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Microarray Missing Value Imputation: A Regularized Local Learning Method
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2019 (English)In: IEEE/ACM Transactions on Computational Biology & Bioinformatics, ISSN 1545-5963, E-ISSN 1557-9964, Vol. 16, no 3, p. 980-993Article in journal (Refereed) Published
Abstract [en]

Microarray experiments on gene expression inevitably generate missing values, which impedes further downstream biological analysis. Therefore, it is key to estimate the missing values accurately. Most of the existing imputation methods tend to suffer from the over-fitting problem. In this study, we propose two regularized local learning methods for microarray missing value imputation. Motivated by the grouping effect of L-2 regularization, after selecting the target gene, we train an L-2 Regularized Local Least Squares imputation model (RLLSimpute_L2) on the target gene and its neighbors to estimate the missing values of the target gene. Furthermore, RLLSimpute_L2 imputes the missing values in an ascending order based on the associated missing rate with each target gene. This contributes to fully utilizing the previously estimated values. Besides L-2, we further explore L-1 regularization and propose an L-1 Regularized Local Least Squares imputation model (RLLSimpute_L1). To evaluate their effectiveness, we conducted extensive experimental studies on six benchmark datasets covering both time series and non-time series cases. Nine state-of-the-art imputation methods are compared with RLLSimpute_L2 and RLLSimpute_L1 in terms of three performance metrics. The comparative experimental results indicate that RLLSimpute_L2 outperforms its competitors by achieving smaller imputation errors and better structure preservation of differentially expressed genes.

Place, publisher, year, edition, pages
IEEE, 2019. Vol. 16, no 3, p. 980-993
Keywords [en]
Microarray data, missing value imputation, regularized model, local learning, similarity measurement
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-161474DOI: 10.1109/TCBB.2018.2810205ISI: 000471070600028PubMedID: 29994588OAI: oai:DiVA.org:umu-161474DiVA, id: diva2:1336293
Available from: 2019-07-09 Created: 2019-07-09 Last updated: 2019-07-09Bibliographically approved

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Lili, Jiang

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CiteExportLink to record
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Citation style
  • apa
  • ieee
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  • de-DE
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