Dataset Information

Web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning.

ABSTRACT: More and more affordable high-throughput techniques for measuring molecular features of biomedical samples have led to a huge increase in availability and size of different types of multi-omic datasets, containing, for example, genetic or histone modification data. Due to the multi-view characteristic of the data, established approaches for exploratory analysis are not directly applicable. Here we present web-rMKL, a web server that provides an integrative dimensionality reduction with subsequent clustering of samples based on data from multiple inputs. The underlying machine learning method rMKL-LPP performed best for clinical enrichment in a recent benchmark of state-of-the-art multi-view clustering algorithms. The method was introduced for a multi-omic cancer subtype discovery setting, however, it is not limited to this application scenario as exemplified by a presented use case for stem cell differentiation. web-rMKL offers an intuitive interface for uploading data and setting the parameters. rMKL-LPP runs on the back end and the user may receive notifications once the results are available. We also introduce a preprocessing tool for generating kernel matrices from tables containing numerical feature values. This program can be used to generate admissible input if no precomputed kernel matrices are available. The web server is freely available at web-rMKL.org.

SUBMITTER: Roder B

PROVIDER: S-EPMC6602472 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning.

Röder Benedict B Kersten Nicolas N Herr Marius M Speicher Nora K NK Pfeifer Nico N

Nucleic acids research 20190701 W1

More and more affordable high-throughput techniques for measuring molecular features of biomedical samples have led to a huge increase in availability and size of different types of multi-omic datasets, containing, for example, genetic or histone modification data. Due to the multi-view characteristic of the data, established approaches for exploratory analysis are not directly applicable. Here we present web-rMKL, a web server that provides an integrative dimensionality reduction with subsequen ...[more]

PMID: 31114892

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Dataset Information

Web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning.

Publications

web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning.

Similar Datasets

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