Wavelet feature extraction and genetic algorithm for biomarker detection in colorectal cancer data

Biomarkers which predict patient’s survival can play an important role in medical diagnosis and treatment. How to select the significant biomarkers from hundreds of protein markers is a key step in survival analysis. In this paper a novel method is proposed to detect the prognostic biomarkers ofsurvival in colorectal cancer patients using wavelet analysis, genetic algorithm, and Bayes classifier. One dimensional discrete wavelet transform (DWT) is normally used to reduce the dimensionality of biomedical data. In this study one dimensional continuous wavelet transform (CWT) was proposed to extract the features of colorectal cancer data. One dimensional CWT has no ability to reduce dimensionality of data, but captures the missing features of DWT, and is complementary part of DWT. Genetic algorithm was performed on extracted wavelet coefficients to select the optimized features, using Bayes classifier to build its fitness function. The corresponding protein markers were located based on the position of optimized features. Kaplan-Meier curve and Cox regression model 2 were used to evaluate the performance of selected biomarkers. Experiments were conducted on colorectal cancer dataset and several significant biomarkers were detected. A new protein biomarker CD46 was found to significantly associate with survival time

Identify submitochondria and subchloroplast locations with pseudo amino acid composition: Approach from the strategy of discrete wavelet transform feature extraction

AbstractIt is very challenging and complicated to predict protein locations at the sub-subcellular level. The key to enhancing the prediction quality for protein sub-subcellular locations is to grasp the core features of a protein that can discriminate among proteins with different subcompartment locations. In this study, a different formulation of pseudoamino acid composition by the approach of discrete wavelet transform feature extraction was developed to predict submitochondria and subchloroplast locations. As a result of jackknife cross-validation, with our method, it can efficiently distinguish mitochondrial proteins from chloroplast proteins with total accuracy of 98.8% and obtained a promising total accuracy of 93.38% for predicting submitochondria locations. Especially the predictive accuracy for mitochondrial outer membrane and chloroplast thylakoid lumen were 82.93% and 82.22%, respectively, showing an improvement of 4.88% and 27.22% when other existing methods were compared. The results indicated that the proposed method might be employed as a useful assistant technique for identifying sub-subcellular locations. We have implemented our algorithm as an online service called SubIdent (http://bioinfo.ncu.edu.cn/services.aspx)

Characterisation and Classification of Protein Sequences by Using Enhanced Amino Acid Indices and Signal Processing-Based Methods

Due to copyright reasons, the authors published papers have been removed from this copy of the thesis.Protein sequencing has produced overwhelming amount of protein sequences, especially in the last decade. Nevertheless, the majority of the proteins' functional and structural classes are still unknown, and experimental methods currently used to determine these properties are very expensive, laborious and time consuming. Therefore, automated computational methods are urgently required to accurately and reliably predict functional and structural classes of the proteins. Several bioinformatics methods have been developed to determine such properties of the proteins directly from their sequence information. Such methods that involve signal processing methods have recently become popular in the bioinformatics area and been investigated for the analysis of DNA and protein sequences and shown to be useful and generally help better characterise the sequences. However, there are various technical issues that need to be addressed in order to overcome problems associated with the signal processing methods for the analysis of the proteins sequences. Amino acid indices that are used to transform the protein sequences into signals have various applications and can represent diverse features of the protein sequences and amino acids. As the majority of indices have similar features, this project proposes a new set of computationally derived indices that better represent the original group of indices. A study is also carried out that resulted in finding a unique and universal set of best discriminating amino acid indices for the characterisation of allergenic proteins. This analysis extracts features directly from the protein sequences by using Discrete Fourier Transform (DFT) to build a classification model based on Support Vector Machines (SVM) for the allergenic proteins. The proposed predictive model yields a higher and more reliable accuracy than those of the existing methods. A new method is proposed for performing a multiple sequence alignment. For this method, DFT-based method is used to construct a new distance matrix in combination with multiple amino acid indices that were used to encode protein sequences into numerical sequences. Additionally, a new type of substitution matrix is proposed where the physicochemical similarities between any given amino acids is calculated. These similarities were calculated based on the 25 amino acids indices selected, where each one represents a unique biological protein feature. The proposed multiple sequence alignment method yields a better and more reliable alignment than the existing methods. In order to evaluate complex information that is generated as a result of DFT, Complex Informational Spectrum Analysis (CISA) is developed and presented. As the results show, when protein classes present similarities or differences according to the Common Frequency Peak (CFP) in specific amino acid indices, then it is probable that these classes are related to the protein feature that the specific amino acid represents. By using only the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient, as biologically related features can appear individually either in the real or the imaginary spectrum. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Upon identification of a new protein, it is important to single out amino acid responsible for the structural and functional classification of the protein, as well as the amino acids contributing to the protein's specific biological characterisation. In this work, a novel approach is presented to identify and quantify the relationship between individual amino acids and the protein. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Characterisation and identification problem of the Influenza A virus protein sequences is tackled through a Subgroup Discovery (SD) algorithm, which can provide ancillary knowledge to the experts. The main objective of the case study was to derive interpretable knowledge for the influenza A virus problem and to consequently better describe the relationships between subtypes of this virus. Finally, by using DFT-based sequence-driven features a Support Vector Machine (SVM)-based classification model was built and tested, that yields higher predictive accuracy than that of SD. The methods developed and presented in this study yield promising results and can be easily applied to proteomic fields

Network and multi-scale signal analysis for the integration of large omic datasets: applications in \u3ci\u3ePopulus trichocarpa\u3c/i\u3e

Poplar species are promising sources of cellulosic biomass for biofuels because of their fast growth rate, high cellulose content and moderate lignin content. There is an increasing movement on integrating multiple layers of ’omics data in a systems biology approach to understand gene-phenotype relationships and assist in plant breeding programs. This dissertation involves the use of network and signal processing techniques for the combined analysis of these various data types, for the goals of (1) increasing fundamental knowledge of P. trichocarpa and (2) facilitating the generation of hypotheses about target genes and phenotypes of interest. A data integration “Lines of Evidence” method is presented for the identification and prioritization of target genes involved in functions of interest. A new post-GWAS method, Pleiotropy Decomposition, is presented, which extracts pleiotropic relationships between genes and phenotypes from GWAS results, allowing for identification of genes with signatures favorable to genome editing. Continuous wavelet transform signal processing analysis is applied in the characterization of genome distributions of various features (including variant density, gene density, and methylation profiles) in order to identify chromosome structures such as the centromere. This resulted in the approximate centromere locations on all P. trichocarpa chromosomes, which had previously not been adequately reported in the scientific literature. Discrete wavelet transform signal processing followed by correlation analysis was applied to genomic features from various data types including transposable element density, methylation density, SNP density, gene density, centromere position and putative ancestral centromere position. Subsequent correlation analysis of the resulting wavelet coefficients identified scale-specific relationships between these genomic features, and provide insights into the evolution of the genome structure of P. trichocarpa. These methods have provided strategies to both increase fundamental knowledge about the P. trichocarpa system, as well as to identify new target genes related to biofuels targets. We intend that these approaches will ultimately be used in the designing of better plants for more efficient and sustainable production of bioenergy

Conditions for propagation and block of excitation in an asymptotic model of atrial tissue

Detailed ionic models of cardiac cells are difficult for numerical simulations because they consist of a large number of equations and contain small parameters. The presence of small parameters, however, may be used for asymptotic reduction of the models. Earlier results have shown that the asymptotics of cardiac equations are non-standard. Here we apply such a novel asymptotic method to an ionic model of human atrial tissue in order to obtain a reduced but accurate model for the description of excitation fronts. Numerical simulations of spiral waves in atrial tissue show that wave fronts of propagating action potentials break-up and self-terminate. Our model, in particular, yields a simple analytical criterion of propagation block, which is similar in purpose but completely different in nature to the `Maxwell rule' in the FitzHugh-Nagumo type models. Our new criterion agrees with direct numerical simulations of break-up of re-entrant waves.Comment: Revised manuscript submitted to Biophysical Journal (30 pages incl. 10 figures

Advances in Digital Processing of Low-Amplitude Components of Electrocardiosignals

This manual has been published within the framework of the BME-ENA project under the responsibility of National Technical University of Ukraine. The BME-ENA “Biomedical Engineering Education Tempus Initiative in Eastern Neighbouring Area”, Project Number: 543904-TEMPUS-1-2013-1-GR-TEMPUS-JPCR is a Joint Project within the TEMPUS IV program. This project has been funded with support from the European Commission.Навчальний посібник присвячено розробці методів та засобів для неінвазивного виявлення та дослідження тонких проявів електричної активності серця. Особлива увага приділяється вдосконаленню інформаційного та алгоритмічного забезпечення систем електрокардіографії високого розрізнення для ранньої діагностики електричної нестабільності міокарда, а також для оцінки функціонального стану плоду під час вагітності. Теоретичні основи супроводжуються прикладами реалізації алгоритмів за допомогою системи MATLAB. Навчальний посібник призначений для студентів, аспірантів, а також фахівців у галузі біомедичної електроніки та медичних працівників.The teaching book is devoted to development and research of methods and tools for non-invasive detection of subtle manifistations of heart electrical activity. Particular attention is paid to the improvement of information and algorithmic support of high resolution electrocardiography for early diagnosis of myocardial electrical instability, as well as for the evaluation of the functional state of the fetus during pregnancy examination. The theoretical basis accompanied by the examples of implementation of the discussed algorithms with the help of MATLAB. The teaching book is intended for students, graduate students, as well as specialists in the field of biomedical electronics and medical professionals

Efficient smile detection by Extreme Learning Machine

Smile detection is a specialized task in facial expression analysis with applications such as photo selection, user experience analysis, and patient monitoring. As one of the most important and informative expressions, smile conveys the underlying emotion status such as joy, happiness, and satisfaction. In this paper, an efficient smile detection approach is proposed based on Extreme Learning Machine (ELM). The faces are first detected and a holistic flow-based face registration is applied which does not need any manual labeling or key point detection. Then ELM is used to train the classifier. The proposed smile detector is tested with different feature descriptors on publicly available databases including real-world face images. The comparisons against benchmark classifiers including Support Vector Machine (SVM) and Linear Discriminant Analysis (LDA) suggest that the proposed ELM based smile detector in general performs better and is very efficient. Compared to state-of-the-art smile detector, the proposed method achieves competitive results without preprocessing and manual registration

Hidden Markov Models

Hidden Markov Models (HMMs), although known for decades, have made a big career nowadays and are still in state of development. This book presents theoretical issues and a variety of HMMs applications in speech recognition and synthesis, medicine, neurosciences, computational biology, bioinformatics, seismology, environment protection and engineering. I hope that the reader will find this book useful and helpful for their own research