Block HSIC Lasso: Model-free biomarker detection for ultra-high dimensional data
Research output: Contribution to journal › Article › Scientific › peer-review
Researchers
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 language | English |
---|---|
Article number | btz333 |
Pages (from-to) | i427-i435 |
Journal | Bioinformatics |
Volume | 35 |
Issue number | 14 |
Publication status | Published - 15 Jul 2019 |
MoE publication type | A1 Journal article-refereed |
Download statistics
ID: 35580978