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Low-rank graph optimization for multi-view dimensionality reduction.

ABSTRACT: Graph-based dimensionality reduction methods have attracted substantial attention due to their successful applications in many tasks, including classification and clustering. However, most classical graph-based dimensionality reduction approaches are only applied to data from one view. Hence, combining information from different data views has attracted considerable attention in the literature. Although various multi-view graph-based dimensionality reduction algorithms have been proposed, the graph construction strategies utilized in them do not adequately take noise and different importance of multiple views into account, which may degrade their performance. In this paper, we propose a novel algorithm, namely, Low-Rank Graph Optimization for Multi-View Dimensionality Reduction (LRGO-MVDR), that overcomes these limitations. First, we construct a low-rank shared matrix and a sparse error matrix from the graph that corresponds to each view for capturing potential noise. Second, an adaptive nonnegative weight vector is learned to explore complementarity among views. Moreover, an effective optimization procedure based on the Alternating Direction Method of Multipliers scheme is utilized. Extensive experiments are carried out to evaluate the effectiveness of the proposed algorithm. The experimental results demonstrate that the proposed LRGO-MVDR algorithm outperforms related methods.

SUBMITTER: Qian Y

PROVIDER: S-EPMC6919611 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Low-rank graph optimization for multi-view dimensionality reduction.

Qian Youcheng Y Yin Xueyan X Kong Jun J Wang Jianzhong J Gao Wei W

PloS one 20191218 12

Graph-based dimensionality reduction methods have attracted substantial attention due to their successful applications in many tasks, including classification and clustering. However, most classical graph-based dimensionality reduction approaches are only applied to data from one view. Hence, combining information from different data views has attracted considerable attention in the literature. Although various multi-view graph-based dimensionality reduction algorithms have been proposed, the gr ...[more]

PMID: 31851696

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Project description:Despite new developments in machine learning classification techniques, improving the accuracy of spam filtering is a difficult task due to linguistic phenomena that limit its effectiveness. In particular, we highlight polysemy, synonymy, the usage of hypernyms/hyponyms, and the presence of irrelevant/confusing words. These problems should be solved at the pre-processing stage to avoid using inconsistent information in the building of classification models. Previous studies have suggested that the use of synset-based representation strategies could be successfully used to solve synonymy and polysemy problems. Complementarily, it is possible to take advantage of hyponymy/hypernymy-based to implement dimensionality reduction strategies. These strategies could unify textual terms to model the intentions of the document without losing any information (e.g., bringing together the synsets "viagra", "ciallis", "levitra" and other representing similar drugs by using "virility drug" which is a hyponym for all of them). These feature reduction schemes are known as lossless strategies as the information is not removed but only generalised. However, in some types of text classification problems (such as spam filtering) it may not be worthwhile to keep all the information and let dimensionality reduction algorithms discard information that may be irrelevant or confusing. In this work, we are introducing the feature reduction as a multi-objective optimisation problem to be solved using a Multi-Objective Evolutionary Algorithm (MOEA). Our algorithm allows, with minor modifications, to implement lossless (using only semantic-based synset grouping), low-loss (discarding irrelevant information and using semantic-based synset grouping) or lossy (discarding only irrelevant information) strategies. The contribution of this study is two-fold: (i) to introduce different dimensionality reduction methods (lossless, low-loss and lossy) as an optimization problem that can be solved using MOEA and (ii) to provide an experimental comparison of lossless and low-loss schemes for text representation. The results obtained support the usefulness of the low-loss method to improve the efficiency of classifiers.

Project description:BackgroundIdentifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionality reduction (MDR) is a popular approach for detecting gene-gene interactions that has been extended in various forms to handle binary and continuous phenotypes. However, only few multivariate MDR methods are available for multiple related phenotypes. Current approaches use Hotelling's T2 statistic to evaluate interaction models, but it is well known that Hotelling's T2 statistic is highly sensitive to heavily skewed distributions and outliers.ResultsWe propose a robust approach based on nonparametric statistics such as spatial signs and ranks. The new multivariate rank-based MDR (MR-MDR) is mainly suitable for analyzing multiple continuous phenotypes and is less sensitive to skewed distributions and outliers. MR-MDR utilizes fuzzy k-means clustering and classifies multi-locus genotypes into two groups. Then, MR-MDR calculates a spatial rank-sum statistic as an evaluation measure and selects the best interaction model with the largest statistic. Our novel idea lies in adopting nonparametric statistics as an evaluation measure for robust inference. We adopt tenfold cross-validation to avoid overfitting. Intensive simulation studies were conducted to compare the performance of MR-MDR with current methods. Application of MR-MDR to a real dataset from a Korean genome-wide association study demonstrated that it successfully identified genetic interactions associated with four phenotypes related to kidney function. The R code for conducting MR-MDR is available at https://github.com/statpark/MR-MDR .ConclusionsIntensive simulation studies comparing MR-MDR with several current methods showed that the performance of MR-MDR was outstanding for skewed distributions. Additionally, for symmetric distributions, MR-MDR showed comparable power. Therefore, we conclude that MR-MDR is a useful multivariate non-parametric approach that can be used regardless of the phenotype distribution, the correlations between phenotypes, and sample size.

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Low-rank graph optimization for multi-view dimensionality reduction.

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Low-rank graph optimization for multi-view dimensionality reduction.

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