Search results for: cancer classification

Authors: Hassan Ezzaidi, Jean Rouat

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Recently many research has been conducted to retrieve pertinent parameters and adequate models for automatic music genre classification. In this paper, two measures based upon information theory concepts are investigated for mapping the features space to decision space. A Gaussian Mixture Model (GMM) is used as a baseline and reference system. Various strategies are proposed for training and testing sessions with matched or mismatched conditions, long training and long testing, long training and short testing. For all experiments, the file sections used for testing are never been used during training. With matched conditions all examined measures yield the best and similar scores (almost 100%). With mismatched conditions, the proposed measures yield better scores than the GMM baseline system, especially for the short testing case. It is also observed that the average discrimination information measure is most appropriate for music category classifications and on the other hand the divergence measure is more suitable for music subcategory classifications.

Keywords: Audio feature, information measures, music genre.

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Authors: B. A. Lawal, A. G. Ojanuga, P. A. Tsado, A. Mohammed

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This work assessed some properties of three pedons on a toposequence in Ijah-Gbagyi district in Niger State, Nigeria. The pedons were designated as JG1, JG2 and JG3 representing the upper, middle and lower slopes respectively. The surface soil was characterized by dark yellowish brown (10YR3/4) color at the JG1 and JG2 and very dark grayish brown (10YR3/2) color at JG3. Sand dominated the mineral fraction and its content in the surface horizon decreased down the slope, whereas silt content increased down the slope due to sorting by geological and pedogenic processes. Although organic carbon (OC), total nitrogen (TN) and available phosphorus (P) were rated high, TN and available P decreased down the slope. High cation exchange capacity (CEC) was an indication that the soils have high potential for plant nutrients retention. The pedons were classified as Typic Haplustepts/ Haplic Cambisols (Eutric), Plinthic Petraquepts/ Petric Plinthosols (Abruptic) and Typic Endoaquepts/ Endogleyic Cambisols (Endoclayic).

Keywords: Ecological region, landscape positions, soil characterization, soil classification.

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Authors: Mohammed Mustapha Alhaji, Salawu Sadiku

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A clay soil classified as A-7-6 and CH soil according to AASHTO and unified soil classification system respectively, was stabilized using A-3 soil (AASHTO soil classification system). The clay soil was replaced with 0%, 10%, 20%, to 100% A-3 soil, compacted at both British Standard Light (BSL) and British Standard Heavy (BSH) compaction energy levels and using Unconfined Compressive Strength (UCS) as evaluation criteria. The Maximum Dry Density (MDD) of the treated soils at both the BSL and BSH compaction energy levels showed increase from 0% to 40% A-3 soil replacement after which the values reduced to 100% replacement. The trend of the Optimum Moisture Content (OMC) with varied A-3 soil replacement was similar to that of MDD but in a reversed order. The OMC reduced from 0% to 40% A-3 soil replacement after which the values increased to 100% replacement. This trend was attributed to the observed reduction in void ratio from 0% to 40% replacement after which the void ratio increased to 100% replacement. The maximum UCS for the soil at varied A-3 soil replacement increased from 272 and 770 kN/m2 for BSL and BSH compaction energy level at 0% replacement to 295 and 795 kN/m2 for BSL and BSH compaction energy level respectively at 10% replacement after which the values reduced to 22 and 60 kN/m2 for BSL and BSH compaction energy level respectively at 70% replacement. Beyond 70% replacement, the mixtures could not be moulded for UCS test.

Keywords: A-3 soil, clay soil, pozzolanic action, stabilization.

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Authors: M. Chaichanyut, S. Tungjitkusolmun

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This paper is concerned with microwave (MW) ablation for a liver cancer tissue by using helix antenna. The antenna structure supports the propagation of microwave energy at 2.45 GHz. A 1½ turn spiral catheter-based microwave antenna applicator has been developed. We utilize the three-dimensional finite element method (3D FEM) simulation to analyze where the tissue heat flux, lesion pattern and volume destruction during MW ablation. The configurations of helix antenna where Helix air-core antenna and Helix Dielectric-core antenna. The 3D FEMs solutions were based on Maxwell and bio-heat equations. The simulation protocol was power control (10 W, 300s). Our simulation result, both helix antennas have heat flux occurred around the helix antenna and that can be induced the temperature distribution similar (teardrop). The region where the temperature exceeds 50°C the microwave ablation was successful (i.e. complete destruction). The Helix air-core antenna and Helix Dielectric-core antenna, ablation zone or axial ratios (Widest/length) were respectively 0.82 and 0.85; the complete destructions were respectively 4.18 cm³ and 5.64 cm³

Keywords: Liver cancer, Helix antenna, Finite element, Microwave ablation.

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Authors: Cheng-Hong Yang, Tsung-Mu Shih, Li-Yeh Chuang

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Serial Analysis of Gene Expression is a powerful quantification technique for generating cell or tissue gene expression data. The profile of the gene expression of cell or tissue in several different states is difficult for biologists to analyze because of the large number of genes typically involved. However, feature selection in machine learning can successfully reduce this problem. The method allows reducing the features (genes) in specific SAGE data, and determines only relevant genes. In this study, we used a genetic algorithm to implement feature selection, and evaluate the classification accuracy of the selected features with the K-nearest neighbor method. In order to validate the proposed method, we used two SAGE data sets for testing. The results of this study conclusively prove that the number of features of the original SAGE data set can be significantly reduced and higher classification accuracy can be achieved.

Keywords: Serial Analysis of Gene Expression, Feature selection, Genetic Algorithm, K-nearest neighbor method.

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Authors: L. Lindsay, S. A. Coleman, D. Kerr, B. J. Taylor, A. Moorhead

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Cognitive decline and frailty is apparent in older adults leading to an increased likelihood of the risk of falling. Currently health care professionals have to make professional decisions regarding such risks, and hence make difficult decisions regarding the future welfare of the ageing population. This study uses health data from The Irish Longitudinal Study on Ageing (TILDA), focusing on adults over the age of 50 years, in order to analyse health risk factors and predict the likelihood of falls. This prediction is based on the use of machine learning algorithms whereby health risk factors are used as inputs to predict the likelihood of falling. Initial results show that health risk factors such as long-term health issues contribute to the number of falls. The identification of such health risk factors has the potential to inform health and social care professionals, older people and their family members in order to mitigate daily living risks.

Keywords: Classification, falls, health risk factors, machine learning, older adults.

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Authors: Kasra Majbouri Yazdi, Adel Majbouri Yazdi, Saeid Khodayi, Jingyu Hou, Wanlei Zhou, Saeed Saedy

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Fake news and false information are big challenges of all types of media, especially social media. There is a lot of false information, fake likes, views and duplicated accounts as big social networks such as Facebook and Twitter admitted. Most information appearing on social media is doubtful and in some cases misleading. They need to be detected as soon as possible to avoid a negative impact on society. The dimensions of the fake news datasets are growing rapidly, so to obtain a better result of detecting false information with less computation time and complexity, the dimensions need to be reduced. One of the best techniques of reducing data size is using feature selection method. The aim of this technique is to choose a feature subset from the original set to improve the classification performance. In this paper, a feature selection method is proposed with the integration of K-means clustering and Support Vector Machine (SVM) approaches which work in four steps. First, the similarities between all features are calculated. Then, features are divided into several clusters. Next, the final feature set is selected from all clusters, and finally, fake news is classified based on the final feature subset using the SVM method. The proposed method was evaluated by comparing its performance with other state-of-the-art methods on several specific benchmark datasets and the outcome showed a better classification of false information for our work. The detection performance was improved in two aspects. On the one hand, the detection runtime process decreased, and on the other hand, the classification accuracy increased because of the elimination of redundant features and the reduction of datasets dimensions.

Keywords: Fake news detection, feature selection, support vector machine, K-means clustering, machine learning, social media.

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Authors: Mukesh Singh Boori, Vít Voženílek

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Olomouc is a unique and complex landmark with widespread forestation and land use. This research work was conducted to assess important and complex land use change trajectories in Olomouc region. Multi-temporal satellite data from 1991, 2001 and 2013 were used to extract land use/cover types by object oriented classification method. To achieve the objectives, three different aspects were used: (1) Calculate the quantity of each transition; (2) Allocate location based landscape pattern (3) Compare land use/cover evaluation procedure. Land cover change trajectories shows that 16.69% agriculture, 54.33% forest and 21.98% other areas (settlement, pasture and water-body) were stable in all three decade. Approximately 30% of the study area maintained as a same land cove type from 1991 to 2013. Here broad scale of political and socioeconomic factors was also affect the rate and direction of landscape changes. Distance from the settlements was the most important predictor of land cover change trajectories. This showed that most of landscape trajectories were caused by socio-economic activities and mainly led to virtuous change on the ecological environment.

Keywords: Remote Sensing, land use/cover, Change trajectories, Image classification.

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Authors: Tsair-Fwu Lee , Hui-Min Ting , Pei-Ju Chao, Jing-Chuan Jiang, Min-Yuan Chao, Wen-Cheng Chen, Long-Chang Chen, Jia-Ming Wu

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The purpose of this study is to derive parameters estimating for the Lyman–Kutcher–Burman (LKB) normal tissue complication probability (NTCP) model using analysis of scintigraphy assessments and quality of life (QoL) measurement questionnaires for the parotid gland (xerostomia). In total, 31 patients with head-and-neck (HN) cancer were enrolled. Salivary excretion factor (SEF) and EORTC QLQ-H&N35 questionnaires datasets are used for the NTCP modeling to describe the incidence of grade 4 xerostomia. Assuming that n= 1, NTCP fitted parameters are given as TD50= 43.6 Gy, m= 0.18 in SEF analysis, and as TD50= 44.1 Gy, m= 0.11 in QoL measurements, respectively. SEF and QoL datasets can validate the Quantitative Analyses of Normal Tissue Effects in the Clinic (QUANTEC) guidelines well, resulting in NPV-s of 100% for the both datasets and suggests that the QUANTEC 25/20Gy gland-spared guidelines are suitable for clinical used for the HN cohort to effectively avoid xerostomia.

Keywords: HN, NTCP, SEF, QoL, QUANTEC

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Authors: Vickneswaran Jeyabalan, Andrews Samraj, Loo Chu Kiong

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The noteworthy point in the advancement of Brain Machine Interface (BMI) research is the ability to accurately extract features of the brain signals and to classify them into targeted control action with the easiest procedures since the expected beneficiaries are of disabled. In this paper, a new feature extraction method using the combination of adaptive band pass filters and adaptive autoregressive (AAR) modelling is proposed and applied to the classification of right and left motor imagery signals extracted from the brain. The introduction of the adaptive bandpass filter improves the characterization process of the autocorrelation functions of the AAR models, as it enhances and strengthens the EEG signal, which is noisy and stochastic in nature. The experimental results on the Graz BCI data set have shown that by implementing the proposed feature extraction method, a LDA and SVM classifier outperforms other AAR approaches of the BCI 2003 competition in terms of the mutual information, the competition criterion, or misclassification rate.

Keywords: Adaptive autoregressive, adaptive bandpass filter, brain machine Interface, EEG, motor imaginary.

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Authors: S. Rokhsari, M. Delavar, A. Sadeghi-Niaraki, A. Abed-Elmdoust, B. Moshiri

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Traffic incident has bad effect on all parts of society so controlling road networks with enough traffic devices could help to decrease number of accidents, so using the best method for optimum site selection of these devices could help to implement good monitoring system. This paper has considered here important criteria for optimum site selection of traffic camera based on aggregation methods such as Bagging and Dempster-Shafer concepts. In the first step, important criteria such as annual traffic flow, distance from critical places such as parks that need more traffic controlling were identified for selection of important road links for traffic camera installation, Then classification methods such as Artificial neural network and Decision tree algorithms were employed for classification of road links based on their importance for camera installation. Then for improving the result of classifiers aggregation methods such as Bagging and Dempster-Shafer theories were used.

Keywords: Aggregation, Bagging theory, Dempster-Shafer theory, Site selection

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Authors: Tahseen A. Jilani, S. M. Aqil Burney, C. Ardil

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In this paper, we have presented a new multivariate fuzzy time series forecasting method. This method assumes mfactors with one main factor of interest. History of past three years is used for making new forecasts. This new method is applied in forecasting total number of car accidents in Belgium using four secondary factors. We also make comparison of our proposed method with existing methods of fuzzy time series forecasting. Experimentally, it is shown that our proposed method perform better than existing fuzzy time series forecasting methods. Practically, actuaries are interested in analysis of the patterns of causalities in road accidents. Thus using fuzzy time series, actuaries can define fuzzy premium and fuzzy underwriting of car insurance and life insurance for car insurance. National Institute of Statistics, Belgium provides region of risk classification for each road. Thus using this risk classification, we can predict premium rate and underwriting of insurance policy holders.

Keywords: Average forecasting error rate (AFER), Fuzziness offuzzy sets Fuzzy, If-Then rules, Multivariate fuzzy time series.

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Authors: S. K. Aruna, S. Chitra

Abstract:

This research paper presents a framework for classifying Magnetic Resonance Imaging (MRI) images for Dementia. Dementia, an age-related cognitive decline is indicated by degeneration of cortical and sub-cortical structures. Characterizing morphological changes helps understand disease development and contributes to early prediction and prevention of the disease. Modelling, that captures the brain’s structural variability and which is valid in disease classification and interpretation is very challenging. Features are extracted using Gabor filter with 0, 30, 60, 90 orientations and Gray Level Co-occurrence Matrix (GLCM). It is proposed to normalize and fuse the features. Independent Component Analysis (ICA) selects features. Support Vector Machine (SVM) classifier with different kernels is evaluated, for efficiency to classify dementia. This study evaluates the presented framework using MRI images from OASIS dataset for identifying dementia. Results showed that the proposed feature fusion classifier achieves higher classification accuracy.

Keywords: Magnetic resonance imaging, dementia, Gabor filter, gray level co-occurrence matrix, support vector machine.

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Authors: Maha Shamseddine, Amjad Nusayr, Wassim Itani

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In this paper, we present a Platform-as-a-Service (PaaS) model for controlling the privacy enforcement mechanisms applied on user data when stored and processed in Cloud data centers. The proposed architecture consists of establishing user configurable ‘sticky’ policies on the Graphical User Interface (GUI) data-bound components during the application development phase to specify the details of privacy enforcement on the contents of these components. Various privacy classification classes on the data components are formally defined to give the user full control on the degree and scope of privacy enforcement including the type of execution containers to process the data in the Cloud. This not only enhances the privacy-awareness of the developed Cloud services, but also results in major savings in performance and energy efficiency due to the fact that the privacy mechanisms are solely applied on sensitive data units and not on all the user content. The proposed design is implemented in a real PaaS cloud computing environment on the Microsoft Azure platform.

Keywords: Privacy enforcement, Platform-as-a-Service privacy awareness, cloud computing privacy.

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Authors: El-Sayed Atlam, Masao Fuketa, Kazuhiro Morita, Jun-ichi Aoe

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Field Association (FA) terms are a limited set of discriminating terms that give us the knowledge to identify document fields which are effective in document classification, similar file retrieval and passage retrieval. But the problem lies in the lack of an effective method to extract automatically relevant Arabic FA Terms to build a comprehensive dictionary. Moreover, all previous studies are based on FA terms in English and Japanese, and the extension of FA terms to other language such Arabic could be definitely strengthen further researches. This paper presents a new method to extract, Arabic FA Terms from domain-specific corpora using part-of-speech (POS) pattern rules and corpora comparison. Experimental evaluation is carried out for 14 different fields using 251 MB of domain-specific corpora obtained from Arabic Wikipedia dumps and Alhyah news selected average of 2,825 FA Terms (single and compound) per field. From the experimental results, recall and precision are 84% and 79% respectively. Therefore, this method selects higher number of relevant Arabic FA Terms at high precision and recall.

Keywords: Arabic Field Association Terms, information extraction, document classification, information retrieval.

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Authors: Khaled Abduesslam. M, Mohammed Ali, Basher H Alsdai, Muhammad Nizam, Inayati

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This paper presents the voltage problem location classification using performance of Least Squares Support Vector Machine (LS-SVM) and Learning Vector Quantization (LVQ) in electrical power system for proper voltage problem location implemented by IEEE 39 bus New- England. The data was collected from the time domain simulation by using Power System Analysis Toolbox (PSAT). Outputs from simulation data such as voltage, phase angle, real power and reactive power were taken as input to estimate voltage stability at particular buses based on Power Transfer Stability Index (PTSI).The simulation data was carried out on the IEEE 39 bus test system by considering load bus increased on the system. To verify of the proposed LS-SVM its performance was compared to Learning Vector Quantization (LVQ). The results showed that LS-SVM is faster and better as compared to LVQ. The results also demonstrated that the LS-SVM was estimated by 0% misclassification whereas LVQ had 7.69% misclassification.

Keywords: IEEE 39 bus, Least Squares Support Vector Machine, Learning Vector Quantization, Voltage Collapse.

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Authors: Laila Salah Seada, Ashraf Ibrahim, Fawaz Al Rashid, Ihab Abdo, Hassan Kasim, Waleed Al Mansi, Saud Al Shabli

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Background and Objectives: Colorectal carcinoma is increasing among both men and women worldwide. It has a multifactorial etiology including genetic factors, environmental factors and inflammatory conditions of the digestive tract. A clinicopathologic assessment of colorectal carcinoma in Hail region is done, considering any changing patterns in two 5-year periods from 2005-2009 (A) and from 2012 to 2017 (B). All data had been retrieved from histopathology files of King Khalid Hospital, Hail. Results: During period (A), 75 cases were diagnosed as colorectal carcinoma. Male patients comprised 56/75 (74.7%) of the study, with a mean age of 58.4 (36-97), while females were 19/75 (25.3%) with a mean age of 50.3(30-85) and the difference was significant (p = 0.05). M:F ratio was 2.9:1. Most common histological type was adenocarcioma in 68/75 (90.7%) patients mostly well differentiated in 44/68 (64.7%). Mucinous neoplasms comprised only 7/75 (9.3%) of cases and tended to have a higher stage (p = 0.04). During period (B), 115 cases were diagnosed with an increase of 53.3% in number of cases than period (A). Male to female ratio also decreased to 1.35:1, females being 44.83% more affected. Adenocarcinoma remained the prevalent type (93.9%), while mucinous type was still rare (5.2%). No distal metastases found at time of presentation. Localization of tumors was rectosigmoid in group (A) in 41.4%, which increased to 56.6% in group (B), with an increase of 15.2%. Iliocecal location also decreased from 8% to 3.5%, being 56.25% less. Other proximal areas of the colon were decreased by 25.75%, from 53.9% in group (A) to 40% in group (B). Conclusion: Colorectal carcinoma in Hail region has increased by 53.3% in the past 5 years, with more females being diagnosed. Localization has also shifted distally by 15.2%. These findings are different from Western world patterns which experienced a decrease in incidence and proximal shift of the colon cancer localization. This might be due to better diagnostic tools, population awareness of the disease, as well as changing of life style and/or food habits in the region.

Keywords: Colorectal cancer, Hail Region, changing pattern, distal shift.

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Authors: Sung Ho Ha, Seong Hyeon Joo, Eun Kyung Kwon

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Until recently, researchers have developed various tools and methodologies for effective clinical decision-making. Among those decisions, chest pain diseases have been one of important diagnostic issues especially in an emergency department. To improve the ability of physicians in diagnosis, many researchers have developed diagnosis intelligence by using machine learning and data mining. However, most of the conventional methodologies have been generally based on a single classifier for disease classification and prediction, which shows moderate performance. This study utilizes an ensemble strategy to combine multiple different classifiers to help physicians diagnose chest pain diseases more accurately than ever. Specifically the ensemble strategy is applied by using the integration of decision trees, neural networks, and support vector machines. The ensemble models are applied to real-world emergency data. This study shows that the performance of the ensemble models is superior to each of single classifiers.

Keywords: Diagnosis intelligence, ensemble approach, data mining, emergency department

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Authors: Marzieh Ebrahimi, Vahid Changizi, Mohammad Reza Kardan, Seyed Mahdi Hosseini Pooya, Parham Geramifar

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Radiation exposure to the patient's family members is one of the major concerns during thyroid cancer radionuclide therapy. The aim of this study was to measure the total effective dose of the family members by means of thermoluminescence personal dosimeter, and compare with those calculated by analytical methods. Eighty-five adult family members of fifty-one patients volunteered to participate in this research study. Considering the minimum and maximum range of dose rate from 15 µsv/h to 120 µsv/h at patients' release time, the calculated mean and median dose values of family members were 0.45 mSv and 0.28 mSv, respectively. Moreover, almost all family members’ doses were measured to be less than the dose constraint of 5 mSv recommended by Basic Safety Standards. Considering the influence parameters such as patient dose rate and administrated activity, the total effective doses of family members were calculated by TEDE and NRC formulas and compared with those of experimental results. The results indicated that, it is fruitful to use the quantitative calculations for releasing patients treated with I-131 and correct estimation of patients' family doses.

Keywords: Effective dose, thermoluminescence, I-131, Thyroid cancer.

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Authors: Jian-Wei Li, Yao-Tien Wang, Yi-Chun Chang

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Cooperative learning has been defined as learners working together as a team to solve a problem to complete a task or to accomplish a common goal, which emphasizes the importance of interactions among members to promote the whole learning performance. With the popularity of society networks, cooperative learning is no longer limited to traditional classroom teaching activities. Since society networks facilitate to organize online learners, to establish common shared visions, and to advance learning interaction, the online community and online learning community have triggered the establishment of web-based societies. Numerous research literatures have indicated that the collaborative learning community is a critical issue to enhance learning performance. Hence, this paper proposes a learning community recommendation approach to facilitate that a learner joins the appropriate learning communities, which is based on k-nearest neighbor (kNN) classification. To demonstrate the viability of the proposed approach, the proposed approach is implemented for 117 students to recommend learning communities. The experimental results indicate that the proposed approach can effectively recommend appropriate learning communities for learners.

Keywords: k-nearest neighbor classification, learning community, Cooperative/Collaborative Learning and Environments.

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Authors: Imran Ahmed, Muhammad Islam, Syed Inayat Ali Shah, Awais Adnan

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The identification and classification of weeds are of major technical and economical importance in the agricultural industry. To automate these activities, like in shape, color and texture, weed control system is feasible. The goal of this paper is to build a real-time, machine vision weed control system that can detect weed locations. In order to accomplish this objective, a real-time robotic system is developed to identify and locate outdoor plants using machine vision technology and pattern recognition. The algorithm is developed to classify images into broad and narrow class for real-time selective herbicide application. The developed algorithm has been tested on weeds at various locations, which have shown that the algorithm to be very effectiveness in weed identification. Further the results show a very reliable performance on weeds under varying field conditions. The analysis of the results shows over 90 percent classification accuracy over 140 sample images (broad and narrow) with 70 samples from each category of weeds.

Keywords: Weed detection, Image Processing, real-timerecognition, Standard Deviation.

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Authors: Ameur Abdelkader, Abed Bouarfa Hafida

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Since its inception, predictive analysis has revolutionized the IT industry through its robustness and decision-making facilities. It involves the application of a set of data processing techniques and algorithms in order to create predictive models. Its principle is based on finding relationships between explanatory variables and the predicted variables. Past occurrences are exploited to predict and to derive the unknown outcome. With the advent of big data, many studies have suggested the use of predictive analytics in order to process and analyze big data. Nevertheless, they have been curbed by the limits of classical methods of predictive analysis in case of a large amount of data. In fact, because of their volumes, their nature (semi or unstructured) and their variety, it is impossible to analyze efficiently big data via classical methods of predictive analysis. The authors attribute this weakness to the fact that predictive analysis algorithms do not allow the parallelization and distribution of calculation. In this paper, we propose to extend the predictive analysis algorithm, Classification And Regression Trees (CART), in order to adapt it for big data analysis. The major changes of this algorithm are presented and then a version of the extended algorithm is defined in order to make it applicable for a huge quantity of data.

Keywords: Predictive analysis, big data, predictive analysis algorithms. CART algorithm.

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Authors: K.Manimala, Dr.K.Selvi, R.Ahila

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Artificial Intelligence (AI) methods are increasingly being used for problem solving. This paper concerns using AI-type learning machines for power quality problem, which is a problem of general interest to power system to provide quality power to all appliances. Electrical power of good quality is essential for proper operation of electronic equipments such as computers and PLCs. Malfunction of such equipment may lead to loss of production or disruption of critical services resulting in huge financial and other losses. It is therefore necessary that critical loads be supplied with electricity of acceptable quality. Recognition of the presence of any disturbance and classifying any existing disturbance into a particular type is the first step in combating the problem. In this work two classes of AI methods for Power quality data mining are studied: Artificial Neural Networks (ANNs) and Support Vector Machines (SVMs). We show that SVMs are superior to ANNs in two critical respects: SVMs train and run an order of magnitude faster; and SVMs give higher classification accuracy.

Keywords: back propagation network, power quality, probabilistic neural network, radial basis function support vector machine

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Authors: Frank Emmert Streib

Abstract:

The classification of the protein structure is commonly not performed for the whole protein but for structural domains, i.e., compact functional units preserved during evolution. Hence, a first step to a protein structure classification is the separation of the protein into its domains. We approach the problem of protein domain identification by proposing a novel graph theoretical algorithm. We represent the protein structure as an undirected, unweighted and unlabeled graph which nodes correspond the secondary structure elements of the protein. This graph is call the protein graph. The domains are then identified as partitions of the graph corresponding to vertices sets obtained by the maximization of an objective function, which mutually maximizes the cycle distributions found in the partitions of the graph. Our algorithm does not utilize any other kind of information besides the cycle-distribution to find the partitions. If a partition is found, the algorithm is iteratively applied to each of the resulting subgraphs. As stop criterion, we calculate numerically a significance level which indicates the stability of the predicted partition against a random rewiring of the protein graph. Hence, our algorithm terminates automatically its iterative application. We present results for one and two domain proteins and compare our results with the manually assigned domains by the SCOP database and differences are discussed.

Keywords: Graph partitioning, unweighted graph, protein domains.

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Authors: M. Rahimnejad, B. Vahidi, B. Ebrahimi Hoseinzadeh, F. Yazdian, P. Motamed Fath, R. Jamjah

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In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.

Keywords: Anti-cancer drug, center of Mass, interaction energy, molecular dynamics simulation, nanocarrier.

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Authors: Mahdieh Khalilinezhad, Silvana Dellepiane, Gianni Vernazza

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The aim of this work is to build a model based on tissue characterization that is able to discriminate pathological and non-pathological regions from three-phasic CT images. With our research and based on a feature selection in different phases, we are trying to design a neural network system with an optimal neuron number in a hidden layer. Our approach consists of three steps: feature selection, feature reduction, and classification. For each region of interest (ROI), 6 distinct sets of texture features are extracted such as: first order histogram parameters, absolute gradient, run-length matrix, co-occurrence matrix, autoregressive model, and wavelet, for a total of 270 texture features. When analyzing more phases, we show that the injection of liquid cause changes to the high relevant features in each region. Our results demonstrate that for detecting HCC tumor phase 3 is the best one in most of the features that we apply to the classification algorithm. The percentage of detection between pathology and healthy classes, according to our method, relates to first order histogram parameters with accuracy of 85% in phase 1, 95% in phase 2, and 95% in phase 3.

Keywords: Feature selection, Multi-phasic liver images, Neural network, Texture analysis.

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Authors: Walsh Joe, Climstein Mike, Heazlewood Ian Timothy, Burke Stephen, Kettunen Jyrki, Adams Kent, DeBeliso Mark

Abstract:

Whilst there is growing evidence that activity across the lifespan is beneficial for improved health, there are also many changes involved with the aging process and subsequently the potential for reduced indices of health. Data gathered on a subsample of 535 football code athletes, aged 31-72 yrs ( = 47.4, s = ±7.1), competing at the Sydney World Masters Games (2009) demonstrated a significantly (p < 0.001), reduced classification of obesity using Body Mass Index (BMI) when compared to the general Australian population. This evidence of improved classification in one index of health (BMI < 30) for master athletes (when compared to the general population) implies there are either improved levels of this index of health due to adherence to sport or possibly the reduced BMI is advantageous and contributes to this cohort adhering (or being attracted) to masters sport. Demonstration of this proportionately under-investigated World Masters Games population having improved health over the general population is of particular interest.

Keywords: BMI, masters athlete, rugby union, soccer, touch football.

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Authors: Ali A. Bazzi, Ameer Hamza, Riley O’Hara, Kimberly Kado, Karen H. Hagglund, Lamia Fathallah, Robert T. Morris

Abstract:

Introduction: Endometrial Cancer is a common gynecologic malignancy primarily treated with complete surgical staging, which may include complete pelvic and para-aortic lymphadenectomy. The role of lymphadenectomy is controversial, especially the intraoperative indications for the procedure. Three factors are important in decision to proceed with lymphadenectomy: Myometrial invasion, maximum tumor dimension, and histology. Many institutions incorporate these criteria in varying degrees in the decision to proceed with lymphadenectomy. This investigation assesses the use of intraoperatively measured MTD with and without pre-operative histologic grade. Methods: This study compared retrospectively EEC patients with intraoperatively measured MTD ≤2 cm to those with MTD >2 cm from January 1, 2002 to August 31, 2017. This assessment compared those with MTD ≤ 2cm with endometrial biopsy (EB) grade 1-2 to patients with MTD > 2cm with EB grade 3. Lymph node metastasis (LNM), recurrence, and survival were compared in these groups. Results: This study reviewed 222 patient cases. In tumors > 2 cm, LNM occurred in 20% cases while in tumors ≤ 2 cm, LNM was found in 6% cases (p=0.04). Recurrence and mean survival based on last follow up visit in these two groups were not statistically different (p=0.78 and 0.36 respectively). Data demonstrated a trend that when combined with preoperative EB International Federation of Gynecology and Obstetrics (FIGO) grade, a higher proportion of patients with EB FIGO Grade 3 and MTD > 2 cm had LNM compared to those with EB FIGO Grade 1-2 and MTD ≤ 2 cm (43% vs, 11%, p=0.06). LNM was found in 15% of cases in which lymphadenectomy was performed based on current practices, whereas if the criteria of EB FIGO 3 and MTD > 2 cm were used the incidence of LNM would have been 44% cases. However, using this criterion, two patients would not have had their nodal metastases detected. Compared to the current practice, the sensitivity and specificity of the proposed criteria would be 60% and 81%, respectively. The PPV and NPV would be 43% and 90%, respectively. Conclusion: The results indicate that MTD combined with EB FIGO grade can detect LNM in a higher proportion of cases when compared to current practice. MTD combined with EB FIGO grade may eliminate the need of frozen section sampling in a substantial number of cases.

Keywords: Endometrial cancer, FIGO grade, lymphadenectomy, tumor size.

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Authors: Elif Derya UBEYLI, Inan GULER

Abstract:

A new approach based on the consideration that electroencephalogram (EEG) signals are chaotic signals was presented for automated diagnosis of electroencephalographic changes. This consideration was tested successfully using the nonlinear dynamics tools, like the computation of Lyapunov exponents. This paper presented the usage of statistics over the set of the Lyapunov exponents in order to reduce the dimensionality of the extracted feature vectors. Since classification is more accurate when the pattern is simplified through representation by important features, feature extraction and selection play an important role in classifying systems such as neural networks. Multilayer perceptron neural network (MLPNN) architectures were formulated and used as basis for detection of electroencephalographic changes. Three types of EEG signals (EEG signals recorded from healthy volunteers with eyes open, epilepsy patients in the epileptogenic zone during a seizure-free interval, and epilepsy patients during epileptic seizures) were classified. The selected Lyapunov exponents of the EEG signals were used as inputs of the MLPNN trained with Levenberg- Marquardt algorithm. The classification results confirmed that the proposed MLPNN has potential in detecting the electroencephalographic changes.

Keywords: Chaotic signal, Electroencephalogram (EEG) signals, Feature extraction/selection, Lyapunov exponents

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Authors: Huyen T. Pham, Nhue P. Nguyen, Tien Q. Phi, Phuong T. Dang, Hy G. Le

Abstract:

Since the marine environmental conditions are extremely different from the other ones, marine actinomycetes might produce novel bioactive compounds. Therefore, actinomycete strains were screened from marine water and sediment samples collected from the coastal areas of Northern Vietnam. Ninety-nine actinomycete strains were obtained on starch-casein agar media by dilution technique, only seven strains, named HP112, HP12, HP411, HPN11, HP 11, HPT13 and HPX12, showed significant antibacterial activity against both gram-positive and gram-negative bacteria (Bacillus subtilis ATCC 6633, Staphylococcus epidemidis ATCC 12228, Escherichia coli ATCC 11105). Further studies were carried out with the most active HP411 strain against Candida albicans ATCC 10231. This strain could grow rapidly on starch casein agar and other media with high salt containing 7-10% NaCl at 28-30oC. Spore-chain of HP411 showed an elongated and circular shape with 10 to 30 spores/chain. Identification of the strain was carried out by employing the taxonomical studies including the 16S rRNA sequence. Based on phylogenetic and phenotypic evidence it is proposed that HP411 to be belongs to species Streptomyces variabilis. The potent of the crude extract of fermentation broth of HP411 that are effective against wide range of pathogens: both grampositive, gram-negative and fungi. Further studies revealed that the crude extract HP411 could obtain the anticancer activity for cancer cell lines: Hep-G2 (liver cancer cell line); RD (cardiac and skeletal muscle letters cell line); FL (membrane of the uterus cancer cell line). However, the actinomycetes from marine ecosystem will be useful for the discovery of new drugs in the future.

Keywords: Marine actinomycetes, antibacterial, anticancer, Streptomyces variabilis.

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