Search results for: facial expression classifier.

Authors: V. T. S. Dao, T. G. Etoh, C. Vo Le, H. D. Nguyen, K. Takehara, T. Akino, K. Nishi

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We present an explicit expression to estimate driving voltage attenuation through RC networks representation of an ultrahigh- speed image sensor. Elmore delay metric for a fundamental RC chain is employed as the first-order approximation. By application of dimensional analysis to SPICE simulation data, we found a simple expression that significantly improves the accuracy of the approximation. Estimation error of the resultant expression for uniform RC networks is less than 2%. Similarly, another simple closed-form model to estimate 50 % delay through fundamental RC networks is also derived with sufficient accuracy. The framework of this analysis can be extended to address delay or attenuation issues of other VLSI structures.

Keywords: Dimensional Analysis, Elmore model, RC network, Signal Attenuation, Ultra-High-Speed Image Sensor.

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Authors: Dewan Md. Farid, Nguyen Huu Hoa, Jerome Darmont, Nouria Harbi, Mohammad Zahidur Rahman

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In this paper, we present a new learning algorithm for anomaly based network intrusion detection using improved self adaptive naïve Bayesian tree (NBTree), which induces a hybrid of decision tree and naïve Bayesian classifier. The proposed approach scales up the balance detections for different attack types and keeps the false positives at acceptable level in intrusion detection. In complex and dynamic large intrusion detection dataset, the detection accuracy of naïve Bayesian classifier does not scale up as well as decision tree. It has been successfully tested in other problem domains that naïve Bayesian tree improves the classification rates in large dataset. In naïve Bayesian tree nodes contain and split as regular decision-trees, but the leaves contain naïve Bayesian classifiers. The experimental results on KDD99 benchmark network intrusion detection dataset demonstrate that this new approach scales up the detection rates for different attack types and reduces false positives in network intrusion detection.

Keywords: Detection rates, false positives, network intrusiondetection, naïve Bayesian tree.

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Authors: Seo Young Kim, Tai Myong Choi

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The main goal of microarray experiments is to quantify the expression of every object on a slide as precisely as possible, with a further goal of clustering the objects. Recently, many studies have discussed clustering issues involving similar patterns of gene expression. This paper presents an application of fuzzy-type methods for clustering DNA microarray data that can be applied to typical comparisons. Clustering and analyses were performed on microarray and simulated data. The results show that fuzzy-possibility c-means clustering substantially improves the findings obtained by others.

Keywords: Clustering, microarray data, Fuzzy-type clustering, Validation

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Authors: Ghada Esheba, Fatimah Alturkistani, Arwa Obaid, Ahdab Bashehab, Moayad Alturkistani

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Introduction: Craniopharyngiomas (CPs) are rare epithelial tumors located mainly in the sellar/parasellar region. CPs have been classified histopathologically, genetically, clinically and prognostically into two distinctive subtypes: adamantinomatous and papillary variants. Aim: To examine the pattern of expression of both the β-catenin and epidermal growth factor receptor (EGFR) in surgically resected samples of adamantinomatous CP, and to asses for the possibility of using anti-EGFR in the management of ACP patients. Materials and methods: β-catenin and EGFR immunostaining was performed on paraffin-embedded tissue sections of 18 ACP cases. Result: 17 out of 18 cases (94%) of ACP exhibited strong nuclear/cytoplasmic expression of β-catenin, 15 (83%) of APC cases were positive for EGFR. Conclusion: Nuclear accumulation of β-catenin is a diagnostic hallmark of ACP. EGFR positivity in most cases of ACP could qualify the use of anti-EGFR therapy. 

Keywords: Craniopharyngioma, adamantinomatous, papillary, epidermal growth factor receptor, B-catenin.

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Authors: K. Akilandeswari, G. M. Nasira

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Brain-Computer Interfaces (BCIs) measure brain signals activity, intentionally and unintentionally induced by users, and provides a communication channel without depending on the brain’s normal peripheral nerves and muscles output pathway. Feature Selection (FS) is a global optimization machine learning problem that reduces features, removes irrelevant and noisy data resulting in acceptable recognition accuracy. It is a vital step affecting pattern recognition system performance. This study presents a new Binary Particle Swarm Optimization (BPSO) based feature selection algorithm. Multi-layer Perceptron Neural Network (MLPNN) classifier with backpropagation training algorithm and Levenberg-Marquardt training algorithm classify selected features.

Keywords: Brain-Computer Interfaces (BCI), Feature Selection (FS), Walsh–Hadamard Transform (WHT), Binary Particle Swarm Optimization (BPSO), Multi-Layer Perceptron (MLP), Levenberg–Marquardt algorithm.

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Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

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The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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Authors: Sukrit Shankar, Chetana Shanta Patsa, Jaydev Sharma

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Fractional Fourier Transform is a generalization of the classical Fourier Transform. The Fractional Fourier span in general depends on the amplitude and phase functions of the signal and varies with the transform order. However, with the development of the Fractional Fourier filter banks, it is advantageous in some cases to have different transform orders for different filter banks to achieve better decorrelation of the windowed and overlapped time signal. We present an expression that is useful for finding the perturbation in the Fractional Fourier span due to the erroneous transform order and the possible variation in the window shape and length. The expression is based on the dependency of the time-Fractional Fourier span Uncertainty on the amplitude and phase function of the signal. We also show with the help of the developed expression that the perturbation of span has a varying degree of sensitivity for varying degree of transform order and the window coefficients.

Keywords: Fractional Fourier Transform, Perturbation, Fractional Fourier span, amplitude, phase, transform order, filterbanks.

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Authors: Hong Ding, Fatiha Benslimane, Isra Marei, Chris R. Triggle

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Hyperglycaemia is a key factor that contributes to the development of diabetes-related microvascular disease and a major risk factor for endothelial dysfunction. In the current study, we have explored glucose-induced abnormal intracellular calcium (Ca2+ i) homeostasis in mouse microvessel endothelial cells (MMECs) in high glucose (HG) (40mmol/L) versus control (low glucose, LG) (11 mmol/L). We demonstrated that the exposure of MMECs to HG for 3 days did not change basal Ca2+ i, however, there was a significant increase of acetylcholine-induced Ca2+ entry. Western blots illustrated that exposure to HG also increased STIM1 (Stromal Interaction Molecule 1), but not Orai1 (the pore forming subunit), protein expression levels. Although the link between HG-induced changes in STIM1 expression, enhanced Ca2+ entry and endothelial dysfunction requires further study, the current data are suggestive that targeting these pathways may reduce the impact of HG on endothelial function.

Keywords: store-operated calcium entry, hyperglycaemia, STIM1, endothelial dysfunction

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Authors: Johann Barbier, Eric Filiol, Kichenakoumar Mayoura

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We present in this paper a new approach for specific JPEG steganalysis and propose studying statistics of the compressed DCT coefficients. Traditionally, steganographic algorithms try to preserve statistics of the DCT and of the spatial domain, but they cannot preserve both and also control the alteration of the compressed data. We have noticed a deviation of the entropy of the compressed data after a first embedding. This deviation is greater when the image is a cover medium than when the image is a stego image. To observe this deviation, we pointed out new statistic features and combined them with the Multiple Embedding Method. This approach is motivated by the Avalanche Criterion of the JPEG lossless compression step. This criterion makes possible the design of detectors whose detection rates are independent of the payload. Finally, we designed a Fisher discriminant based classifier for well known steganographic algorithms, Outguess, F5 and Hide and Seek. The experiemental results we obtained show the efficiency of our classifier for these algorithms. Moreover, it is also designed to work with low embedding rates (< 10-5) and according to the avalanche criterion of RLE and Huffman compression step, its efficiency is independent of the quantity of hidden information.

Keywords: Compressed frequency domain, Fisher discriminant, specific JPEG steganalysis.

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Authors: Ebipatei Victoria Tunyan, T. A. Cao, Cheol Young Ock

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Detecting subjectively biased statements is a vital task. This is because this kind of bias, when present in the text or other forms of information dissemination media such as news, social media, scientific texts, and encyclopedias, can weaken trust in the information and stir conflicts amongst consumers. Subjective bias detection is also critical for many Natural Language Processing (NLP) tasks like sentiment analysis, opinion identification, and bias neutralization. Having a system that can adequately detect subjectivity in text will boost research in the above-mentioned areas significantly. It can also come in handy for platforms like Wikipedia, where the use of neutral language is of importance. The goal of this work is to identify the subjectively biased language in text on a sentence level. With machine learning, we can solve complex AI problems, making it a good fit for the problem of subjective bias detection. A key step in this approach is to train a classifier based on BERT (Bidirectional Encoder Representations from Transformers) as upstream model. BERT by itself can be used as a classifier; however, in this study, we use BERT as data preprocessor as well as an embedding generator for a Bi-LSTM (Bidirectional Long Short-Term Memory) network incorporated with attention mechanism. This approach produces a deeper and better classifier. We evaluate the effectiveness of our model using the Wiki Neutrality Corpus (WNC), which was compiled from Wikipedia edits that removed various biased instances from sentences as a benchmark dataset, with which we also compare our model to existing approaches. Experimental analysis indicates an improved performance, as our model achieved state-of-the-art accuracy in detecting subjective bias. This study focuses on the English language, but the model can be fine-tuned to accommodate other languages.

Keywords: Subjective bias detection, machine learning, BERT–BiLSTM–Attention, text classification, natural language processing.

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Authors: Prasad Senadheera, Younousse Saidi, Frans JM Maathuis

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Rice seed expression (cDNA) library in the Lambda Zap 11® phage constructed from the developing grain 10-20 days after flowering was transformed into yeast for functional complementation assays in three salt sensitive yeast mutants S. cerevisiae strain CY162, G19 and Axt3K. Transformed cells of G19 and Axt3K with pYES vector with cDNA inserts showed enhance tolerance than those with empty pYes vector. Sequencing of the cDNA inserts revealed that they encode for the putative proteins with the sequence homologous to rice putative protein PROLM24 (Os06g31070), a prolamin precursor. Expression of this cDNA did not affect yeast growth in absence of salt. Axt3k and G19 strains expressing the PROLM24 were able to grow upto 400 mM and 600 mM of NaCl respectively. Similarly, Axt3k mutant with PROLM24 expression showed comparatively higher growth rate in the medium with excess LiCl (50 mM). The observation that expression of PROLM24 rescued the salt sensitive phenotypes of G19 and Axt3k indicates the existence of a regulatory system that ameliorates the effect of salt stress in the transformed yeast mutants. However, the exact function of the cDNA sequence, which shows partial sequence homology to yeast UTR1 is not clear. Although UTR1 involved in ferrous uptake and iron homeostasis in yeast cells, there is no evidence to prove its role in Na+ homeostasis in yeast cells. Absence of transmembrane regions in Os06g31070 protein indicates that salt tolerance is achieved not through the direct functional complementation of the mutant genes but through an alternative mechanism.

Keywords: Rice seed expression, salt stress, prolamin, salinitytolerance, Oryza sativa

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Authors: Kjersti Engan, Thor Ole Gulsrud, Karl Fredrik Fretheim, Barbro Furebotten Iversen, Liv Eriksen

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Clusters of microcalcifications in mammograms are an important sign of breast cancer. This paper presents a complete Computer Aided Detection (CAD) scheme for automatic detection of clustered microcalcifications in digital mammograms. The proposed system, MammoScan μCaD, consists of three main steps. Firstly all potential microcalcifications are detected using a a method for feature extraction, VarMet, and adaptive thresholding. This will also give a number of false detections. The goal of the second step, Classifier level 1, is to remove everything but microcalcifications. The last step, Classifier level 2, uses learned dictionaries and sparse representations as a texture classification technique to distinguish single, benign microcalcifications from clustered microcalcifications, in addition to remove some remaining false detections. The system is trained and tested on true digital data from Stavanger University Hospital, and the results are evaluated by radiologists. The overall results are promising, with a sensitivity > 90 % and a low false detection rate (approx 1 unwanted pr. image, or 0.3 false pr. image).

Keywords: mammogram, microcalcifications, detection, CAD, MammoScan μCaD, VarMet, dictionary learning, texture, FTCM, classification, adaptive thresholding

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Authors: Yungeng Xie, Cong Liu, Yi Liu, Xuanao Wan

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The study aims to explore microblog users’ emotion expression and sharing behaviors on the Chinese microblog (Weibo). The first theme of study analyzed whether microblog emotions impact readers’ message sharing behaviors, specifically, how the strength of emotion (positive and negative) in microblog messages facilitate/inhibit readers’ sharing behaviors. The second theme compared the differences among the three types of microblog users (i.e., verified enterprise users, verified individual users and unverified users) in terms of their profiles and microblog behaviors. A total of 7114 microblog messages about 24 hot public events in China were sampled from Sina Weibo. The first study results show that strength of negative emotions that microblog messages carry significantly increase the possibility of the message being shared. The second study results indicate that there are significant differences across the three types of users in terms of their emotion expression and its influence on microblog behaviors.

Keywords: Microblog, emotion expression, information diffusion.

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Authors: A. F. Ali, D. M. Shawky

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Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.

Keywords: Bioinformatics, Artificial Neural Networks, Protein Sequence Analysis, Feature Extraction.

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Authors: R. Haddad, K. Morris, V. Buchanan-Wollaston

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Biochemical and molecular analysis of some antioxidant enzyme genes revealed different level of gene expression on oilseed (Brassica napus). For molecular and biochemical analysis, leaf tissues were harvested from plants at eight different developmental stages, from young to senescence. The levels of total protein and chlorophyll were increased during maturity stages of plant, while these were decreased during the last stages of plant growth. Structural analysis (nucleotide and deduced amino acid sequence, and phylogenic tree) of a complementary DNA revealed a high level of similarity for a family of Catalase genes. The expression of the gene encoded by different Catalase isoforms was assessed during different plant growth phase. No significant difference between samples was observed, when Catalase activity was statistically analyzed at different developmental stages. EST analysis exhibited different transcripts levels for a number of other relevant antioxidant genes (different isoforms of SOD and glutathione). The high level of transcription of these genes at senescence stages was indicated that these genes are senescenceinduced genes.

Keywords: Biochemical analysis, Oilseed, Expression pattern, Growth phases

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Authors: W. Kultangwattana, K. Somkantha, P. Phuangsuwan

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This paper presents a technique for diagnosis of the abdominal aorta aneurysm in magnetic resonance imaging (MRI) images. First, our technique is designed to segment the aorta image in MRI images. This is a required step to determine the volume of aorta image which is the important step for diagnosis of the abdominal aorta aneurysm. Our proposed technique can detect the volume of aorta in MRI images using a new external energy for snakes model. The new external energy for snakes model is calculated from Law-s texture. The new external energy can increase the capture range of snakes model efficiently more than the old external energy of snakes models. Second, our technique is designed to diagnose the abdominal aorta aneurysm by Bayesian classifier which is classification models based on statistical theory. The feature for data classification of abdominal aorta aneurysm was derived from the contour of aorta images which was a result from segmenting of our snakes model, i.e., area, perimeter and compactness. We also compare the proposed technique with the traditional snakes model. In our experiment results, 30 images are trained, 20 images are tested and compared with expert opinion. The experimental results show that our technique is able to provide more accurate results than 95%.

Keywords: Adbominal Aorta Aneurysm, Bayesian Classifier, Snakes Model, Texture Feature.

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Authors: Seung Pil Pack

Abstract:

Carbonic anhydrases (CAs) has been focused as biological catalysis for CO2 sequestration process because it can catalyze the conversion of CO2 to bicarbonate. Here, codon-optimized sequence of α type-CA cloned from Duneliala species. (DsCAopt) was constructed, expressed, and characterized. The expression level in E. coli BL21(DE3) was better for codon-optimized DsCAopt than intact sequence of DsCAopt. DsCAopt enzyme shows high-stability at pH 7.6/10.0. In final, we demonstrated that in the Ca2+ solution, DsCAopt enzyme can catalyze well the conversion of CO2 to CaCO3, as the calcite form.

Keywords: Carbonic anhydrase, Codon-optimization, Duneliala species, CO2 sequestration

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Authors: M. K. Bhuyan, P. K. Bora, D. Ghosh

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One very interesting field of research in Pattern Recognition that has gained much attention in recent times is Gesture Recognition. In this paper, we consider a form of dynamic hand gestures that are characterized by total movement of the hand (arm) in space. For these types of gestures, the shape of the hand (palm) during gesturing does not bear any significance. In our work, we propose a model-based method for tracking hand motion in space, thereby estimating the hand motion trajectory. We employ the dynamic time warping (DTW) algorithm for time alignment and normalization of spatio-temporal variations that exist among samples belonging to the same gesture class. During training, one template trajectory and one prototype feature vector are generated for every gesture class. Features used in our work include some static and dynamic motion trajectory features. Recognition is accomplished in two stages. In the first stage, all unlikely gesture classes are eliminated by comparing the input gesture trajectory to all the template trajectories. In the next stage, feature vector extracted from the input gesture is compared to all the class prototype feature vectors using a distance classifier. Experimental results demonstrate that our proposed trajectory estimator and classifier is suitable for Human Computer Interaction (HCI) platform.

Keywords: Hand gesture, human computer interaction, key video object plane, dynamic time warping.

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Authors: R. Sutjiati, Rubianto, I. B. Narmada, I. K. Sudiana, R. P. Rahayu

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The prevalence of post-treatment relapse in orthodontics in the community is high enough; therefore, relapses in orthodontic treatment must be prevented well. The aim of this study is to experimentally test the inhibition of relapse of orthodontics tooth movement in NaF of expression TGF-β1, Runx2, alkaline phosphatase (ALP) and microscopic of woven bone. The research method used was experimental laboratory research involving 30 rats, which were divided into three groups. Group A: rats were not given orthodontic tooth movement and without NaF. Group B: rats were given orthodontic tooth movement and without 11.5 ppm by topical application. Group C: rats were given orthodontic tooth movement and 11.75 ppm by topical application. Orthodontic tooth movement was conducted by applying ligature wires of 0.02 mm in diameter on the molar-1 (M-1) of left permanent maxilla and left insisivus of maxilla. Immunohistochemical examination was conducted to calculate the number of osteoblast to determine TGF β1, Runx2, ALP and haematoxylin to determine woven bone on day 7 and day 14. Results: It was shown that administrations of Natrium Fluoride topical application proved effective to increase the expression of TGF-β1, Runx2, ALP and to increase woven bone in the tension area greater than administration without natrium fluoride topical application (p < 0.05), except the expression of ALP on day 7 and day 14 which was significant. The results of the study show that NaF significantly increases the expressions of TGF-β1, Runx2, ALP and woven bone. The expression of the variables enhanced on day 7 compared on that on day 14, except ALP. Thus, it can be said that the acceleration of woven bone occurs on day 7.

Keywords: TGF-β1, Runx2, ALP, woven bone, natrium fluoride.

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Authors: Taeung Yoon, Dahae Chong, Sangho Ahn, Seokho Yoon

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In a chirp spread spectrum (CSS) system, the overlap technique is used for increasing bit rate. More overlaps can offer higher data throughput; however, they may cause more intersymbol interference (ISI) at the same time, resulting in serious bit error rate (BER) performance degradation. In this paper, we perform the BER analysis and derive a closed form BER expression for the overlap-based CSS system. The derived BER expression includes the number of overlaps as a parameter, and thus, would be very useful in determining the number of overlaps for a specified BER. The numerical results demonstrate that the BER derived in a closed form closely agrees with the simulated BER.

Keywords: CSS, DM, chirp, overlap.

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Authors: Luay A. Fraiwan, Natheer Y. Khaswaneh, Khaldon Y. Lweesy

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Sleep stage scoring is the process of classifying the stage of the sleep in which the subject is in. Sleep is classified into two states based on the constellation of physiological parameters. The two states are the non-rapid eye movement (NREM) and the rapid eye movement (REM). The NREM sleep is also classified into four stages (1-4). These states and the state wakefulness are distinguished from each other based on the brain activity. In this work, a classification method for automated sleep stage scoring based on a single EEG recording using wavelet packet decomposition was implemented. Thirty two ploysomnographic recording from the MIT-BIH database were used for training and validation of the proposed method. A single EEG recording was extracted and smoothed using Savitzky-Golay filter. Wavelet packets decomposition up to the fourth level based on 20th order Daubechies filter was used to extract features from the EEG signal. A features vector of 54 features was formed. It was reduced to a size of 25 using the gain ratio method and fed into a classifier of regression trees. The regression trees were trained using 67% of the records available. The records for training were selected based on cross validation of the records. The remaining of the records was used for testing the classifier. The overall correct rate of the proposed method was found to be around 75%, which is acceptable compared to the techniques in the literature.

Keywords: Features selection, regression trees, sleep stagescoring, wavelet packets.

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Authors: Aleksandra Zysk, Pawel Badura

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Recognizing and controlling vocal registers during singing is a difficult task for beginner vocalist. It requires among others identifying which part of natural resonators is being used when a sound propagates through the body. Thus, an application has been designed allowing for sound recording, automatic vocal register recognition (VRR), and a graphical user interface providing real-time visualization of the signal and recognition results. Six spectral features are determined for each time frame and passed to the support vector machine classifier yielding a binary decision on the head or chest register assignment of the segment. The classification training and testing data have been recorded by ten professional female singers (soprano, aged 19-29) performing sounds for both chest and head register. The classification accuracy exceeded 93% in each of various validation schemes. Apart from a hard two-class clustering, the support vector classifier returns also information on the distance between particular feature vector and the discrimination hyperplane in a feature space. Such an information reflects the level of certainty of the vocal register classification in a fuzzy way. Thus, the designed recognition and training application is able to assess and visualize the continuous trend in singing in a user-friendly graphical mode providing an easy way to control the vocal emission.

Keywords: Classification, singing, spectral analysis, vocal emission, vocal register.

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Authors: Loai AbdAllah, Mahmoud Kaiyal

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Missing values in real-world datasets are a common problem. Many algorithms were developed to deal with this problem, most of them replace the missing values with a fixed value that was computed based on the observed values. In our work, we used a distance function based on Bhattacharyya distance to measure the distance between objects with missing values. Bhattacharyya distance, which measures the similarity of two probability distributions. The proposed distance distinguishes between known and unknown values. Where the distance between two known values is the Mahalanobis distance. When, on the other hand, one of them is missing the distance is computed based on the distribution of the known values, for the coordinate that contains the missing value. This method was integrated with Wikaya, a digital health company developing a platform that helps to improve prevention of chronic diseases such as diabetes and cancer. In order for Wikaya’s recommendation system to work distance between users need to be measured. Since there are missing values in the collected data, there is a need to develop a distance function distances between incomplete users profiles. To evaluate the accuracy of the proposed distance function in reflecting the actual similarity between different objects, when some of them contain missing values, we integrated it within the framework of k nearest neighbors (kNN) classifier, since its computation is based only on the similarity between objects. To validate this, we ran the algorithm over diabetes and breast cancer datasets, standard benchmark datasets from the UCI repository. Our experiments show that kNN classifier using our proposed distance function outperforms the kNN using other existing methods.

Keywords: Missing values, distance metric, Bhattacharyya distance.

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Authors: Kemal Polat

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In this paper, an attribute weighting method called fuzzy C-means clustering based attribute weighting (FCMAW) for classification of Diabetes disease dataset has been used. The aims of this study are to reduce the variance within attributes of diabetes dataset and to improve the classification accuracy of classifier algorithm transforming from non-linear separable datasets to linearly separable datasets. Pima Indians Diabetes dataset has two classes including normal subjects (500 instances) and diabetes subjects (268 instances). Fuzzy C-means clustering is an improved version of K-means clustering method and is one of most used clustering methods in data mining and machine learning applications. In this study, as the first stage, fuzzy C-means clustering process has been used for finding the centers of attributes in Pima Indians diabetes dataset and then weighted the dataset according to the ratios of the means of attributes to centers of theirs. Secondly, after weighting process, the classifier algorithms including support vector machine (SVM) and k-NN (k- nearest neighbor) classifiers have been used for classifying weighted Pima Indians diabetes dataset. Experimental results show that the proposed attribute weighting method (FCMAW) has obtained very promising results in the classification of Pima Indians diabetes dataset.

Keywords: Fuzzy C-means clustering, Fuzzy C-means clustering based attribute weighting, Pima Indians diabetes dataset, SVM.

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Authors: Wafa' S.Al-Sharafat, Reyadh Naoum

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Society has grown to rely on Internet services, and the number of Internet users increases every day. As more and more users become connected to the network, the window of opportunity for malicious users to do their damage becomes very great and lucrative. The objective of this paper is to incorporate different techniques into classier system to detect and classify intrusion from normal network packet. Among several techniques, Steady State Genetic-based Machine Leaning Algorithm (SSGBML) will be used to detect intrusions. Where Steady State Genetic Algorithm (SSGA), Simple Genetic Algorithm (SGA), Modified Genetic Algorithm and Zeroth Level Classifier system are investigated in this research. SSGA is used as a discovery mechanism instead of SGA. SGA replaces all old rules with new produced rule preventing old good rules from participating in the next rule generation. Zeroth Level Classifier System is used to play the role of detector by matching incoming environment message with classifiers to determine whether the current message is normal or intrusion and receiving feedback from environment. Finally, in order to attain the best results, Modified SSGA will enhance our discovery engine by using Fuzzy Logic to optimize crossover and mutation probability. The experiments and evaluations of the proposed method were performed with the KDD 99 intrusion detection dataset.

Keywords: MSSGBML, Network Intrusion Detection, SGA, SSGA.

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Authors: Ahmad Ali Shahid, Muhammad Shakil Shaukat, Kamran Shehzad Bajwa, Abdul Qayyum Rao, Tayyab Husnain

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Agriculture is the backbone of economy of Pakistan and cotton is the major agricultural export and supreme source of raw fiber for our textile industry. To combat severe problems of insect and weed, combination of three genes namely Cry1Ac, Cry2A and EPSPS genes was transferred in locally cultivated cotton variety MNH-786 with the use of Agrobacterium mediated genetic transformation. The present study focused on the molecular screening of transgenic cotton plants at T3 generation in order to confirm integration and expression of all three genes (Cry1Ac, Cry2A and EPSP synthase) into the cotton genome. Initially, glyphosate spray assay was used for screening of transgenic cotton plants containing EPSP synthase gene at T3 generation. Transgenic cotton plants which were healthy and showed no damage on leaves were selected after 07 days of spray. For molecular analysis of transgenic cotton plants in the laboratory, the genomic DNA of these transgenic cotton plants were isolated and subjected to amplification of the three genes. Thus, seventeen out of twenty (Cry1Ac gene), ten out of twenty (Cry2A gene) and all twenty (EPSP synthase gene) were produced positive amplification. On the base of PCR amplification, ten transgenic plant samples were subjected to protein expression analysis through ELISA. The results showed that eight out of ten plants were actively expressing the three transgenes. Real-time PCR was also done to quantify the mRNA expression levels of Cry1Ac and EPSP synthase gene. Finally, eight plants were confirmed for the presence and active expression of all three genes at T3 generation.

Keywords: Agriculture, Cotton, Transformation, Cry Genes, ELISA and PCR.

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Authors: M R Asadi, G Torkaman, M Hedayati

Abstract:

We evaluated the effect of sensory (direct current (DC), 600μA) and motor (monophasic current, pulse duration 300μs, 100 Hz, 2.5-3mA) intensities of cathodal electrical stimulation (ES) current to release VEGF and biomechanical properties of wound. 54 male Sprague-dawley rats were randomly assigned into one control and two experimental groups. A full thickness skin incision was made on animals- dorsal region. The experimental groups received ES for 1h/day and every other day. VEGF expression was measured in skin on the 7th day after surgical incision and tensile strength was measured on 21st day. On the 7th day, the values of skin VEGF in the sensory group were significantly greater than those of the other groups (p < 0.05). Sensory and Motor intensity stimulation, can not improve the biomechanical properties of the repaired wounds. It seems the mechanical environment induced by sensory and motor intensity of electrical stimulation, could not simulate the role of normal daily stress and strain to maturation of collagen fibers and their cross links. Further work is needed to determine the relationship between VEGF expression after ES and its effect on tensile strength of healed wound.

Keywords: Biomechanical properties Direct current, Monophasic current, Skin, VEGF

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Authors: Ankit Agrawal, Ankush Mittal

Abstract:

A gene network gives the knowledge of the regulatory relationships among the genes. Each gene has its activators and inhibitors that regulate its expression positively and negatively respectively. Genes themselves are believed to act as activators and inhibitors of other genes. They can even activate one set of genes and inhibit another set. Identifying gene networks is one of the most crucial and challenging problems in Bioinformatics. Most work done so far either assumes that there is no time delay in gene regulation or there is a constant time delay. We here propose a Dynamic Time- Lagged Correlation Based Method (DTCBM) to learn the gene networks, which uses time-lagged correlation to find the potential gene interactions, and then uses a post-processing stage to remove false gene interactions to common parents, and finally uses dynamic correlation thresholds for each gene to construct the gene network. DTCBM finds correlation between gene expression signals shifted in time, and therefore takes into consideration the multi time delay relationships among the genes. The implementation of our method is done in MATLAB and experimental results on Saccharomyces cerevisiae gene expression data and comparison with other methods indicate that it has a better performance.

Keywords: Activators, correlation, dynamic time-lagged correlation based method, inhibitors, multi-time delay gene network.

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Authors: Aref Aasi, Sahar Ebrahimi Bajgani, Erfan Aasi

Abstract:

Breast cancer (BC) continues to be the most frequent cancer in females and causes the highest number of cancer-related deaths in women worldwide. Inspired by recent advances in studying the relationship between different patient attributes and features and the disease, in this paper, we have tried to investigate the different classification methods for better diagnosis of BC in the early stages. In this regard, datasets from the University Hospital Centre of Coimbra were chosen, and different machine learning (ML)-based and neural network (NN) classifiers have been studied. For this purpose, we have selected favorable features among the nine provided attributes from the clinical dataset by using a random forest algorithm. This dataset consists of both healthy controls and BC patients, and it was noted that glucose, BMI, resistin, and age have the most importance, respectively. Moreover, we have analyzed these features with various ML-based classifier methods, including Decision Tree (DT), K-Nearest Neighbors (KNN), eXtreme Gradient Boosting (XGBoost), Logistic Regression (LR), Naive Bayes (NB), and Support Vector Machine (SVM) along with NN-based Multi-Layer Perceptron (MLP) classifier. The results revealed that among different techniques, the SVM and MLP classifiers have the most accuracy, with amounts of 96% and 92%, respectively. These results divulged that the adopted procedure could be used effectively for the classification of cancer cells, and also it encourages further experimental investigations with more collected data for other types of cancers.

Keywords: Breast cancer, health diagnosis, Machine Learning, biomarker classification, Neural Network.

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Authors: Tzyy Rong Jinn, Nguyen Tiep Khac, Tzong Yuan Wu

Abstract:

Highly pathogenic avian influenza (HPAI) H5N1 viruses have created demand for a cost-effective vaccine to prevent a pandemic of the disease. Here, we report that Trichoplusia ni (T. ni) larvae can act as a cost-effective bioreactor to produce recombinant HA5 (rH5HA) proteins as an potential effective vaccine for chickens. To facilitate the recombinant virus identification, virus titer determination and access the infected larvae, we employed the internal ribosome entry site (IRES) derived from Perina nuda virus (PnV, belongs to insect picorna like Iflavirus genus) to construct a bi-cistronic baculovirus expression vector that can express the rH5HA protein and enhanced green fluorescent protein (EGFP) simultaneously. Western blot analysis revealed that the 70 kDa rH5HA protein and partially cleaved products (40 kDa H5HA1) were generated in T. ni larvae infected with recombinant baculovirus carrying the H5HA gene. These data suggest that the baculovirus-larvae recombinant protein expression system could be a cost-effective platform for H5N1 vaccine production.

Keywords: Avian Influenza, baculovirus, hemagglutinin, Trichoplusia ni larvae

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