Optimization of Spaced K-mer Frequency Feature Extraction using Genetic Algorithms for Metagenome Fragment Classification

K-mer frequencies are commonly used in extracting features from metagenome fragments. In spite of this, researchers have found that their use is still inefficient. In this research, a genetic algorithm was employed to find optimally spaced k-mers. These were obtained by generating the possible combinations of match positions and don't care positions (written as *). This approach was adopted from the concept of spaced seeds in PatternHunter. The use of spaced k-mers could reduce the size of the k-mer frequency feature's dimension. To measure the accuracy of the proposed method we used the naïve Bayesian classifier (NBC). The result showed that the chromosome 111111110001, representing spaced k-mer model [111 1111 10001], was the best chromosome, with a higher fitness (85.42) than that of the k-mer frequency feature. Moreover, the proposed approach also reduced the feature extraction time.

A Survey of Feature Selection Strategies for DNA Microarray Classification

Classification tasks are difficult and challenging in the bioinformatics field, that used to predict or diagnose patients at an early stage of disease by utilizing DNA microarray technology. However, crucial characteristics of DNA microarray technology are a large number of features and small sample sizes, which means the technology confronts a "dimensional curse" in its classification tasks because of the high computational execution needed and the discovery of biomarkers difficult. To reduce the dimensionality of features to find the significant features that can employ feature selection algorithms and not affect the performance of classification tasks. Feature selection helps decrease computational time by removing irrelevant and redundant features from the data. The study aims to briefly survey popular feature selection methods for classifying DNA microarray technology, such as filters, wrappers, embedded, and hybrid approaches. Furthermore, this study describes the steps of the feature selection process used to accomplish classification tasks and their relationships to other components such as datasets, cross-validation, and classifier algorithms. In the case study, we chose four different methods of feature selection on two-DNA microarray datasets to evaluate and discuss their performances, namely classification accuracy, stability, and the subset size of selected features. Keywords: Brief survey; DNA microarray data; feature selection; filter methods; wrapper methods; embedded methods; and hybrid methods. DOI: 10.7176/CEIS/14-2-01 Publication date:March 31st 202

An enhanced binary bat and Markov clustering algorithms to improve event detection for heterogeneous news text documents

Event Detection (ED) works on identifying events from various types of data. Building an ED model for news text documents greatly helps decision-makers in various disciplines in improving their strategies. However, identifying and summarizing events from such data is a non-trivial task due to the large volume of published heterogeneous news text documents. Such documents create a high-dimensional feature space that influences the overall performance of the baseline methods in ED model. To address such a problem, this research presents an enhanced ED model that includes improved methods for the crucial phases of the ED model such as Feature Selection (FS), ED, and summarization. This work focuses on the FS problem by automatically detecting events through a novel wrapper FS method based on Adapted Binary Bat Algorithm (ABBA) and Adapted Markov Clustering Algorithm (AMCL), termed ABBA-AMCL. These adaptive techniques were developed to overcome the premature convergence in BBA and fast convergence rate in MCL. Furthermore, this study proposes four summarizing methods to generate informative summaries. The enhanced ED model was tested on 10 benchmark datasets and 2 Facebook news datasets. The effectiveness of ABBA-AMCL was compared to 8 FS methods based on meta-heuristic algorithms and 6 graph-based ED methods. The empirical and statistical results proved that ABBAAMCL surpassed other methods on most datasets. The key representative features demonstrated that ABBA-AMCL method successfully detects real-world events from Facebook news datasets with 0.96 Precision and 1 Recall for dataset 11, while for dataset 12, the Precision is 1 and Recall is 0.76. To conclude, the novel ABBA-AMCL presented in this research has successfully bridged the research gap and resolved the curse of high dimensionality feature space for heterogeneous news text documents. Hence, the enhanced ED model can organize news documents into distinct events and provide policymakers with valuable information for decision making