Dataset Information

Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer.

ABSTRACT: High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve proper integration, joint Dimensionality Reduction (jDR) methods are among the most efficient approaches. However, several jDR methods are available, urging the need for a comprehensive benchmark with practical guidelines. We perform a systematic evaluation of nine representative jDR methods using three complementary benchmarks. First, we evaluate their performances in retrieving ground-truth sample clustering from simulated multi-omics datasets. Second, we use TCGA cancer data to assess their strengths in predicting survival, clinical annotations and known pathways/biological processes. Finally, we assess their classification of multi-omics single-cell data. From these in-depth comparisons, we observe that intNMF performs best in clustering, while MCIA offers an effective behavior across many contexts. The code developed for this benchmark study is implemented in a Jupyter notebook-multi-omics mix (momix)-to foster reproducibility, and support users and future developers.

SUBMITTER: Cantini L

PROVIDER: S-EPMC7785750 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer.

Cantini Laura L Zakeri Pooya P Hernandez Celine C Naldi Aurelien A Thieffry Denis D Remy Elisabeth E Baudot Anaïs A

Nature communications 20210105 1

High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve proper integration, joint Dimensionality Reduction (jDR) methods are among the most efficient approaches. However, several jDR methods are available, urging the need for a comprehensive benchmark with practical guidelines. We perform a systematic evaluation of nine representative jDR methods using three complementary benchmarks. F ...[more]

PMID: 33402734

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Project description:Despite new developments in machine learning classification techniques, improving the accuracy of spam filtering is a difficult task due to linguistic phenomena that limit its effectiveness. In particular, we highlight polysemy, synonymy, the usage of hypernyms/hyponyms, and the presence of irrelevant/confusing words. These problems should be solved at the pre-processing stage to avoid using inconsistent information in the building of classification models. Previous studies have suggested that the use of synset-based representation strategies could be successfully used to solve synonymy and polysemy problems. Complementarily, it is possible to take advantage of hyponymy/hypernymy-based to implement dimensionality reduction strategies. These strategies could unify textual terms to model the intentions of the document without losing any information (e.g., bringing together the synsets "viagra", "ciallis", "levitra" and other representing similar drugs by using "virility drug" which is a hyponym for all of them). These feature reduction schemes are known as lossless strategies as the information is not removed but only generalised. However, in some types of text classification problems (such as spam filtering) it may not be worthwhile to keep all the information and let dimensionality reduction algorithms discard information that may be irrelevant or confusing. In this work, we are introducing the feature reduction as a multi-objective optimisation problem to be solved using a Multi-Objective Evolutionary Algorithm (MOEA). Our algorithm allows, with minor modifications, to implement lossless (using only semantic-based synset grouping), low-loss (discarding irrelevant information and using semantic-based synset grouping) or lossy (discarding only irrelevant information) strategies. The contribution of this study is two-fold: (i) to introduce different dimensionality reduction methods (lossless, low-loss and lossy) as an optimization problem that can be solved using MOEA and (ii) to provide an experimental comparison of lossless and low-loss schemes for text representation. The results obtained support the usefulness of the low-loss method to improve the efficiency of classifiers.

Dataset Information

Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer.

Publications

Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer.

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