Robust Data Integration Method for Classification of Biomedical Data.
We present a protocol for integrating two types of biological data – clinical and molecular – for more effective classification of patients with cancer. The proposed approach is a hybrid between early and late data integration strategy. In this hybrid protocol, the set of informative clinical featur...
| Published in: | Journal of Medical Systems Vol. 45; no. 4; pp. 1 - 15 |
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| Main Authors: | , , |
| Format: | algorithm research tables/charts Journal Article |
| Published: |
Springer Nature
Apr2021
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| Online Access: | View this record in EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=149631222&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 149631222 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 01485598 4N0 jtl: Journal of Medical Systems issn: 01485598 maglogo: N pubinfo: dt: Apr2021 vid: 45 iid: 4 pid: 237 pub: Springer Nature place: New York, New York artinfo: ui: 149631222 149631222 149631222 10.1007/s10916-021-01718-7 149631222 ppf: 1 ppct: 14 formats: fmt: @attributes: type: P tig: atl: Robust Data Integration Method for Classification of Biomedical Data. aug: au: Polewko-Klim, Aneta Mnich, Krzysztof Rudnicki, Witold R. affil: Institute of Computer Science, University of Bialystok, Bialystok, Poland sug: subj: Medical Informatics Methods Neoplasms Cancer Patients Classification Human Protocols Breast Neoplasms Bladder Neoplasms Gene Expression Sequence Analysis Machine Learning Algorithms Biological Markers Genes, BRCA ab: We present a protocol for integrating two types of biological data – clinical and molecular – for more effective classification of patients with cancer. The proposed approach is a hybrid between early and late data integration strategy. In this hybrid protocol, the set of informative clinical features is extended by the classification results based on molecular data sets. The results are then treated as new synthetic variables. The hybrid protocol was applied to METABRIC breast cancer samples and TCGA urothelial bladder carcinoma samples. Various data types were used for clinical endpoint prediction: clinical data, gene expression, somatic copy number aberrations, RNA-Seq, methylation, and reverse phase protein array. The performance of the hybrid data integration was evaluated with a repeated cross validation procedure and compared with other methods of data integration: early integration and late integration via super learning. The hybrid method gave similar results to those obtained by the best of the tested variants of super learning. What is more, the hybrid method allowed for further sensitivity analysis and recursive feature elimination, which led to compact predictive models for cancer clinical endpoints. For breast cancer, the final model consists of eight clinical variables and two synthetic features obtained from molecular data. For urothelial bladder carcinoma, only two clinical features and one synthetic variable were necessary to build the best predictive model. We have shown that the inclusion of the synthetic variables based on the RNA expression levels and copy number alterations can lead to improved quality of prognostic tests. Thus, it should be considered for inclusion in wider medical practice. pubtype: Academic Journal doctype: algorithm research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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