Unsupervised multiple kernel learning for heterogeneous data integration

Bioinformatics
Jérôme Mariette, Nathalie Villa-Vialaneix

Abstract

Recent high-throughput sequencing advances have expanded the breadth of available omics datasets and the integrated analysis of multiple datasets obtained on the same samples has allowed to gain important insights in a wide range of applications. However, the integration of various sources of information remains a challenge for systems biology since produced datasets are often of heterogeneous types, with the need of developing generic methods to take their different specificities into account. We propose a multiple kernel framework that allows to integrate multiple datasets of various types into a single exploratory analysis. Several solutions are provided to learn either a consensus meta-kernel or a meta-kernel that preserves the original topology of the datasets. We applied our framework to analyse two public multi-omics datasets. First, the multiple metagenomic datasets, collected during the TARA Oceans expedition, was explored to demonstrate that our method is able to retrieve previous findings in a single kernel PCA as well as to provide a new image of the sample structures when a larger number of datasets are included in the analysis. To perform this analysis, a generic procedure is also proposed to improve the interpret...Continue Reading

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Citations

Jun 28, 2019·Molecular & Cellular Proteomics : MCP·Chen MengAedín C Culhane
Jan 9, 2020·Bioinformatics·Xiaqiong Wang, Yalu Wen
Nov 19, 2019·Bioinformatics·Laura M ZingarettiYuliaxis Ramayo-Caldas
Jul 2, 2020·Briefings in Bioinformatics·Ruiling FangYuehua Cui
Sep 18, 2020·PloS One·Shengbing RenChaudry Naeem Siddique
Dec 4, 2019·Briefings in Bioinformatics·Morgane Pierre-JeanFlorence Mauger
Jul 23, 2020·Frontiers in Oncology·Giovanna NicoraRiccardo Bellazzi
Apr 25, 2020·BMC Bioinformatics·Xingheng YuHao Jiang
Aug 9, 2019·Molecular & Cellular Proteomics : MCP·Chen MengAedín C Culhane
Apr 20, 2021·Computational and Structural Biotechnology Journal·Yongqing WuYuehua Cui
May 15, 2021·Computers in Biology and Medicine·Hua ChaiYuedong Yang
Jun 16, 2021·Artificial Intelligence in Medicine·E ParimbelliM Peleg
Aug 13, 2021·PLoS Computational Biology·Ran DuanSongwei Jia

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