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Sparse partial least squares classification for high dimensional data.

ABSTRACT: Partial least squares (PLS) is a well known dimension reduction method which has been recently adapted for high dimensional classification problems in genome biology. We develop sparse versions of the recently proposed two PLS-based classification methods using sparse partial least squares (SPLS). These sparse versions aim to achieve variable selection and dimension reduction simultaneously. We consider both binary and multicategory classification. We provide analytical and simulation-based insights about the variable selection properties of these approaches and benchmark them on well known publicly available datasets that involve tumor classification with high dimensional gene expression data. We show that incorporation of SPLS into a generalized linear model (GLM) framework provides higher sensitivity in variable selection for multicategory classification with unbalanced sample sizes between classes. As the sample size increases, the two-stage approach provides comparable sensitivity with better specificity in variable selection. In binary classification and multicategory classification with balanced sample sizes, the two-stage approach provides comparable variable selection and prediction accuracy as the GLM version and is computationally more efficient.

SUBMITTER: Chung D

PROVIDER: S-EPMC2861314 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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Sparse partial least squares classification for high dimensional data.

Chung Dongjun D Keles Sunduz S

Statistical applications in genetics and molecular biology 20100303

Partial least squares (PLS) is a well known dimension reduction method which has been recently adapted for high dimensional classification problems in genome biology. We develop sparse versions of the recently proposed two PLS-based classification methods using sparse partial least squares (SPLS). These sparse versions aim to achieve variable selection and dimension reduction simultaneously. We consider both binary and multicategory classification. We provide analytical and simulation-based insi ...[more]

PMID: 20361856

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Project description:BACKGROUND:Recent technological developments have enabled the measurement of a plethora of biomolecular data from various omics domains, and research is ongoing on statistical methods to leverage these omics data to better model and understand biological pathways and genetic architectures of complex phenotypes. Current reviews report that the simultaneous analysis of multiple (i.e. three or more) high dimensional omics data sources is still challenging and suitable statistical methods are unavailable. Often mentioned challenges are the lack of accounting for the hierarchical structure between omics domains and the difficulty of interpretation of genomewide results. This study is motivated to address these challenges. We propose multiset sparse Partial Least Squares path modeling (msPLS), a generalized penalized form of Partial Least Squares path modeling, for the simultaneous modeling of biological pathways across multiple omics domains. msPLS simultaneously models the effect of multiple molecular markers, from multiple omics domains, on the variation of multiple phenotypic variables, while accounting for the relationships between data sources, and provides sparse results. The sparsity in the model helps to provide interpretable results from analyses of hundreds of thousands of biomolecular variables. RESULTS:With simulation studies, we quantified the ability of msPLS to discover associated variables among high dimensional data sources. Furthermore, we analysed high dimensional omics datasets to explore biological pathways associated with Marfan syndrome and with Chronic Lymphocytic Leukaemia. Additionally, we compared the results of msPLS to the results of Multi-Omics Factor Analysis (MOFA), which is an alternative method to analyse this type of data. CONCLUSIONS:msPLS is an multiset multivariate method for the integrative analysis of multiple high dimensional omics data sources. It accounts for the relationship between multiple high dimensional data sources while it provides interpretable results through its sparse solutions. The biomarkers found by msPLS in the omics datasets can be interpreted in terms of biological pathways associated with the pathophysiology of Marfan syndrome and of Chronic Lymphocytic Leukaemia. Additionally, msPLS outperforms MOFA in terms of variation explained in the chronic lymphocytic leukaemia dataset while it identifies the two most important clinical markers for Chronic Lymphocytic Leukaemia AVAILABILITY: http://uva.csala.me/mspls.https://github.com/acsala/2018_msPLS.

Project description:MotivationA complex disease is usually driven by a number of genes interwoven into networks, rather than a single gene product. Network comparison or differential network analysis has become an important means of revealing the underlying mechanism of pathogenesis and identifying clinical biomarkers for disease classification. Most studies, however, are limited to network correlations that mainly capture the linear relationship among genes, or rely on the assumption of a parametric probability distribution of gene measurements. They are restrictive in real application.ResultsWe propose a new Joint density based non-parametric Differential Interaction Network Analysis and Classification (JDINAC) method to identify differential interaction patterns of network activation between two groups. At the same time, JDINAC uses the network biomarkers to build a classification model. The novelty of JDINAC lies in its potential to capture non-linear relations between molecular interactions using high-dimensional sparse data as well as to adjust confounding factors, without the need of the assumption of a parametric probability distribution of gene measurements. Simulation studies demonstrate that JDINAC provides more accurate differential network estimation and lower classification error than that achieved by other state-of-the-art methods. We apply JDINAC to a Breast Invasive Carcinoma dataset, which includes 114 patients who have both tumor and matched normal samples. The hub genes and differential interaction patterns identified were consistent with existing experimental studies. Furthermore, JDINAC discriminated the tumor and normal sample with high accuracy by virtue of the identified biomarkers. JDINAC provides a general framework for feature selection and classification using high-dimensional sparse omics data.Availability and implementationR scripts available at https://github.com/jijiadong/JDINAC.Contactlxie@iscb.org.Supplementary informationSupplementary data are available at Bioinformatics online.

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Sparse partial least squares classification for high dimensional data.

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Sparse partial least squares classification for high dimensional data.

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