Semi-supervised Naive Hubness Bayesian k-Nearest Neighbor for Gene Expression Data

The purpose of this paper is to introduce transductive inference with support vector machines (TSVM) as a powerful methodology for classification of gene expression data, using training and prediction data sets. The following classification problems will be considered: determination of cancer diagnosis categories and classification of genes from the budding yeast Saccharomyces cerevisiae in functional groups. In the case of training samples, experts have already classified the samples in their respective classes. So, given each prediction sample, the purpose is to determine its corresponding class. The main aspect of TSVM is that the classification task will be implemented in just one step, improving the generalization capability of the classifier. The TSVM will be compared with the traditional inductive method (SVM) in a series of experiments concerning the two classification problems, with promising results.

Chapter 9 - Effective dimensionality reduction model with machine learning classification for microarray gene expression data

Though DNA microarray technology simultaneously measures the expression levels of thousands of genes, only a few underlying gene features may account for significant data variation in gene classification problems. Selection of features from huge data set is difficult and so dimension reduction of gene expression data set is essential in order to determining important features, which play key role in predicting an outcome. Rough set theory (RST) has been used recently for dimension reduction of data, however, the existing methods are inadequate to finding minimal reduct. The paper proposes a RST based technique, applied on gene expression data for dimension reduction by obtaining single reduct in one pass. The gene expression data are discretized using linguistic terms with proper semantics and represented by fuzzy sets. The discretized values are calculated using Gaussian membership function with varied mean and standard deviation in order to eliminate the ambiguity between different linguistic terms. The genes are classified using linguistic decision attribute values based on the frequency of gene expression data. Discritization and classification of gene expression data are performed simultaneously, which significantly reduces time complexity of the procedure. Thus, the proposed framework selects the most significant samples for gene classification, resulting dimension reduction. The Proposed method produces output, which exhibits no variation with experimental microarray gene information unlike other existing methods.

One of the most significant research topics in bioinformatics is the classification of gene expression. Gene expression data commonly have a large number of features and a small number of samples. The gene expression data are very different from one to another, this differentiation among data and the feature's large number make the classification for gene expression data challenging. In this study, for classification we assessed the accuracy for most powerful deep learning's algorithms such as Deep Neural Network, Recurrent Neural Network, Convolutional Neural Network and improved Deep Neural Network with the preprocessing technique. The DNN was improved by adding Dropout to it by which the overfitting problem was overcame. Our results showed that the proposed improved-DNN outperforms the other algorithms among all used datasets.

Analysis of large-scale gene expression data is a research hotspot in the field of bioinformatics, which can be used to study abnormal phenomenon in plant growth process. This paper proposes a biological knowledge integration method based on parallel clustering to select gene subsets effectively. Gene ontology is utilised to obtain the biological functional similarity, and combined with gene expression data. Parallelised affinity propagation algorithm is used to cluster data since it can not only obtain more biologically meaningful subsets, but also avoid the loss of some potential value in genes from simple gene primary selection. The algorithm is verified with four typical plant datasets and compared with other well-known integration methods. Experimental results on plant stress response datasets demonstrate that the proposed method can select genes with stronger classification ability.

BackgroundInterpretation of high-throughput gene expression data continues to require mathematical tools in data analysis that recognizes the shape of the data in high dimensions. Topological data analysis (TDA) has recently been successful in extracting robust features in several applications dealing with high dimensional constructs. In this work, we utilize some recent developments in TDA to curate gene expression data. Our work differs from the predecessors in two aspects: (1) Traditional TDA pipelines use topological signatures called barcodes to enhance feature vectors which are used for classification. In contrast, this work involves curating relevant features to obtain somewhat better representatives with the help of TDA. This representatives of the entire data facilitates better comprehension of the phenotype labels. (2) Most of the earlier works employ barcodes obtained using topological summaries as fingerprints for the data. Even though they are stable signatures, there exists no direct mapping between the data and said barcodes.ResultsThe topology relevant curated data that we obtain provides an improvement in shallow learning as well as deep learning based supervised classifications. We further show that the representative cycles we compute have an unsupervised inclination towards phenotype labels. This work thus shows that topological signatures are able to comprehend gene expression levels and classify cohorts accordingly.ConclusionsIn this work, we engender representative persistent cycles to discern the gene expression data. These cycles allow us to directly procure genes entailed in similar processes.

Machine Learning algorithms have been widely used for gene expression data classification, despite the fact that these data have often intrinsic limitations, such as high dimensionality and a small number of examples. Few studies try to characterize to which extent these aspects can influence the performance of the classification models induced. In this paper we compute different measures characterizing the complexity of gene expression data sets for cancer diagnosis. We then investigate how these measures relate to the classification performances achieved by support vector machines, a popular Machine Learning technique usually employed in the analysis of gene expression data. The results obtained indicate that some of the complexity indices utilized are indeed successful in explaining the difficulty involved in the classification of cancer gene expression data.

Rapid technological advancements in microarray analysis continue to generate enormous amounts of genomic data. However, neither hardware nor software computational capabilities have kept pace with this drastic increase. This paper presents a novel framework designed to achieve fast, robust, and accurate (biologically-significant) multi-class classification of gene expression data using distributed knowledge discovery and computational integration routines, specifically for cancer applications. The proposed paradigm consists of the following key computational steps: (a) preprocessing normalization and discretization of gene expression data, (b) partition data using two methods: overlapped windows and adaptive selection, (c) perform association rule discovery on partitioned data-spaces using FP-growth method, (d) integrate derived association rules on distributed processor nodes using a novel knowledge integration algorithm, (e) further prune rules to reduce dimensionality using parametric significance estimation, and (f) cluster remaining rules using a novel clustering algorithm for enhanced visualization and interpretation of discovered gene rule sets.

Microarray technology has transformed the biotechnological research to next level in the recent years. It provides the expression levels of various genes involved in a particular disease. Prostate cancer disease turned into life threatening cancer. The genes causing this disease are identified through the classification methods. These gene expression data have problems like high dimensional with low sample size which imposes active challenges in the existing classification algorithms. Feature selection techniques are applied in order to address the dimensionality issues. . This paper aims in analyzing the feature selection methods for classification of gene expression data of Prostate and identify the significant genes that have a major influence on the disease. The three different feature selection methods such as Filters, wrappers and embedded selectors are applied before the classification process for selecting the top ranked genes. Then, the extracted top ranked genes are applied on the classification algorithms such as SVM, k-NN, Random Forest and Artificial Neural Network. After the inclusion of feature selection technique, the classification accuracy is significantly boosted even with less number of genes. Random Forest classification algorithm outperforms other classification methods. The significant genes that has the major influence in prostate cancer disease are identified such as KLK3, GFI1, CXCR2 and TNFRSF10C.

The process of merging data of different data sources is referred to as record linkage. A medical environment with increased preconditions on privacy protection demands the transformation of clear-text attributes like first name or date of birth into one-way encrypted pseudonyms. When performing an automated or privacy preserving record linkage there might be the need of a binary classification deciding whether two records should be classified as the same entity. The classification is the final of the four main phases of the record linkage process: Preprocessing, indexing, matching and classification. The choice of binary classification techniques in dependence of project specifications in particular data quality has not extensively been studied yet. The aim of this work is the introduction and evaluation of an automatable semi-supervised binary classification system applied within the field of record linkage capable of competing or even surpassing advanced automated techniques of the domain of unsupervised classification. This work describes the rationale leading to the model and the final implementation of an automatable semi-supervised binary classification system and the comparison of its classification performance to an advanced active learning approach out of the domain of unsupervised learning. The performance of both systems has been measured on a broad variety of artificial test sets (n = 400), based on real patient data, with distinct and unique characteristics. While the classification performance for both methods measured as F-measure was relatively close on test sets with maximum defined data quality, 0.996 for semi-supervised classification, 0.993 for unsupervised classification, it incrementally diverged for test sets of worse data quality dropping to 0.964 for semi-supervised classification and 0.803 for unsupervised classification. Aside from supplying a viable model for semi-supervised classification for automated probabilistic record linkage, the tests conducted on a large amount of test sets suggest that semi-supervised techniques might generally be capable of outperforming unsupervised techniques especially on data with lower levels of data quality.

Microarray experiments generate data sets containing valuable information on the gene expression levels of millions of genes in the form of a set of biological samples. Inference of gene regulatory networks from microarray data has become an important research area in bioinformatics. Several computational methods have been proposed to infer important relationships between transcription factors with target genes from gene expression and transcription factor data sets. The inferences from these methods are consistent with the biological literature and can help researchers design reasonable and efficient drugs to resist different diseases. This paper is a survey of different methods used for preprocessing and inferring the gene regulatory networks from a data set of gene expression.

Gene expression profiles are sequences of numbers, and the need to analyze them has now increased significantly. Gene expression data contain a large number of genes and models used for cancer classification. As the wealth of these data being produced, new prediction, classification and clustering techniques are applied to the analysis of the data. Although there are a number of proposed methods with good results, there is still limited diagnostics and a lot of problems still to be solved. To solve the difficulty, in this paper, an efficient gene expression data classification is proposed. To predict the cancer class of patients from the gene expression profile, this paper presents a novel classification framework in the manner of three steps namely, Pre-processing, feature selection and classification. In pre-processing, missing value is filled and redundant data are removed. To attain the enhanced classification outcomes, the important features are selected from the database with the help of Adaptive Salp Swarm Optimization (ASSO) algorithm. Then, the selected features are given to the multi kernel SVM (MKSVM) to classify the gene expression data namely, BRCA, KIRC, COAD, LUAD and PRAD. The performance of proposed methodology is analyzed in terms of different metrics namely, accuracy, sensitivity and specificity. The performance of proposed methodology is 4.5% better than existing method in terms of accuracy.

Analysis of temporal gene expression data poses a significant challenge due to the combination of high dimensionality and low sample size. The purpose of this paper is to present a methodology for classification, modelling, and analysis of short time-series gene expression data using spiking neural networks (SNN) and to uncover temporal expression patterns for knowledge discovery. The classification is based on the NeuCube SNN model. Time-series gene expression data of mouse primary cortical neurons is examined as a case study. The results of the analysis are promising, indicating that SNN methodologies can be effectively used to model and analyse temporal gene expression data with surpassing performance over traditional machine learning algorithms. Additionally, a gene interaction network is constructed from the temporal gene activity modelled using the NeuCube architecture offering a new way of knowledge discovery. Future work will be directed towards using gene interactions networks to help guide pharmacological research for dementia.

In recent years, many studies have shown that microarray gene expression data is useful for disease identification and cancer classification. However, since gene expression data may contain thousands of genes simultaneously, successful microarray classification can be rather difficult. Feature (gene) selection is a frequently used pre-processing technology for successful classification of microarray gene expression data. Selecting a useful gene subset as a classifier not only decreases the computational time and cost, but also increases the classification accuracy. It is therefore imperative to extract only a small number of genes, which are exclusively relevant for the classification of a particular cancer/disease type. In this paper, correlation-based binary particle swarm optimizations is proposed to select the relevant genes, and a K-nearest neighbor with the leave-one-out cross-validation method serves as a classifier to evaluate the classification performance on six published cancer classification data sets. The experimental results show that the proposed method selects fewer gene subsets, while still resulting in higher prediction accuracy than the other literature methods.

Most of the traditional gene selection approaches are borrowed from other fields such as statistics and computer science, However, they do not prioritize biologically relevant genes since the ultimate goal is to determine features that optimize model performance metrics not to build a biologically meaningful model. Therefore, there is an imminent need for new computational tools that integrate the biological knowledge about the data in the process of gene selection and machine learning. Integrative gene selection enables incorporation of biological domain knowledge from external biological resources. In this study, we propose a new computational approach named CogNet that is an integrative gene selection tool that exploits biological knowledge for grouping the genes for the computational modeling tasks of ranking and classification. In CogNet, the pathfindR serves as the biological grouping tool to allow the main algorithm to rank active-subnetwork-oriented KEGG pathway enrichment analysis results to build a biologically relevant model. CogNet provides a list of significant KEGG pathways that can classify the data with a very high accuracy. The list also provides the genes belonging to these pathways that are differentially expressed that are used as features in the classification problem. The list facilitates deep analysis and better interpretability of the role of KEGG pathways in classification of the data thus better establishing the biological relevance of these differentially expressed genes. Even though the main aim of our study is not to improve the accuracy of any existing tool, the performance of the CogNet outperforms a similar approach called maTE while obtaining similar performance compared to other similar tools including SVM-RCE. CogNet was tested on 13 gene expression datasets concerning a variety of diseases.