12,558 research outputs found
An embedded two-layer feature selection approach for microarray data analysis
Feature selection is an important technique in dealing with application problems with large number of variables and limited training samples, such as image processing, combinatorial chemistry, and microarray analysis. Commonly employed feature selection strategies can be divided into filter and wrapper. In this study, we propose an embedded two-layer feature selection approach to combining the advantages of filter and wrapper algorithms while avoiding their drawbacks. The hybrid algorithm, called GAEF (Genetic Algorithm with embedded filter), divides the feature selection process into two stages. In the first stage, Genetic Algorithm (GA) is employed to pre-select features while in the second stage a filter selector is used to further identify a small feature subset for accurate sample classification. Three benchmark microarray datasets are used to evaluate the proposed algorithm. The experimental results suggest that this embedded two-layer feature selection strategy is able to improve the stability of the selection results as well as the sample classification accuracy.<br /
Infinite Latent Feature Selection: A Probabilistic Latent Graph-Based Ranking Approach
Feature selection is playing an increasingly significant role with respect to
many computer vision applications spanning from object recognition to visual
object tracking. However, most of the recent solutions in feature selection are
not robust across different and heterogeneous set of data. In this paper, we
address this issue proposing a robust probabilistic latent graph-based feature
selection algorithm that performs the ranking step while considering all the
possible subsets of features, as paths on a graph, bypassing the combinatorial
problem analytically. An appealing characteristic of the approach is that it
aims to discover an abstraction behind low-level sensory data, that is,
relevancy. Relevancy is modelled as a latent variable in a PLSA-inspired
generative process that allows the investigation of the importance of a feature
when injected into an arbitrary set of cues. The proposed method has been
tested on ten diverse benchmarks, and compared against eleven state of the art
feature selection methods. Results show that the proposed approach attains the
highest performance levels across many different scenarios and difficulties,
thereby confirming its strong robustness while setting a new state of the art
in feature selection domain.Comment: Accepted at the IEEE International Conference on Computer Vision
(ICCV), 2017, Venice. Preprint cop
Feature Selection for Big Visual Data: Overview and Challenges
International Conference Image Analysis and Recognition (ICIAR 2018, Póvoa de Varzim, Portugal
Correcting for selection bias via cross-validation in the classification of microarray data
There is increasing interest in the use of diagnostic rules based on
microarray data. These rules are formed by considering the expression levels of
thousands of genes in tissue samples taken on patients of known classification
with respect to a number of classes, representing, say, disease status or
treatment strategy. As the final versions of these rules are usually based on a
small subset of the available genes, there is a selection bias that has to be
corrected for in the estimation of the associated error rates. We consider the
problem using cross-validation. In particular, we present explicit formulae
that are useful in explaining the layers of validation that have to be
performed in order to avoid improperly cross-validated estimates.Comment: Published in at http://dx.doi.org/10.1214/193940307000000284 the IMS
Collections (http://www.imstat.org/publications/imscollections.htm) by the
Institute of Mathematical Statistics (http://www.imstat.org
Machine Learning and Integrative Analysis of Biomedical Big Data.
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues
Ranking to Learn: Feature Ranking and Selection via Eigenvector Centrality
In an era where accumulating data is easy and storing it inexpensive, feature
selection plays a central role in helping to reduce the high-dimensionality of
huge amounts of otherwise meaningless data. In this paper, we propose a
graph-based method for feature selection that ranks features by identifying the
most important ones into arbitrary set of cues. Mapping the problem on an
affinity graph-where features are the nodes-the solution is given by assessing
the importance of nodes through some indicators of centrality, in particular,
the Eigen-vector Centrality (EC). The gist of EC is to estimate the importance
of a feature as a function of the importance of its neighbors. Ranking central
nodes individuates candidate features, which turn out to be effective from a
classification point of view, as proved by a thoroughly experimental section.
Our approach has been tested on 7 diverse datasets from recent literature
(e.g., biological data and object recognition, among others), and compared
against filter, embedded and wrappers methods. The results are remarkable in
terms of accuracy, stability and low execution time.Comment: Preprint version - Lecture Notes in Computer Science - Springer 201
Listen to genes : dealing with microarray data in the frequency domain
Background: We present a novel and systematic approach to analyze temporal microarray data. The approach includes
normalization, clustering and network analysis of genes.
Methodology: Genes are normalized using an error model based uniform normalization method aimed at identifying and
estimating the sources of variations. The model minimizes the correlation among error terms across replicates. The
normalized gene expressions are then clustered in terms of their power spectrum density. The method of complex Granger
causality is introduced to reveal interactions between sets of genes. Complex Granger causality along with partial Granger
causality is applied in both time and frequency domains to selected as well as all the genes to reveal the interesting
networks of interactions. The approach is successfully applied to Arabidopsis leaf microarray data generated from 31,000
genes observed over 22 time points over 22 days. Three circuits: a circadian gene circuit, an ethylene circuit and a new
global circuit showing a hierarchical structure to determine the initiators of leaf senescence are analyzed in detail.
Conclusions: We use a totally data-driven approach to form biological hypothesis. Clustering using the power-spectrum
analysis helps us identify genes of potential interest. Their dynamics can be captured accurately in the time and frequency
domain using the methods of complex and partial Granger causality. With the rise in availability of temporal microarray
data, such methods can be useful tools in uncovering the hidden biological interactions. We show our method in a step by
step manner with help of toy models as well as a real biological dataset. We also analyse three distinct gene circuits of
potential interest to Arabidopsis researchers
AutoEncoder Inspired Unsupervised Feature Selection
High-dimensional data in many areas such as computer vision and machine
learning tasks brings in computational and analytical difficulty. Feature
selection which selects a subset from observed features is a widely used
approach for improving performance and effectiveness of machine learning models
with high-dimensional data. In this paper, we propose a novel AutoEncoder
Feature Selector (AEFS) for unsupervised feature selection which combines
autoencoder regression and group lasso tasks. Compared to traditional feature
selection methods, AEFS can select the most important features by excavating
both linear and nonlinear information among features, which is more flexible
than the conventional self-representation method for unsupervised feature
selection with only linear assumptions. Experimental results on benchmark
dataset show that the proposed method is superior to the state-of-the-art
method.Comment: accepted by ICASSP 201
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