Block HSIC Lasso: Model-free biomarker detection for ultra-high dimensional data

Research output: Contribution to journalArticleScientificpeer-review

Researchers

  • Héctor Climente-González
  • Chloé Agathe Azencott
  • Samuel Kaski

  • Makoto Yamada

Research units

  • Institut Curie
  • Institut National de la Santé et de la Recherche Médicale
  • Ecole des Mines de Paris
  • RIKEN
  • Kyoto University

Abstract

Motivation: Finding non-linear relationships between biomolecules and a biological outcome is computationally expensive and statistically challenging. Existing methods have important drawbacks, including among others lack of parsimony, non-convexity and computational overhead. Here we propose block HSIC Lasso, a non-linear feature selector that does not present the previous drawbacks. Results: We compare block HSIC Lasso to other state-of-the-art feature selection techniques in both synthetic and real data, including experiments over three common types of genomic data: gene-expression microarrays, single-cell RNA sequencing and genome-wide association studies. In all cases, we observe that features selected by block HSIC Lasso retain more information about the underlying biology than those selected by other techniques. As a proof of concept, we applied block HSIC Lasso to a single-cell RNA sequencing experiment on mouse hippocampus. We discovered that many genes linked in the past to brain development and function are involved in the biological differences between the types of neurons.

Details

Original languageEnglish
Article numberbtz333
Pages (from-to)i427-i435
JournalBioinformatics
Volume35
Issue number14
Publication statusPublished - 15 Jul 2019
MoE publication typeA1 Journal article-refereed

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