Log-ratio Lasso: scalable, sparse estimation for log-ratio models

DOI10.1111/BIOM.12995MaRDI QIDQ5214522zbMATH OpenOpenAlexWikidataFDO

Authors Stephen Bates, Robert Tibshirani

Publication date 7 February 2020

Published in Biometrics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1709.01139

zbMATH Keywords

Lassovariable selectioncompositional datamass spectrometrylog-ratio

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Ridge regression; shrinkage estimators (Lasso) (62J07)

Abstract: Positive-valued signal data is common in many biological and medical applications, where the data are often generated from imaging techniques such as mass spectrometry. In such a setting, the relative intensities of the raw features are often the scientifically meaningful quantities, so it is of interest to identify relevant features that take the form of log-ratios of the raw inputs. When including the log-ratios of all pairs of predictors, the dimensionality of this predictor space becomes large, so computationally efficient statistical procedures are required. We introduce an embedding of the log-ratio parameter space into a space of much lower dimension and develop efficient penalized fitting procedure using this more tractable representation. This procedure serves as the foundation for a two-step fitting procedure that combines a convex filtering step with a second non-convex pruning step to yield highly sparse solutions. On a cancer proteomics data set we find that these methods fit highly sparse models with log-ratio features of known biological relevance while greatly improving upon the predictive accuracy of less interpretable methods.

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(6)

• Robust logistic zero-sum regression for microbiome compositional data
• PALAR: Estimation of Absolute Abundance Effects in Regression with Relative Abundance Predictors
• Three approaches to supervised learning for compositional data with pairwise logratios
• SLASSO: a scaled LASSO for multicollinear situations
• Fundamentals of convex optimization for compositional data
• Robust regression with compositional covariates

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