE, Public Library of Science, vol. 15(8), pages 1-18, August.
    8. N. Neykov & P. Filzmoser & P. Neytchev, 2014. "Ultrahigh dimensional variable selection through the penalized maximum trimmed likelihood estimator," Statistical Papers, Springer, vol. 55(1), pages 187-207, February.
    9. Wei Lin & Pixu Shi & Rui Feng & Hongzhe Li, 2014. "Variable selection in regression with compositional covariates," Biometrika, Biometrika Trust, vol. 101(4), pages 785-797.
    10. Jiarui Lu & Pixu Shi & Hongzhe Li, 2019. "Generalized linear models with linear constraints for microbiome compositional data," Biometrics, The International Biometric Society, vol. 75(1), pages 235-244, March.
    11. Hui Zou & Trevor Hastie, 2005. "Addendum: Regularization and variable selection via the elastic net," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(5), pages 768-768, November.
    12. Hui Zou & Trevor Hastie, 2005. "Regularization and variable selection via the elastic net," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(2), pages 301-320, April.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Jordi Saperas-Riera & Glòria Mateu-Figueras & Josep Antoni Martín-Fernández, 2024. "L p -Norm for Compositional Data: Exploring the CoDa L 1 -Norm in Penalised Regression," Mathematics, MDPI, vol. 12(9), pages 1-16, May.

    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. Jan Pablo Burgard & Joscha Krause & Dennis Kreber & Domingo Morales, 2021. "The generalized equivalence of regularization and min–max robustification in linear mixed models," Statistical Papers, Springer, vol. 62(6), pages 2857-2883, December.
    2. Mishra, Aditya & Müller, Christian L., 2022. "Robust regression with compositional covariates," Computational Statistics & Data Analysis, Elsevier, vol. 165(C).
    3. Lingjing Jiang & Niina Haiminen & Anna‐Paola Carrieri & Shi Huang & Yoshiki Vázquez‐Baeza & Laxmi Parida & Ho‐Cheol Kim & Austin D. Swafford & Rob Knight & Loki Natarajan, 2022. "Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data," Biometrics, The International Biometric Society, vol. 78(3), pages 1155-1167, September.
    4. Ning Li & Hu Yang, 2021. "Nonnegative estimation and variable selection under minimax concave penalty for sparse high-dimensional linear regression models," Statistical Papers, Springer, vol. 62(2), pages 661-680, April.
    5. Luca Insolia & Ana Kenney & Martina Calovi & Francesca Chiaromonte, 2021. "Robust Variable Selection with Optimality Guarantees for High-Dimensional Logistic Regression," Stats, MDPI, vol. 4(3), pages 1-17, August.
    6. Dries Cornilly & Lise Tubex & Stefan Van Aelst & Tim Verdonck, 2024. "Robust and sparse logistic regression," 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. 18(3), pages 663-679, September.
    7. 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.
    8. Mkhadri, Abdallah & Ouhourane, Mohamed, 2013. "An extended variable inclusion and shrinkage algorithm for correlated variables," Computational Statistics & Data Analysis, Elsevier, vol. 57(1), pages 631-644.
    9. Chuliá, Helena & Garrón, Ignacio & Uribe, Jorge M., 2024. "Daily growth at risk: Financial or real drivers? The answer is not always the same," International Journal of Forecasting, Elsevier, vol. 40(2), pages 762-776.
    10. Christopher J Greenwood & George J Youssef & Primrose Letcher & Jacqui A Macdonald & Lauryn J Hagg & Ann Sanson & Jenn Mcintosh & Delyse M Hutchinson & John W Toumbourou & Matthew Fuller-Tyszkiewicz &, 2020. "A comparison of penalised regression methods for informing the selection of predictive markers," PLOS ONE, Public Library of Science, vol. 15(11), pages 1-14, November.
    11. Gustavo A. Alonso-Silverio & Víctor Francisco-García & Iris P. Guzmán-Guzmán & Elías Ventura-Molina & Antonio Alarcón-Paredes, 2021. "Toward Non-Invasive Estimation of Blood Glucose Concentration: A Comparative Performance," Mathematics, MDPI, vol. 9(20), pages 1-13, October.
    12. Christopher Kath & Florian Ziel, 2018. "The value of forecasts: Quantifying the economic gains of accurate quarter-hourly electricity price forecasts," Papers 1811.08604, arXiv.org.
    13. Gurgul Henryk & Machno Artur, 2017. "Trade Pattern on Warsaw Stock Exchange and Prediction of Number of Trades," Statistics in Transition New Series, Statistics Poland, vol. 18(1), pages 91-114, March.
    14. Michael Funke & Kadri Männasoo & Helery Tasane, 2023. "Regional Economic Impacts of the Øresund Cross-Border Fixed Link: Cui Bono?," CESifo Working Paper Series 10557, CESifo.
    15. Zichen Zhang & Ye Eun Bae & Jonathan R. Bradley & Lang Wu & Chong Wu, 2022. "SUMMIT: An integrative approach for better transcriptomic data imputation improves causal gene identification," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    16. Štefan Lyócsa & Petra Vašaničová & Branka Hadji Misheva & Marko Dávid Vateha, 2022. "Default or profit scoring credit systems? Evidence from European and US peer-to-peer lending markets," Financial Innovation, Springer;Southwestern University of Finance and Economics, vol. 8(1), pages 1-21, December.
    17. Peter Bühlmann & Jacopo Mandozzi, 2014. "High-dimensional variable screening and bias in subsequent inference, with an empirical comparison," Computational Statistics, Springer, vol. 29(3), pages 407-430, June.
    18. Capanu, Marinela & Giurcanu, Mihai & Begg, Colin B. & Gönen, Mithat, 2023. "Subsampling based variable selection for generalized linear models," Computational Statistics & Data Analysis, Elsevier, vol. 184(C).
    19. Abhinav Kaushik & Diane Dunham & Xiaorui Han & Evan Do & Sandra Andorf & Sheena Gupta & Andrea Fernandes & Laurie Elizabeth Kost & Sayantani B. Sindher & Wong Yu & Mindy Tsai & Robert Tibshirani & Sco, 2022. "CD8+ T cell differentiation status correlates with the feasibility of sustained unresponsiveness following oral immunotherapy," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    20. Tomáš Plíhal, 2021. "Scheduled macroeconomic news announcements and Forex volatility forecasting," Journal of Forecasting, John Wiley & Sons, Ltd., vol. 40(8), pages 1379-1397, December.

    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:spr:advdac:v:16:y:2022:i:2:d:10.1007_s11634-021-00465-4. 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: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    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.