Pomegranate MR image analysis using fuzzy clustering algorithms

In this paper, the process of the pomegranate magnetic resonance (MR) images was studied.  Its internal structure is composed of tissue and seeds, which indicate the dependency between the maturity and internal quality.  The latter properties are important in pomegranate’s sorting and cannot be measured manually.  In this paper, an automatic algorithm was proposed to segment the internal structure of pomegranates.  Since the intensities of the calyx and stem of the pomegranate MR image are closely related to that of the soft tissue, their corresponding pixels are therefore labeled in the same class of the internal soft tissues.  In order to solve this problem, the exact shape of the pomegranate is first extracted from the background of the image using active contour models (ACMs).  Then, the stem and calyx are removed using morphological filters.  We have also proposed an improved version of the fuzzy c-means algorithm (FCM), the spatial FCM (SFCM), for segmentation of MR images of pomegranate.  SFCM is realized by incorporating the spatial neighborhood information into the standard FCM and modifying the membership weighting of each cluster.  SFCM employs spatial information of adjacent pixels leading to an improvement of the results.  It thus outperforms other techniques like FCM, even in the presence of Gaussian, salt and pepper, and speckle noises. Keywords: MRI, pomegranate, image segmentation, spatial fuzzy c-means, morphological filter&nbsp

Automatic Facial Skin Segmentation Using Possibilistic C-Means Algorithm for Evaluation of Facial Surgeries

Human face has a fundamental role in the appearance of individuals. So the importance of facial surgeries is undeniable. Thus, there is a need for the appropriate and accurate facial skin segmentation in order to extract different features. Since Fuzzy C-Means (FCM) clustering algorithm doesn't work appropriately for noisy images and outliers, in this paper we exploit Possibilistic C-Means (PCM) algorithm in order to segment the facial skin. For this purpose, first, we convert facial images from RGB to YCbCr color space. To evaluate performance of the proposed algorithm, the database of Sahand University of Technology, Tabriz, Iran was used. In order to have a better understanding from the proposed algorithm; FCM and Expectation-Maximization (EM) algorithms are also used for facial skin segmentation. The proposed method shows better results than the other segmentation methods. Results include misclassification error (0.032) and the region's area error (0.045) for the proposed algorithm

Automatic Facial Skin Segmentation Using Possibilistic C-Means Algorithm for Evaluation of Facial Surgeries

Human face has a fundamental role in the appearance of individuals. So the importance of facial surgeries is undeniable. Thus, there is a need for the appropriate and accurate facial skin segmentation in order to extract different features. Since Fuzzy C-Means (FCM) clustering algorithm doesn't work appropriately for noisy images and outliers, in this paper we exploit Possibilistic C-Means (PCM) algorithm in order to segment the facial skin. For this purpose, first, we convert facial images from RGB to YCbCr color space. To evaluate performance of the proposed algorithm, the database of Sahand University of Technology, Tabriz, Iran was used. In order to have a better understanding from the proposed algorithm; FCM and Expectation-Maximization (EM) algorithms are also used for facial skin segmentation. The proposed method shows better results than the other segmentation methods. Results include misclassification error (0.032) and the region's area error (0.045) for the proposed algorithm

Automatic Facial Skin Segmentation Using Possibilistic C-Means Algorithm for Evaluation of Facial Surgeries

Human face has a fundamental role in the appearance of individuals. So the importance of facial surgeries is undeniable. Thus, there is a need for the appropriate and accurate facial skin segmentation in order to extract different features. Since Fuzzy C-Means (FCM) clustering algorithm doesn't work appropriately for noisy images and outliers, in this paper we exploit Possibilistic C-Means (PCM) algorithm in order to segment the facial skin. For this purpose, first, we convert facial images from RGB to YCbCr color space. To evaluate performance of the proposed algorithm, the database of Sahand University of Technology, Tabriz, Iran was used. In order to have a better understanding from the proposed algorithm; FCM and Expectation-Maximization (EM) algorithms are also used for facial skin segmentation. The proposed method shows better results than the other segmentation methods. Results include misclassification error (0.032) and the region's area error (0.045) for the proposed algorithm

Development of a new sequential block finding strategy for detection of conserved sequences in riboswitches

Introduction: Some non-coding RNAs have an important role in the regulation of gene expression and consequently cellular function. Riboswitches are examples of these regulatory RNAs. Riboswitches are classified into various families according to sequential and structural similarities. Methods: In this study, a block finder algorithm for identification of frequently appearing sequential blocks in five families of riboswitches from Rfam 12.0 database, without the use of alignment methods, was developed. Results: The developed program identified 21 frequently appearing blocks in five families of riboswitches. Conclusion: Comparison of the results of the proposed algorithm with those of sequential alignment methods revealed that our method can recognize most of the patterns present in conserved areas of individual riboswitch families and determine them as specific blocks, implying potential of the developed program as a platform for further studies and developments

Classification of seed members of five riboswitch families as short sequences based on the features extracted by Block Location-Based Feature Extraction (BLBFE) method

Introduction: Riboswitches are short regulatory elements generally found in the untranslated regions of prokaryotes’ mRNAs and classified into several families. Due to the binding possibility between riboswitches and antibiotics, their usage as engineered regulatory elements and also their evolutionary contribution, the need for bioinformatics tools of riboswitch detection is increasing. We have previously introduced an alignment independent algorithm for the identification of frequent sequential blocks in the families of riboswitches. Herein, we report the application of block location-based feature extraction strategy (BLBFE), which uses the locations of detected blocks on riboswitch sequences as features for classification of seed sequences. Besides, mono- and dinucleotide frequencies, k-mer, DAC, DCC, DACC, PC-PseDNC-General and SC-PseDNC-General methods as some feature extraction strategies were investigated. Methods: The classifiers of the Decision tree, KNN, LDA, and Naïve Bayes, as well as k-fold cross-validation, were employed for all methods of feature extraction to compare their performances based on the criteria of accuracy, sensitivity, specificity, and f-score performance measures. Results: The outcome of the study showed that the BLBFE strategy classified the riboswitches indicating 87.65% average correct classification rate (CCR). Moreover, the performance of the proposed feature extraction method was confirmed with average values of 94.31%, 85.01%, 95.45% and 85.38% for accuracy, sensitivity, specificity, and f-score, respectively. Conclusion: Our result approved the performance of the BLBFE strategy in the classification and discrimination of the riboswitch groups showing remarkable higher values of CCR, accuracy, sensitivity, specificity and f-score relative to previously studied feature extraction methods

A Novel Flexible Inertia Weight Particle Swarm Optimization Algorithm.

Particle swarm optimization (PSO) is an evolutionary computing method based on intelligent collective behavior of some animals. It is easy to implement and there are few parameters to adjust. The performance of PSO algorithm depends greatly on the appropriate parameter selection strategies for fine tuning its parameters. Inertia weight (IW) is one of PSO's parameters used to bring about a balance between the exploration and exploitation characteristics of PSO. This paper proposes a new nonlinear strategy for selecting inertia weight which is named Flexible Exponential Inertia Weight (FEIW) strategy because according to each problem we can construct an increasing or decreasing inertia weight strategy with suitable parameters selection. The efficacy and efficiency of PSO algorithm with FEIW strategy (FEPSO) is validated on a suite of benchmark problems with different dimensions. Also FEIW is compared with best time-varying, adaptive, constant and random inertia weights. Experimental results and statistical analysis prove that FEIW improves the search performance in terms of solution quality as well as convergence rate

Punctual Algorithm for Small Gene Prediction in DNA Sequences Using a Time-Frequency Approach Based on the Z-Curve

Identification of protein-coding regions inDeoxyribonucleic Acid (DNA) sequences because of their 3-baseperiodicity has been a challenging issue in bioinformatics. ManyDSP (Digital Signal Processing) techniques have been applied foridentification task and concentrated on assigning numericalvalues to the symbolic DNA sequence and then applying spectralanalysis tools such as the short-time discrete Fourier transform(ST-DFT) to locate periodicity components. In this paper, weinvestigate the location of exons in DNA strand using VariableLength Window approach based on z-curve. Z-curve is a unique3-D curve to illustrate DNA's sequence which presents a completedescription of DNA's sequence biological behavior. The proposedalgorithm has a high accuracy and resolution due to applyingGaussian window with an adjustable length to identify andestimate exonic areas and non-coding regions are totallyeliminated. In order to extract period-3 component we used anarrow-band band-pass filter with a central frequency of . Theproposed algorithm was applied on some gene sequences existedin GenBank dataset and its results were compared by otherexisting methods at the nucleotide level. Simulation results showthat our algorithm increases the accuracy of exon detectionrelative to other methods for exon prediction