Gene selection from microarray expression data
Genomics / bioinformaticsA cancer classification study has gene-expression measurements for roughly 20,000 genes but only a few hundred patient samples () — the classic high-dimensional, low-sample-size setting where ordinary least squares is not even computable because is singular.
Researchers fit an L1-penalized (Lasso) regression/logistic model relating gene expression to a clinical outcome (e.g. tumor recurrence), sweeping via cross-validation. Elastic Net is often preferred in practice over pure Lasso because many genes in the same biological pathway are highly co-expressed (correlated), and pure Lasso would arbitrarily select just one gene per pathway while ignoring its correlated partners.
The penalty drives the vast majority of the ~20,000 gene coefficients to exactly zero, typically leaving a panel of only a few dozen genes (often 20-100) with non-zero weight — a result that is both statistically tractable and biologically interpretable as a candidate biomarker panel, at a modest cost in predictive accuracy compared to an (infeasible) unregularized fit.
Source: The Elements of Statistical Learning (Ch. 18, High-Dimensional Problems) — Hastie, T., Tibshirani, R. and Friedman, J.