Data Mining of Gene Expression Data by Fuzzy and Hybrid Fuzzy Methods

Uncertainty, imprecision, and many-valued logics in protein bioinformatics

Understanding proteins, their structures, functions, mutual interactions, activity in cellular reactions, interactions with drugs, and expression in body cells is a key to efficient medical diagnosis, drug production, and treatment of patients. Machine learning and data exploration methods supported by many-valued logics allow to grasp the imprecision and uncertainties that naturally occur in proteins and other biomolecules. Many-valued logics, like Łukasiewicz logic or fuzzy logic, are non-classical logics that do not restrict the number of truth values to only two values of true or false, but they allow for a larger set of truth degrees. In this paper, we briefly review the use of many-valued logics, especially the fuzzy logic, in bioinformatics. Then, we focus on protein bioinformatics, and present selected applications of many-valued logics in the analysis of complex protein structures, including; (1) potential-based protein similarity searching, (2) matching proteins on the basis of secondary structures, (3) 3D protein structure alignment, (4) prediction of intrinsically disordered proteins, and (5) fuzzy querying in large collections of Big macromolecular Data. Results of presented studies show that the utilization of many-valued logics can enrich the investigations of protein molecules, in which uncertainty and imprecision are prevalent problems. The paper discusses all observed benefits brought by the application of many-valued logics in investigations related to selected protein analyzes carried out by the author.

BGFS: Design and Development of Brain Genetic Fuzzy System for Data Classification

Recently, classification systems have received significant attention among researchers due to the important characteristics and behaviors of analysis required in real-time databases. Among the various classification-based methods suitable for real-time databases, fuzzy rule-based classification is effectively used by different researchers in various fields. An important issue in the design of fuzzy rule-based classification is the automatic generation of fuzzy if-then rules and the membership functions. The literature presents different techniques for automatic fuzzy design. Among the different techniques available in the literature, choosing the type, the number of membership functions, and defining parameters of membership function are still challenging tasks. In order to handle these challenges in the fuzzy rule-based classification system, this paper proposes a brain genetic fuzzy system (BGFS) for data classification by newly devising the exponential genetic brain storm optimization. Here, membership functions are optimally devised using exponential genetic brain storm optimization algorithm and rules are derived using the exponential brain storm optimization algorithm. The designed membership function and fuzzy rules are then effectively utilized for data classification. The proposed BGFS is analyzed with four datasets, using sensitivity, specificity, and accuracy. The outcome ensures that the proposed BGFS obtained the maximum accuracy of 88.8%, which is high as compared with the existing adaptive genetic fuzzy system.

BSFS: Design and Development of Exponential Brain Storm Fuzzy System for Data Classification

The inductive learning of fuzzy rule classifier suffers in the rule generation and rule optimization when the search space or variables becomes high. This creates the new idea of making the fuzzy system with precise rules leading to less scalability and improved accuracy. Accordingly, different approaches have been presented in the literature for optimal finding of fuzzy rules using optimization algorithms. Here, we make use of the brain storm optimization algorithm for rule optimization. In this paper, a new fuzzy system called, exponential brain storm fuzzy system is developed by modifying the traditional fuzzy system in rule definition process. In rule derivation, we have presented an algorithm called, EBSO by modifying the BSO algorithm with exponential model. Also, the membership function is designed using simple uniform distribution-based approach. Finally, data classification is performed with a new BSFS system using three medical databases such as, PID, Cleveland and DRD. The experimentation proved that the proposed BSFS clearly outperformed in all the three datasets by reaching the maximum accuracy.

Automated Detection of Cancer Associated Genes Using a Combined Fuzzy-Rough-Set-Based F-Information and Water Swirl Algorithm of Human Gene Expression Data

This study describes a novel approach to reducing the challenges of highly nonlinear multiclass gene expression values for cancer diagnosis. To build a fruitful system for cancer diagnosis, in this study, we introduced two levels of gene selection such as filtering and embedding for selection of potential genes and the most relevant genes associated with cancer, respectively. The filter procedure was implemented by developing a fuzzy rough set (FR)-based method for redefining the criterion function of f-information (FI) to identify the potential genes without discretizing the continuous gene expression values. The embedded procedure is implemented by means of a water swirl algorithm (WSA), which attempts to optimize the rule set and membership function required to classify samples using a fuzzy-rule-based multiclassification system (FRBMS). Two novel update equations are proposed in WSA, which have better exploration and exploitation abilities while designing a self-learning FRBMS. The efficiency of our new approach was evaluated on 13 multicategory and 9 binary datasets of cancer gene expression. Additionally, the performance of the proposed FRFI-WSA method in designing an FRBMS was compared with existing methods for gene selection and optimization such as genetic algorithm (GA), particle swarm optimization (PSO), and artificial bee colony algorithm (ABC) on all the datasets. In the global cancer map with repeated measurements (GCM_RM) dataset, the FRFI-WSA showed the smallest number of 16 most relevant genes associated with cancer using a minimal number of 26 compact rules with the highest classification accuracy (96.45%). In addition, the statistical validation used in this study revealed that the biological relevance of the most relevant genes associated with cancer and their linguistics detected by the proposed FRFI-WSA approach are better than those in the other methods. The simple interpretable rules with most relevant genes and effectively classified samples suggest that the proposed FRFI-WSA approach is reliable for classification of an individual’s cancer gene expression data with high precision and therefore it could be helpful for clinicians as a clinical decision support system.

A Novel Hybrid Feature Selection Model for Classification of Neuromuscular Dystrophies Using Bhattacharyya Coefficient, Genetic Algorithm and Radial Basis Function Based Support Vector Machine

An accurate classification of neuromuscular disorders is important in providing proper treatment facilities to the patients. Recently, the microarray technology is employed to monitor the level of activity or expression of large number of genes simultaneously. The gene expression data derived from the microarray experiment usually involve a large number of genes but a very few number of samples. There is a need to reduce the dimension of gene expression data which intends to find a small set of discriminative genes that accurately classifies the samples of various kinds of diseases. So, our goal is to find a small subset of genes which ensures the accurate classification of neuromuscular disorders. In the present paper, we propose a novel hybrid feature selection model for classification of neuromuscular disorders. The process of feature selection is done in two phases by integrating Bhattacharyya coefficient and genetic algorithm (GA). In the first phase, we find Bhattacharyya coefficient to choose a candidate gene subset by removing the most redundant genes. In the second phase, the target gene subset is created by selecting the most discriminative gene subset by applying GA wherein the fitness function is calculated using radial basis function support vector machine (RBF SVM). The proposed hybrid algorithm is applied on two publicly available microarray neuromuscular disorders datasets. The results are compared with two individual techniques of feature selection, namely Bhattacharyya coefficient and GA, and one integrated technique, i.e., Bhattacharyya-GA wherein the fitness function of GA is calculated using four other classifiers, which shows that the proposed integrated method is capable of giving the better classification accuracy.

Hybrid Ant Bee Algorithm for Fuzzy Expert System Based Sample Classification

Accuracy maximization and complexity minimization are the two main goals of a fuzzy expert system based microarray data classification. Our previous Genetic Swarm Algorithm (GSA) approach has improved the classification accuracy of the fuzzy expert system at the cost of their interpretability. The if-then rules produced by the GSA are lengthy and complex which is difficult for the physician to understand. To address this interpretability-accuracy tradeoff, the rule set is represented using integer numbers and the task of rule generation is treated as a combinatorial optimization task. Ant colony optimization (ACO) with local and global pheromone updations are applied to find out the fuzzy partition based on the gene expression values for generating simpler rule set. In order to address the formless and continuous expression values of a gene, this paper employs artificial bee colony (ABC) algorithm to evolve the points of membership function. Mutual Information is used for idenfication of informative genes. The performance of the proposed hybrid Ant Bee Algorithm (ABA) is evaluated using six gene expression data sets. From the simulation study, it is found that the proposed approach generated an accurate fuzzy system with highly interpretable and compact rules for all the data sets when compared with other approaches.

Using image mapping towards biomedical and biological data sharing

Image-based data integration in eHealth and life sciences is typically concerned with the method used for anatomical space mapping, needed to retrieve, compare and analyse large volumes of biomedical data. In mapping one image onto another image, a mechanism is used to match and find the corresponding spatial regions which have the same meaning between the source and the matching image. Image-based data integration is useful for integrating data of various information structures. Here we discuss a broad range of issues related to data integration of various information structures, review exemplary work on image representation and mapping, and discuss the challenges that these techniques may bring.

MULTISTAGE MUTUAL INFORMATION FOR INFORMATIVE GENE SELECTION

An important issue in the design of gene selection algorithm for microarray data analysis is the formation of suitable criterion function for measuring the relevance between different gene expressions. Mutual information (MI) is a widely used criterion function but it calculates the relevance on the entire samples only once which cannot exactly identify the informative genes. This paper proposes a novel idea of computing MI in stages. The proposed multistage mutual information (MSMI) computes MI, initially using all the samples and based on the classification performance produced by artificial neural network (ANN), MI is repeatedly calculated using only the unclassified samples until there is no improvement in the classification accuracy. The performance of the proposed approach is evaluated using ten gene expression data sets. Simulation result shows that the proposed approach helps to improve the discriminate power of the genes with regard to the target disease of a microarray sample. Statistical analysis of the test result shows that the proposed method selects highly informative genes and produces comparable classification accuracy than the other approaches reported in the literature.