Elephant Search with Deep Learning for Microarray Data Analysis

Even though there is a plethora of research in Microarray gene expression data analysis, still, it poses challenges for researchers to effectively and efficiently analyze the large yet complex expression of genes. The feature (gene) selection method is of paramount importance for understanding the differences in biological and non-biological variation between samples. In order to address this problem, a novel elephant search (ES) based optimization is proposed to select best gene expressions from the large volume of microarray data. Further, a promising machine learning method is envisioned to leverage such high dimensional and complex microarray dataset for extracting hidden patterns inside to make a meaningful prediction and most accurate classification. In particular, stochastic gradient descent based Deep learning (DL) with softmax activation function is then used on the reduced features (genes) for better classification of different samples according to their gene expression levels. The experiments are carried out on nine most popular Cancer microarray gene selection datasets, obtained from UCI machine learning repository. The empirical results obtained by the proposed elephant search based deep learning (ESDL) approach are compared with most recent published article for its suitability in future Bioinformatics research.Comment: 12 pages, 5 Tabl

Inverse Projection Representation and Category Contribution Rate for Robust Tumor Recognition

Sparse representation based classification (SRC) methods have achieved remarkable results. SRC, however, still suffer from requiring enough training samples, insufficient use of test samples and instability of representation. In this paper, a stable inverse projection representation based classification (IPRC) is presented to tackle these problems by effectively using test samples. An IPR is firstly proposed and its feasibility and stability are analyzed. A classification criterion named category contribution rate is constructed to match the IPR and complete classification. Moreover, a statistical measure is introduced to quantify the stability of representation-based classification methods. Based on the IPRC technique, a robust tumor recognition framework is presented by interpreting microarray gene expression data, where a two-stage hybrid gene selection method is introduced to select informative genes. Finally, the functional analysis of candidate's pathogenicity-related genes is given. Extensive experiments on six public tumor microarray gene expression datasets demonstrate the proposed technique is competitive with state-of-the-art methods.Comment: 14 pages, 19 figures, 10 table

A cDNA Microarray Gene Expression Data Classifier for Clinical Diagnostics Based on Graph Theory

Despite great advances in discovering cancer molecular profiles, the proper application of microarray technology to routine clinical diagnostics is still a challenge. Current practices in the classification of microarrays' data show two main limitations: the reliability of the training data sets used to build the classifiers, and the classifiers' performances, especially when the sample to be classified does not belong to any of the available classes. In this case, state-of-the-art algorithms usually produce a high rate of false positives that, in real diagnostic applications, are unacceptable. To address this problem, this paper presents a new cDNA microarray data classification algorithm based on graph theory and is able to overcome most of the limitations of known classification methodologies. The classifier works by analyzing gene expression data organized in an innovative data structure based on graphs, where vertices correspond to genes and edges to gene expression relationships. To demonstrate the novelty of the proposed approach, the authors present an experimental performance comparison between the proposed classifier and several state-of-the-art classification algorithm

Hierarchical Multi-Bottleneck Classification Method And Its Application to DNA Microarray Expression Data

The recent development of DNA microarray technology is creating a wealth of gene expression data. Typically these datasets have high dimensionality and a lot of varieties. Analysis of DNA microarray expression data is a fast growing research area that interfaces various disciplines such as biology, biochemistry, computer science and statistics. It is concluded that clustering and classification techniques can be successfully employed to group genes based on the similarity of their expression patterns. In this paper, a hierarchical multi-bottleneck classification method is proposed, and it is applied to classify a publicly available gene microarray expression data of budding yeast Saccharomyces cerevisiae.Singapore-MIT Alliance (SMA

maigesPack: A Computational Environment for Microarray Data Analysis

Microarray technology is still an important way to assess gene expression in molecular biology, mainly because it measures expression profiles for thousands of genes simultaneously, what makes this technology a good option for some studies focused on systems biology. One of its main problem is complexity of experimental procedure, presenting several sources of variability, hindering statistical modeling. So far, there is no standard protocol for generation and evaluation of microarray data. To mitigate the analysis process this paper presents an R package, named maigesPack, that helps with data organization. Besides that, it makes data analysis process more robust, reliable and reproducible. Also, maigesPack aggregates several data analysis procedures reported in literature, for instance: cluster analysis, differential expression, supervised classifiers, relevance networks and functional classification of gene groups or gene networks

Building interpretable fuzzy models for high dimensional data analysis in cancer diagnosis

Background: Analysing gene expression data from microarray technologies is a very important task in biology and medicine, and particularly in cancer diagnosis. Different from most other popular methods in high dimensional bio-medical data analysis, such as microarray gene expression or proteomics mass spectroscopy data analysis, fuzzy rule-based models can not only provide good classification results, but also easily be explained and interpreted in human understandable terms, by using fuzzy rules. However, the advantages offered by fuzzy-based techniques in microarray data analysis have not yet been fully explored in the literature. Although some recently developed fuzzy-based modeling approaches can provide satisfactory classification results, the rule bases generated by most of the reported fuzzy models for gene expression data are still too large to be easily comprehensible. Results: In this paper, we develop some Multi-Objective Evolutionary Algorithms based Interpretable Fuzzy (MOEAIF) methods for analysing high dimensional bio-medical data sets, such as microarray gene expression data and proteomics mass spectroscopy data. We mainly focus on evaluating our proposed models on microarray gene expression cancer data sets, i.e., the lung cancer data set and the colon cancer data set, but we extend our investigations to other type of cancer data set, such as the ovarian cancer data set. The experimental studies have shown that relatively simple and small fuzzy rule bases, with satisfactory classification performance, can be successfully obtained for challenging microarray gene expression datasets. Conclusions: We believe that fuzzy-based techniques, and in particular the methods proposed in this paper, can be very useful tools in dealing with high dimensional cancer data. We also argue that the potential of applying fuzzy-based techniques to microarray data analysis need to be further explored. </p

Feature selection for microarray gene expression data using simulated annealing guided by the multivariate joint entropy

In this work a new way to calculate the multivariate joint entropy is presented. This measure is the basis for a fast information-theoretic based evaluation of gene relevance in a Microarray Gene Expression data context. Its low complexity is based on the reuse of previous computations to calculate current feature relevance. The mu-TAFS algorithm --named as such to differentiate it from previous TAFS algorithms-- implements a simulated annealing technique specially designed for feature subset selection. The algorithm is applied to the maximization of gene subset relevance in several public-domain microarray data sets. The experimental results show a notoriously high classification performance and low size subsets formed by biologically meaningful genes.Postprint (published version

MapReduce Based Feature Selection and Classification of Microarray Dataset

Gene expression profiling has emerged as an efficient technique for classification, diagnosis and treatment of various diseases. The data retrieved from microarray contains the gene expression values of the genes present in a tissue. The size of such data varies from some kilobytes to thousand of Gigabytes. Therefore, the analysis of microarray dataset in a very short period of time is essential. The major setback of microarray dataset is the presence of a large number of irrelevant information, which hinders the amount of useful information present in the dataset and results in a large number of computations. Therefore, selection of relevant genes is an important step in microarray data analysis. After retrieving the required number of features, classification of the dataset is done. In this project, various methods based on MapReduce are proposed to select the relevant number of feature. After feature selection, Naïve Bayes Classifier and N-Nearest Neighbor is used to classify the datasets. These algorithms are implemented on Hadoop framework. A comparative analysis is done on these methodologies using microarray data of different size

A filter based feature selection algorithm using null space of covariance matrix for DNA microarray gene expression data

We propose a new filter based feature selection algorithm for classification based on DNA microarray gene expression data. It utilizes null space of covariance matrix for feature selection. The algorithm can perform bulk reduction of features (genes) while maintaining the quality information in the reduced subset of features for discriminative purpose. Thus, it can be used as a pre-processing step for other feature selection algorithms. The algorithm does not assume statistical independency among the features. The algorithm shows promising classification accuracy when compared with other existing techniques on several DNA microarray gene expression datasets