Identification of discriminant features from stationary pattern of nucleotide bases and their application to essential gene classification

Introduction: Essential genes are essential for the survival of various species. These genes are a family linked to critical cellular activities for species survival. These genes are coded for proteins that regulate central metabolism, gene translation, deoxyribonucleic acid replication, and fundamental cellular structure and facilitate intracellular and extracellular transport. Essential genes preserve crucial genomics information that may hold the key to a detailed knowledge of life and evolution. Essential gene studies have long been regarded as a vital topic in computational biology due to their relevance. An essential gene is composed of adenine, guanine, cytosine, and thymine and its various combinations.Methods: This paper presents a novel method of extracting information on the stationary patterns of nucleotides such as adenine, guanine, cytosine, and thymine in each gene. For this purpose, some co-occurrence matrices are derived that provide the statistical distribution of stationary patterns of nucleotides in the genes, which is helpful in establishing the relationship between the nucleotides. For extracting discriminant features from each co-occurrence matrix, energy, entropy, homogeneity, contrast, and dissimilarity features are computed, which are extracted from all co-occurrence matrices and then concatenated to form a feature vector representing each essential gene. Finally, supervised machine learning algorithms are applied for essential gene classification based on the extracted fixed-dimensional feature vectors.Results: For comparison, some existing state-of-the-art feature representation techniques such as Shannon entropy (SE), Hurst exponent (HE), fractal dimension (FD), and their combinations have been utilized.Discussion: An extensive experiment has been performed for classifying the essential genes of five species that show the robustness and effectiveness of the proposed methodology

Design and optimal tuning of fraction order controller for multiple stage evaporator system

The tight control of the process parameters through appropriate tuning of controllers is an art that imperatively employed to various process industries. Most of these industries are influenced by the nonlinearity that occurred due to the input parameter variation and presence of disturbances. The aim of this work is to investigate the nonlinear dynamics of a paper industry based energy intensive unit named Multiple Stage Evaporator (MSE) in presence of different Energy Reduction Schemes. MSE is used to concentrate the weak Black Liquor (BL), a biomass based byproduct. Hence, to extract the bioenergy from the BL, the quality of the product liquor needs to be appropriately controlled. The quality of BL is measured by two process parameters, product concentration and temperature. Hence, in this work, an intelligent controller Fraction Order Proportional-Integral-Derivative controller has been studied and employed to resolve the servo and the regulatory problem occurred during the process. A state-of-art metaheuristic approach, Black Widow Optimization Algorithm has been proposed here to tune the controller parameters and compared with another optimization approaches named Water Cycle Algorithm. The simulated result demonstrates the usefulness of the proposed strategy and confirm the performance improvement for the process parameters. To enlighten the advantages of the proposed control scheme, a comparative analysis have also been performed with conventional PID, 2-DOF-PID and FOPID controllers

Table1_Identification of discriminant features from stationary pattern of nucleotide bases and their application to essential gene classification.docx

Introduction: Essential genes are essential for the survival of various species. These genes are a family linked to critical cellular activities for species survival. These genes are coded for proteins that regulate central metabolism, gene translation, deoxyribonucleic acid replication, and fundamental cellular structure and facilitate intracellular and extracellular transport. Essential genes preserve crucial genomics information that may hold the key to a detailed knowledge of life and evolution. Essential gene studies have long been regarded as a vital topic in computational biology due to their relevance. An essential gene is composed of adenine, guanine, cytosine, and thymine and its various combinations.Methods: This paper presents a novel method of extracting information on the stationary patterns of nucleotides such as adenine, guanine, cytosine, and thymine in each gene. For this purpose, some co-occurrence matrices are derived that provide the statistical distribution of stationary patterns of nucleotides in the genes, which is helpful in establishing the relationship between the nucleotides. For extracting discriminant features from each co-occurrence matrix, energy, entropy, homogeneity, contrast, and dissimilarity features are computed, which are extracted from all co-occurrence matrices and then concatenated to form a feature vector representing each essential gene. Finally, supervised machine learning algorithms are applied for essential gene classification based on the extracted fixed-dimensional feature vectors.Results: For comparison, some existing state-of-the-art feature representation techniques such as Shannon entropy (SE), Hurst exponent (HE), fractal dimension (FD), and their combinations have been utilized.Discussion: An extensive experiment has been performed for classifying the essential genes of five species that show the robustness and effectiveness of the proposed methodology.</p