Search results for: Ordinal pairwise partitioning

Authors: Billel Kenidra, Mohamed Benmohammed

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Data mining technique used in the field of clustering is a subject of active research and assists in biological pattern recognition and extraction of new knowledge from raw data. Clustering means the act of partitioning an unlabeled dataset into groups of similar objects. Each group, called a cluster, consists of objects that are similar between themselves and dissimilar to objects of other groups. Several clustering methods are based on partitional clustering. This category attempts to directly decompose the dataset into a set of disjoint clusters leading to an integer number of clusters that optimizes a given criterion function. The criterion function may emphasize a local or a global structure of the data, and its optimization is an iterative relocation procedure. The K-Means algorithm is one of the most widely used partitional clustering techniques. Since K-Means is extremely sensitive to the initial choice of centers and a poor choice of centers may lead to a local optimum that is quite inferior to the global optimum, we propose a strategy to initiate K-Means centers. The improved K-Means algorithm is compared with the original K-Means, and the results prove how the efficiency has been significantly improved.

Keywords: Microarray data mining, biological pattern recognition, partitional clustering, k-means algorithm, centroid initialization.

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Authors: Lu Zou, Dianfu MA, Ying Wang, Xianqi Zhao

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Avionic software architecture has transit from a federated avionics architecture to an integrated modular avionics (IMA) .ARINC 653 (Avionics Application Standard Software Interface) is a software specification for space and time partitioning in Safety-critical avionics Real-time operating systems. Methods to transform the abstract avionics application logic function to the executable model have been brought up, however with less consideration about the code generating input and output model specific for ARINC 653 platform and inner-task synchronous dynamic interaction order sequence. In this paper, we proposed an AADL-based model-driven design methodology to fulfill the purpose to automatically generating Cµ executable model on ARINC 653 platform from the ARINC653 architecture which defined as AADL653 in order to facilitate the development of the avionics software constructed on ARINC653 OS. This paper presents the mapping rules between the AADL653 elements and the elements in Cµ language, and define the code generating rules , designs an automatic C µ code generator .Then, we use a case to illustrate our approach. Finally, we give the related work and future research directions.

Keywords: IMA, ARINC653, AADL653, code generation.

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Authors: Frank Emmert-Streib, Matthias Dehmer, Jing Liu, Max Muhlhauser

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The major objective of this paper is to introduce a new method to select genes from DNA microarray data. As criterion to select genes we suggest to measure the local changes in the correlation graph of each gene and to select those genes whose local changes are largest. More precisely, we calculate the correlation networks from DNA microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to tumor progression. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth. This indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, generalized trees, graph alignment, DNA microarray data, cervical cancer.

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Authors: Fernanda M. Assef, Maria Teresinha A. Steiner, David Gabriel F. de Barros

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Review researches are useful in terms of analysis of research problems. Between the types of review documents, we commonly find bibliometric studies. This type of application often helps the global visualization of a research problem and helps academics worldwide to understand the context of a research area better. In this document, a bibliometric view surrounding clustering techniques and sustainability problems is presented. The authors aimed at which issues mostly use clustering techniques and even which sustainability issue would be more impactful on today’s moment of research. During the bibliometric analysis, we found 10 different groups of research in clustering applications for sustainability issues: Energy; Environmental; Non-urban Planning; Sustainable Development; Sustainable Supply Chain; Transport; Urban Planning; Water; Waste Disposal; and, Others. Moreover, by analyzing the citations of each group, it was discovered that the Environmental group could be classified as the most impactful research cluster in the area mentioned. After the content analysis of each paper classified in the environmental group, it was found that the k-means technique is preferred for solving sustainability problems with clustering methods since it appeared the most amongst the documents. The authors finally conclude that a bibliometric assessment could help indicate a gap of researches on waste disposal – which was the group with the least amount of publications – and the most impactful research on environmental problems.

Keywords: Bibliometric assessment, clustering, sustainability, territorial partitioning.

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Authors: Mounira Taileb, Sid Lamrous, Sami Touati

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In order to accelerate the similarity search in highdimensional database, we propose a new hierarchical indexing method. It is composed of offline and online phases. Our contribution concerns both phases. In the offline phase, after gathering the whole of the data in clusters and constructing a hierarchical index, the main originality of our contribution consists to develop a method to construct bounding forms of clusters to avoid overlapping. For the online phase, our idea improves considerably performances of similarity search. However, for this second phase, we have also developed an adapted search algorithm. Our method baptized NOHIS (Non-Overlapping Hierarchical Index Structure) use the Principal Direction Divisive Partitioning (PDDP) as algorithm of clustering. The principle of the PDDP is to divide data recursively into two sub-clusters; division is done by using the hyper-plane orthogonal to the principal direction derived from the covariance matrix and passing through the centroid of the cluster to divide. Data of each two sub-clusters obtained are including by a minimum bounding rectangle (MBR). The two MBRs are directed according to the principal direction. Consequently, the nonoverlapping between the two forms is assured. Experiments use databases containing image descriptors. Results show that the proposed method outperforms sequential scan and SRtree in processing k-nearest neighbors.

Keywords: K-nearest neighbour search, multi-dimensional indexing, multimedia databases, similarity search.

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Authors: Harshani Uggallage, Kapila D. Dissanayaka

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A Sulforhodamine-B assay-guided fractionation on Nigella sativa seeds was conducted to determine the presence of cytotoxic compounds against human hepatoma (HepG2) cells. Initially, a freeze-dried sample of Nigella sativa seeds was sequentially extracted into solvents of increasing polarities. Crude extracts from the sequential extraction of Nigella sativa seeds in chloroform and ethyl acetate showed the highest cytotoxicity. The combined mixture of these two extracts was subjected to bioassay guided fractionation using a modified Kupchan method of partitioning, followed by Sephadex® LH-20 chromatography. This chromatographic separation process resulted in a column fraction with a convincing IC50 (half-maximal inhibitory concentration) value of 13.07 µg/ml, which is considerable for developing therapeutic drug leads against human hepatoma. Reversed phase High-Performance Liquid Chromatography (HPLC) was finally conducted for the same column fraction and the result indicates the presence of one or several main cytotoxic compounds against human HepG2 cells.

Keywords: Cytotoxic compounds, half-maximal inhibitory concentration, high-performance liquid chromatography, human HepG2 cells, Nigella sativa seeds, Sulforhodamine-B assay-guided fractionation.

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Authors: Paúl I. Cornejo

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The elastic energy released through Strombolian explosions has been quite studied, detailing various processes, sources, and precursory events at several volcanoes. We realized an analysis based on the relative partitioning of the elastic energy radiated into the atmosphere and ground by Strombolian-type explosions recorded at El Reventador volcano, using infrasound and seismic signals at high and moderate seismicity episodes during intense eruptive stages of explosive and effusive activity. Our results show that considerable values of Volcano Acoustic-Seismic Ratio (VASR or η) are obtained at high seismicity stages. VASR is a physical diagnostic of explosive degassing that we used to compare eruption mechanisms at El Reventador volcano for two datasets of explosions recorded at a Broad-Band BB seismic and infrasonic station located at ~5 kilometers from the vent. We conclude that the acoustic energy EA released during explosive activity (VASR η = 0.47, standard deviation σ = 0.8) is higher than the EA released during effusive activity; therefore, producing the highest values of η. Furthermore, we realized the analysis and characterization of the eruptive intensity for two episodes at high seismicity, calculating a η three-time higher for an episode of effusive activity with an occasional explosive component (η = 0.32, and σ = 0.42), than a η for an episode of only effusive activity (η = 0.11, and σ = 0.18), but more energetic.

Keywords: Effusive, explosion quakes, explosive, strombolian, VASR.

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Authors: Mohd. Noor Md. Sap, A. Majid Awan

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Intelligent systems based on machine learning techniques, such as classification, clustering, are gaining wide spread popularity in real world applications. This paper presents work on developing a software system for predicting crop yield, for example oil-palm yield, from climate and plantation data. At the core of our system is a method for unsupervised partitioning of data for finding spatio-temporal patterns in climate data using kernel methods which offer strength to deal with complex data. This work gets inspiration from the notion that a non-linear data transformation into some high dimensional feature space increases the possibility of linear separability of the patterns in the transformed space. Therefore, it simplifies exploration of the associated structure in the data. Kernel methods implicitly perform a non-linear mapping of the input data into a high dimensional feature space by replacing the inner products with an appropriate positive definite function. In this paper we present a robust weighted kernel k-means algorithm incorporating spatial constraints for clustering the data. The proposed algorithm can effectively handle noise, outliers and auto-correlation in the spatial data, for effective and efficient data analysis by exploring patterns and structures in the data, and thus can be used for predicting oil-palm yield by analyzing various factors affecting the yield.

Keywords: Pattern analysis, clustering, kernel methods, spatial data, crop yield

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Authors: Hyun Chul Cho, Hyunkyoung Oh, Hyun Yoon, Jooyeon Jin, Jae Won Lee

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Identifying, structuring, and racking the most important factors related to improving athletes’ performances could pave the way for improve training system. The purpose of this study was to identify the relative importance factors to improve performance of the of judo athletes with visual impairments, including blindness by using the Analytic Hierarchy Process (AHP). After reviewing the literature, the relative importance of factors affecting performance of the blind judo was selected. A group of expert reviewed the first draft of the questionnaires, and then finally selected performance factors were classified into the major categories of techniques, physical fitness, and psychological categories. Later, a pre-selected experts group was asked to review the final version of questionnaire and confirm the priories of performance factors. The order of priority was determined by performing pairwise comparisons using Expert Choice 2000. Results indicated that “grappling” (.303) and “throwing” (.234) were the most important lower hierarchy factors for blind judo skills. In addition, the most important physical factors affecting performance were “muscular strength and endurance” (.238). Further, among other psychological factors “competitive anxiety” (.393) was important factor that affects performance. It is important to offer psychological skills training to reduce anxiety of judo athletes with visual impairments and blindness, so they can compete in their optimal states. These findings offer insights into what should be considered when determining factors to improve performance of judo athletes with visual impairments and blindness.

Keywords: Analytic hierarchy process, blind athlete, judo, sport performance.

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Authors: Achitphol Chookaew, Paramee Thongsukhsai, Patamarerk Engsontia, Narongwit Nakwan, Pritsana Raugrut

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Lung cancer is one of the most common malignancies and primary cause of death due to cancer worldwide. Non-small cell lung cancer (NSCLC) is the main subtype in which majority of patients present with advanced-stage disease. Herein, we analyzed differentially expressed genes to find potential biomarkers for lung cancer diagnosis as well as prognostic markers. We used transcriptome data from our 2 NSCLC patients and public data (GSE81089) composing of 8 NSCLC and 10 normal lung tissues. Differentially expressed genes (DEGs) between NSCLC and normal tissue and between early-stage and late-stage NSCLC were analyzed by the DESeq2. Pairwise correlation was used to find the DEGs with false discovery rate (FDR) adjusted p-value £ 0.05 and |log2 fold change| ³ 4 for NSCLC versus normal and FDR adjusted p-value £ 0.05 with |log2 fold change| ³ 2 for early versus late-stage NSCLC. Bioinformatic tools were used for functional and pathway analysis. Moreover, the top ten genes in each comparison group were verified the expression and survival analysis via GEPIA. We found 150 up-regulated and 45 down-regulated genes in NSCLC compared to normal tissues. Many immnunoglobulin-related genes e.g., IGHV4-4, IGHV5-10-1, IGHV4-31, IGHV4-61, and IGHV1-69D were significantly up-regulated. 22 genes were up-regulated, and five genes were down-regulated in late-stage compared to early-stage NSCLC. The top five DEGs genes were KRT6B, SPRR1A, KRT13, KRT6A and KRT5. Keratin 6B (KRT6B) was the most significantly increased gene in the late-stage NSCLC. From GEPIA analysis, we concluded that IGHV4-31 and IGKV1-9 might be used as diagnostic biomarkers, while KRT6B and KRT6A might be used as prognostic biomarkers. However, further clinical validation is needed.

Keywords: Bioinformatics, differentially expressed genes, non-small cell lung cancer, transcriptomics.

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Authors: Niveditha Domse, Kris Kumar, K. N. Balasubramanya Murthy

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The more recent satellite projects/programs makes extensive usage of real – time embedded systems. 16 bit processors which meet the Mil-Std-1750 standard architecture have been used in on-board systems. Most of the Space Applications have been written in ADA. From a futuristic point of view, 32 bit/ 64 bit processors are needed in the area of spacecraft computing and therefore an effort is desirable in the study and survey of 64 bit architectures for space applications. This will also result in significant technology development in terms of VLSI and software tools for ADA (as the legacy code is in ADA). There are several basic requirements for a special processor for this purpose. They include Radiation Hardened (RadHard) devices, very low power dissipation, compatibility with existing operational systems, scalable architectures for higher computational needs, reliability, higher memory and I/O bandwidth, predictability, realtime operating system and manufacturability of such processors. Further on, these may include selection of FPGA devices, selection of EDA tool chains, design flow, partitioning of the design, pin count, performance evaluation, timing analysis etc. This project deals with a brief study of 32 and 64 bit processors readily available in the market and designing/ fabricating a 64 bit RISC processor named RISC MicroProcessor with added functionalities of an extended double precision floating point unit and a 32 bit signal processing unit acting as co-processors. In this paper, we emphasize the ease and importance of using Open Core (OpenSparc T1 Verilog RTL) and Open “Source" EDA tools such as Icarus to develop FPGA based prototypes quickly. Commercial tools such as Xilinx ISE for Synthesis are also used when appropriate.

Keywords: RISC MicroProcessor, RPC – RISC Processor Core, PBX – Processor to Block Interface part of the Interconnection Network, BPX – Block to Processor Interface part of the Interconnection Network, FPU – Floating Point Unit, SPU – Signal Processing Unit, WB – Wishbone Interface, CTU – Clock and Test Unit

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Authors: Natalia Rudeli, Elisabeth Viles, Adrian Santilli

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Delays in the construction industry are a global phenomenon. Many construction projects experience extensive delays exceeding the initially estimated completion time. The main purpose of this study is to identify construction projects typical behaviors in order to develop a prognosis and management tool. Being able to know a construction projects schedule tendency will enable evidence-based decision-making to allow resolutions to be made before delays occur. This study presents an innovative approach that uses Cluster Analysis Method to support predictions during Earned Value Analyses. A clustering analysis was used to predict future scheduling, Earned Value Management (EVM), and Earned Schedule (ES) principal Indexes behaviors in construction projects. The analysis was made using a database with 90 different construction projects. It was validated with additional data extracted from literature and with another 15 contrasting projects. For all projects, planned and executed schedules were collected and the EVM and ES principal indexes were calculated. A complete linkage classification method was used. In this way, the cluster analysis made considers that the distance (or similarity) between two clusters must be measured by its most disparate elements, i.e. that the distance is given by the maximum span among its components. Finally, through the use of EVM and ES Indexes and Tukey and Fisher Pairwise Comparisons, the statistical dissimilarity was verified and four clusters were obtained. It can be said that construction projects show an average delay of 35% of its planned completion time. Furthermore, four typical behaviors were found and for each of the obtained clusters, the interim milestones and the necessary rhythms of construction were identified. In general, detected typical behaviors are: (1) Projects that perform a 5% of work advance in the first two tenths and maintain a constant rhythm until completion (greater than 10% for each remaining tenth), being able to finish on the initially estimated time. (2) Projects that start with an adequate construction rate but suffer minor delays culminating with a total delay of almost 27% of the planned time. (3) Projects which start with a performance below the planned rate and end up with an average delay of 64%, and (4) projects that begin with a poor performance, suffer great delays and end up with an average delay of a 120% of the planned completion time. The obtained clusters compose a tool to identify the behavior of new construction projects by comparing their current work performance to the validated database, thus allowing the correction of initial estimations towards more accurate completion schedules.

Keywords: Cluster analysis, construction management, earned value, schedule.

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Authors: R. U. Hamzah, H. L. Muhammad, A. Sayyadi, M. B Busari, R. Garba, M. B. Umar, A. N Abubakar

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Lead (Pb) and Cadmium (Cd) are toxic, non-essential transition metals that pose many health risks for both humans and animals. They are environmental toxicants which contribute to testicular damage resulting to infertility problem among male populace worldwide. Chelating agents used for lead and cadmium toxicity are not readily available, toxic, expensive and unable to mop up most of the toxic metals accumulated in various organs. In this study, the effect of crude extract (CE), ethyl acetate fraction (EF) and acetone fraction (AF) of Pterocarpus mildbraedii leaf extract was assessed on cadmium-lead chloride induced testicular damaged in male albino Wistar rats. CE of the leaf was obtained by extracting in absolute methanol which was further subjected to solvent partitioning via vacuum liquid chromatographic (VLC) techniques using ethyl acetate, acetone and 70% methanol. A preliminary phytochemical screening and in vitro antioxidants guided activities on the CE and fractions were determined using standard methods. EF, AF and CE which exhibited significant in vitro activity were subjected to an in vivo study using Wistar rats. In vivo antioxidant markers, male reproductive hormones, testicular enzymes and DNA damage markers were analyzed on the rats’ testes supernatant. AF had the highest quantities of phenols (319.00 mg/g), flavonoids (8.87 mg/g) and tannins (8.87 mg/g) while methanol and EFs were richer in saponins (135.32 µg/g) and alkaloids (38.34 µg/g) respectively. A dose dependent 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, ferric reducing antioxidant power (FRAP) and lipid peroxidation were observed in all the extract with high antioxidants power in CE and AF. Administration of lead-cadmium chloride solution significantly (p > 0.05) decreases the testicular superoxide dismutase (SOD) activity to 6.82 unit/mg protein, Catalase (CAT) activity to 8.07 of H2O2 consumed/unit/mg protein and Glutathione (GSH) concentration to 31.30 ug/mg protein. There was a concomitant increase in the level of Malondialdehyde (MDA) to a value of 23.70 mmol/mg protein. In addition, lead-cadmium chloride solution significantly (p > 0.05) increases the testicular marker enzymes (Alkaline phosphatase (119.57 u/L), lactate dehydrogenase (357.05 u/L), Acid phosphatase (98.65 u/L)) and DNA damage markers (conjugated dienes (93.39 nmol/mg protein), carbonyl protein (35.39 nmol/mg protein), DNA fragmentation percentage (32.12%)) with lowered testicular hormones (Testosterone (3.1 ng/mL), Follicle stimulating (0.35 IU/mL) and Luteinizing hormones (0.15 IU/mL)) of the animals in negative control group when compared with other treated groups. Treatment with Pterocarpus mildbraedii leaf extract reverts the observed changes with the best activities found in the CE and AFs in a dose dependent manner. Pterocarpus mildbraedii leaf extract ameliorated the lead/cadmium induced testicular damage in male albino rats. The restoration of the aforementioned parameters by some of the extract dosages were comparable to the standard drug with higher activities in the crude and AF. Therefore, Pterocarpus mildbraedii leaf extract can be explored further for the management of lead/cadmium induced toxicity.

Keywords: Cadmium, lead, Pterocarpus mildbraedii, testicular damage.

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