Abstract: Clusters of Microcalcifications (MCCs) are most frequent symptoms of Ductal Carcinoma in Situ (DCIS) recognized by mammography. Least-Square Support Vector Machine (LS-SVM) is a variant of the standard SVM. In the paper, LS-SVM is proposed as a classifier for classifying MCCs as benign or malignant based on relevant extracted features from enhanced mammogram. To establish the credibility of LS-SVM classifier for classifying MCCs, a comparative evaluation of the relative performance of LS-SVM classifier for different kernel functions is made. For comparative evaluation, confusion matrix and ROC analysis are used. Experiments are performed on data extracted from mammogram images of DDSM database. A total of 380 suspicious areas are collected, which contain 235 malignant and 145 benign samples, from mammogram images of DDSM database. A set of 50 features is calculated for each suspicious area. After this, an optimal subset of 23 most suitable features is selected from 50 features by Particle Swarm Optimization (PSO). The results of proposed study are quite promising.
Abstract: HIV-1 genome is highly heterogeneous. Due to this
variation, features of HIV-I genome is in a wide range. For this
reason, the ability to infection of the virus changes depending on
different chemokine receptors. From this point of view, R5 HIV
viruses use CCR5 coreceptor while X4 viruses use CXCR5 and
R5X4 viruses can utilize both coreceptors. Recently, in
Bioinformatics, R5X4 viruses have been studied to classify by using
the experiments on HIV-1 genome.
In this study, R5X4 type of HIV viruses were classified using
Auto Regressive (AR) model through Artificial Neural Networks
(ANNs). The statistical data of R5X4, R5 and X4 viruses was
analyzed by using signal processing methods and ANNs. Accessible
residues of these virus sequences were obtained and modeled by AR
model since the dimension of residues is large and different from
each other. Finally the pre-processed data was used to evolve various
ANN structures for determining R5X4 viruses. Furthermore ROC
analysis was applied to ANNs to show their real performances. The
results indicate that R5X4 viruses successfully classified with high
sensitivity and specificity values training and testing ROC analysis
for RBF, which gives the best performance among ANN structures.
Abstract: Automatic segmentation of skin lesions is the first step
towards the automated analysis of malignant melanoma. Although
numerous segmentation methods have been developed, few studies
have focused on determining the most effective color space for
melanoma application. This paper proposes an automatic segmentation
algorithm based on color space analysis and clustering-based histogram
thresholding, a process which is able to determine the optimal
color channel for detecting the borders in dermoscopy images. The
algorithm is tested on a set of 30 high resolution dermoscopy images.
A comprehensive evaluation of the results is provided, where borders
manually drawn by four dermatologists, are compared to automated
borders detected by the proposed algorithm, applying three previously
used metrics of accuracy, sensitivity, and specificity and a new metric
of similarity. By performing ROC analysis and ranking the metrics,
it is demonstrated that the best results are obtained with the X and
XoYoR color channels, resulting in an accuracy of approximately
97%. The proposed method is also compared with two state-of-theart
skin lesion segmentation methods.
Abstract: The feature of HIV genome is in a wide range because
of it is highly heterogeneous. Hence, the infection ability of the virus changes related with different chemokine receptors. From this point,
R5 and X4 HIV viruses use CCR5 and CXCR5 coreceptors respectively while R5X4 viruses can utilize both coreceptors. Recently, in Bioinformatics, R5X4 viruses have been studied to
classify by using the coreceptors of HIV genome.
The aim of this study is to develop the optimal Multilayer
Perceptron (MLP) for high classification accuracy of HIV sub-type viruses. To accomplish this purpose, the unit number in hidden layer
was incremented one by one, from one to a particular number. The statistical data of R5X4, R5 and X4 viruses was preprocessed by the
signal processing methods. Accessible residues of these virus sequences were extracted and modeled by Auto-Regressive Model
(AR) due to the dimension of residues is large and different from each other. Finally the pre-processed dataset was used to evolve MLP with various number of hidden units to determine R5X4
viruses. Furthermore, ROC analysis was used to figure out the optimal MLP structure.
Abstract: Gene, principal unit of inheritance, is an ordered
sequence of nucleotides. The genes of eukaryotic organisms include
alternating segments of exons and introns. The region of
Deoxyribonucleic acid (DNA) within a gene containing instructions
for coding a protein is called exon. On the other hand, non-coding
regions called introns are another part of DNA that regulates gene
expression by removing from the messenger Ribonucleic acid (RNA)
in a splicing process. This paper proposes to determine splice
junctions that are exon-intron boundaries by analyzing DNA
sequences. A splice junction can be either exon-intron (EI) or intron
exon (IE). Because of the popularity and compatibility of the
artificial neural network (ANN) in genetic fields; various ANN
models are applied in this research. Multi-layer Perceptron (MLP),
Radial Basis Function (RBF) and Generalized Regression Neural
Networks (GRNN) are used to analyze and detect the splice junctions
of gene sequences. 10-fold cross validation is used to demonstrate
the accuracy of networks. The real performances of these networks
are found by applying Receiver Operating Characteristic (ROC)
analysis.
Abstract: Automatic segmentation of skin lesions is the first step
towards development of a computer-aided diagnosis of melanoma.
Although numerous segmentation methods have been developed,
few studies have focused on determining the most discriminative
and effective color space for melanoma application. This paper
proposes a novel automatic segmentation algorithm using color space
analysis and clustering-based histogram thresholding, which is able to
determine the optimal color channel for segmentation of skin lesions.
To demonstrate the validity of the algorithm, it is tested on a set of 30
high resolution dermoscopy images and a comprehensive evaluation
of the results is provided, where borders manually drawn by four
dermatologists, are compared to automated borders detected by the
proposed algorithm. The evaluation is carried out by applying three
previously used metrics of accuracy, sensitivity, and specificity and
a new metric of similarity. Through ROC analysis and ranking the
metrics, it is shown that the best results are obtained with the X and
XoYoR color channels which results in an accuracy of approximately
97%. The proposed method is also compared with two state-ofthe-
art skin lesion segmentation methods, which demonstrates the
effectiveness and superiority of the proposed segmentation method.
Abstract: ECG analysis method was developed using ROC
analysis of PVC detecting algorithm. ECG signal of MIT-BIH
arrhythmia database was analyzed by MATLAB. First of all, the
baseline was removed by median filter to preprocess the ECG signal.
R peaks were detected for ECG analysis method, and normal VCG
was extracted for VCG analysis method. Four PVC detecting
algorithm was analyzed by ROC curve, which parameters are
maximum amplitude of QRS complex, width of QRS complex, r-r
interval and geometric mean of VCG. To set cut-off value of
parameters, ROC curve was estimated by true-positive rate
(sensitivity) and false-positive rate. sensitivity and false negative rate
(specificity) of ROC curve calculated, and ECG was analyzed using
cut-off value which was estimated from ROC curve. As a result, PVC
detecting algorithm of VCG geometric mean have high availability,
and PVC could be detected more accurately with amplitude and width
of QRS complex.