Search results for: biomarker discovery

Authors: Alaa E. Abdallah, Bajes Y. Alskarnah

Abstract:

Ant colony based routing algorithms are known to grantee the packet delivery, but they suffer from the huge overhead of control messages which are needed to discover the route. In this paper we utilize the network nodes positions to group the nodes in connected clusters. We use clusters-heads only on forwarding the route discovery control messages. Our simulations proved that the new algorithm has decreased the overhead dramatically without affecting the delivery rate.

Keywords: Ant colony-based routing, position-based routing, MANET.

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Authors: Rezvan Najafi, Korosh Heydari, Massoud Saidijam

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5-FU is a chemotherapeutic agent that has been used in colorectal cancer (CRC) treatment. However, it is usually associated with the acquired resistance, which decreases the therapeutic effects of 5-FU. miR-200c is involved in chemotherapeutic drug resistance, but its mechanism is not fully understood. In this study, the effect of inhibition of miR-200c in sensitivity of HCT-116 CRC cells to 5-FU was evaluated. HCT-116 cells were transfected with LNA-anti- miR-200c for 48 h. mRNA expression of miR-200c was evaluated using quantitative real- time PCR. The protein expression of phosphatase and tensin homolog (PTEN) and E-cadherin were analyzed by western blotting. Annexin V and propidium iodide staining assay were applied for apoptosis detection. The caspase-3 activation was evaluated by an enzymatic assay. The results showed LNA-anti-miR-200c inhibited the expression of PTEN and E-cadherin protein, apoptosis and activation of caspase 3 compared with control cells. In conclusion, these results suggest that miR-200c as a prognostic marker can overcome to 5-FU chemoresistance in CRC.

Keywords: Colorectal cancer, miR-200c, 5-FU resistance, E-cadherin, PTEN.

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Authors: Ricardo Avila, Gabriel Lopes, Vania Vidal, Jose Macedo

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This article offers a approach to the automatic discovery of semantic concepts and links in the domain of Oil Exploration and Production (E&P). Machine learning methods combined with textual pre-processing techniques were used to detect local patterns in texts and, thus, generate new concepts and new semantic links. Even using more specific vocabularies within the oil domain, our approach has achieved satisfactory results, suggesting that the proposal can be applied in other domains and languages, requiring only minor adjustments.

Keywords: Semantic links, data mining, linked data, SKOS.

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Authors: Jorge Cardoso

Abstract:

It has been recognized that due to the autonomy and heterogeneity, of Web services and the Web itself, new approaches should be developed to describe and advertise Web services. The most notable approaches rely on the description of Web services using semantics. This new breed of Web services, termed semantic Web services, will enable the automatic annotation, advertisement, discovery, selection, composition, and execution of interorganization business logic, making the Internet become a common global platform where organizations and individuals communicate with each other to carry out various commercial activities and to provide value-added services. This paper deals with two of the hottest R&D and technology areas currently associated with the Web – Web services and the semantic Web. It describes how semantic Web services extend Web services as the semantic Web improves the current Web, and presents three different conceptual approaches to deploying semantic Web services, namely, WSDL-S, OWL-S, and WSMO.

Keywords: Semantic Web, Web service, Web process, WWW

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Authors: Chia-Feng Lu, Yuh-Jen Wang, Yu-Te Wu, Sui-Hing Yan

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This study aimed at investigating whether the functional brain networks constructed using the initial EEG (obtained when patients first visited hospital) can be correlated with the progression of cognitive decline calculated as the changes of mini-mental state examination (MMSE) scores between the latest and initial examinations. We integrated the time–frequency cross mutual information (TFCMI) method to estimate the EEG functional connectivity between cortical regions, and the network analysis based on graph theory to investigate the organization of functional networks in aMCI. Our finding suggested that higher integrated functional network with sufficient connection strengths, dense connection between local regions, and high network efficiency in processing information at the initial stage may result in a better prognosis of the subsequent cognitive functions for aMCI. In conclusion, the functional connectivity can be a useful biomarker to assist in prediction of cognitive declines in aMCI.

Keywords: Cognitive decline, functional connectivity, MCI, MMSE.

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Authors: A. R. Vazifedoost, M. Rahgozar, F. Oroumchian

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Knowledge discovery from text and ontology learning are relatively new fields. However their usage is extended in many fields like Information Retrieval (IR) and its related domains. Human Plausible Reasoning based (HPR) IR systems for example need a knowledge base as their underlying system which is currently made by hand. In this paper we propose an architecture based on ontology learning methods to automatically generate the needed HPR knowledge base.

Keywords: Ontology Learning, Human Plausible Reasoning, knowledge extraction, knowledge representation.

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Authors: Ahmad M. Khalil, Ahmad M. Alshamali, Marwan H. Gagaa

Abstract:

We investigated oxidative DNA damage caused by radio frequency radiation using 8-oxo-7, 8-dihydro-2'- deoxyguanosine (8-oxodG) generated in mice tissues after exposure to 900 MHz mobile phone radio frequency in three independent experiments. The RF was generated by a Global System for Mobile Communication (GSM) signal generator. The radio frequency field was adjusted to 25 V/m. The whole body specific absorption rate (SAR) was 1.0 W/kg. Animals were exposed to this field for 30 min daily for 30 days. 24 h post-exposure, blood serum, brain and spleen were removed and DNA was isolated. Enzyme-linked immunosorbent assay (ELISA) was used to measure 8-oxodG concentration. All animals survived the whole experimental period. The body weight of animals did not change significantly at the end of the experiment. No statistically significant differences observed in the levels of oxidative stress. Our results are not in favor of the hypothesis that 900 MHz RF induces oxidative damage.

Keywords: Mice, Mobile phone radiation, oxidative stress, 8-oxo-7, 8-dihydro-2'-deoxyguanosine

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Authors: S. B. Kotsiantis, D. Kanellopoulos, P. E. Pintelas

Abstract:

Many factors affect the success of Machine Learning (ML) on a given task. The representation and quality of the instance data is first and foremost. If there is much irrelevant and redundant information present or noisy and unreliable data, then knowledge discovery during the training phase is more difficult. It is well known that data preparation and filtering steps take considerable amount of processing time in ML problems. Data pre-processing includes data cleaning, normalization, transformation, feature extraction and selection, etc. The product of data pre-processing is the final training set. It would be nice if a single sequence of data pre-processing algorithms had the best performance for each data set but this is not happened. Thus, we present the most well know algorithms for each step of data pre-processing so that one achieves the best performance for their data set.

Keywords: Data mining, feature selection, data cleaning.

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Authors: Mehdi Alilou, Mehdi Dehghan

Abstract:

Routing in mobile ad hoc networks is a challenging task because nodes are free to move randomly. In DSR like all On- Demand routing algorithms, route discovery mechanism is associated with great delay. More Clearly in DSR routing protocol to send route reply packet, when current route breaks, destination seeks a new route. In this paper we try to change route selection mechanism proactively. We also define a link stability parameter in which a stability value is assigned to each link. Given this feature, destination node can estimate stability of routes and can select the best and more stable route. Therefore we can reduce the delay and jitter of sending data packets.

Keywords: DSR, MANET, proactive, routing.

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Authors: R. A. Karim, N. M. A. Ghani, N. N. S. Nasari

Abstract:

Wastages such as grated coconut meat, spent tea and used sugarcane had contributed negative impacts to the environment. Vermicomposting method is fully utilized to manage the wastes towards a more sustainable approach. The worms that are used in the vermicomposting are Eisenia foetida and Eudrillus euginae. This research shows that the vermicompost of wastages has voltage of electrical energy and is able to light up the Light-Emitting Diode (LED) device. Based on the experiment, the use of replicated and double compartments of the component will produce double of voltage. Hence, for conclusion, this harmless and low cost technology of vermicompost can act as a dry cell in order to reduce the usage of hazardous chemicals that can contaminate the environment.

Keywords: Wastages, vermiconpose, worm, voltage, organic cell.

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Authors: R. J. Parham, J. D. Knight

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Organic farmers across Saskatchewan face soil phosphorus (P) shortages. Due to the restriction on inputs in organic systems, farmers rely on crop rotation and naturally-occurring arbuscular mycorrhizal fungi (AMF) for plant P supply. Crop rotation is important for disease, pest, and weed management. Crops that are not colonized by AMF (non-mycorrhizal) can decrease colonization of a following crop. An experiment was performed to quantify soil P cycling in four cropping sequences under organic management and determine if mustard (non-mycorrhizal) was delaying the colonization of subsequent wheat. Soils from the four cropping sequences were measured for inorganic soil P (Pi), AMF spore density (SD), phospholipid fatty acid analysis (PLFA, for AMF biomarker counts), and alkaline phosphatase activity (ALPase, related to AMF metabolic activity). Plants were measured for AMF colonization and P content and uptake of above-ground biomass. A lack of difference in AMF activity indicated that mustard was not depressing colonization. Instead, AMF colonization was largely determined by crop type and crop rotation.

Keywords: Arbuscular mycorrhizal fungi, crop rotation, organic farming, phosphorous, soil microbiology.

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Authors: P. Sateesh Kumar , S. Ramachandram

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Genetic Zone Routing Protocol (GZRP) is a new hybrid routing protocol for MANETs which is an extension of ZRP by using Genetic Algorithm (GA). GZRP uses GA on IERP and BRP parts of ZRP to provide a limited set of alternative routes to the destination in order to load balance the network and robustness during node/link failure during the route discovery process. GZRP is studied for its performance compared to ZRP in many folds like scalability for packet delivery and proved with improved results. This paper presents the results of the effect of load balancing on GZRP. The results show that GZRP outperforms ZRP while balancing the load.

Keywords: MANET, routing, ZRP, Genetic algorithm, GZRP, load balancing

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Authors: C. T. S. Ching, P. W. C hen, T. P. Sun, H. L. Shieh

Abstract:

The biomarker for colorectal cancer (CRC) is CEACAM-6 antigen (C6AG). Therefore, this study aims to develop a novel, simple and low-cost CEACAM-6 antigen immumosensor (C6AG-IMS), based on electrical impedance measurement, for precise determination of C6AG. A low-cost screen-printed graphite electrode was constructed and used as the sensor, with CEACAM-6 antibody (C6AB) immobilized on it. The procedures of sensor fabrication and antibody immobilization are simple and low-cost. Measurement of the electrical impedance at a definite frequency ranges (0.43 – 1.26 MHz) showed that the C6AG-IMS has an excellent linear (r2>0.9) response range (8.125 – 65 pg/mL), covering the normal physiological and pathological ranges of blood C6AG levels. Also, the C6AG-IMS has excellent reliability and validity, with the intraclass correlation coefficient being 0.97. In conclusion, a novel, simple, low-cost and reliable C6AG-IMS was designed and developed, being able to accurately determine blood C6AG levels in the range of pathological and normal physiological regions. The C6AG-IMS can provide a point-of-care and immediate screening results to the user at home.

Keywords: Colorectal Cancer, Immunosensor, Electrical Impedance, CEACAM-6, Measurement, Point-of-Care

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Authors: R. AliMohammadzadeh, M. Rahgozar, A. Zarnani

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The inherent flexibilities of XML in both structure and semantics makes mining from XML data a complex task with more challenges compared to traditional association rule mining in relational databases. In this paper, we propose a new model for the effective extraction of generalized association rules form a XML document collection. We directly use frequent subtree mining techniques in the discovery process and do not ignore the tree structure of data in the final rules. The frequent subtrees based on the user provided support are split to complement subtrees to form the rules. We explain our model within multi-steps from data preparation to rule generation.

Keywords: XML, Data Mining, Association Rule Mining.

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Authors: Arshia Azam, J. Amarnath, Ch. D. V. Paradesi Rao

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The advantage of solving the complex nonlinear problems by utilizing fuzzy logic methodologies is that the experience or expert-s knowledge described as a fuzzy rule base can be directly embedded into the systems for dealing with the problems. The current limitation of appropriate and automated designing of fuzzy controllers are focused in this paper. The structure discovery and parameter adjustment of the Branched T-S fuzzy model is addressed by a hybrid technique of type constrained sparse tree algorithms. The simulation result for different system model is evaluated and the identification error is observed to be minimum.

Keywords: Fuzzy logic, branch T-S fuzzy model, tree modeling, complex nonlinear system.

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Authors: Manpreet Singh, Parminder Kaur Wadhwa, Surinder Kaur

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The drug discovery process starts with protein identification because proteins are responsible for many functions required for maintenance of life. Protein identification further needs determination of protein function. Proposed method develops a classifier for human protein function prediction. The model uses decision tree for classification process. The protein function is predicted on the basis of matched sequence derived features per each protein function. The research work includes the development of a tool which determines sequence derived features by analyzing different parameters. The other sequence derived features are determined using various web based tools.

Keywords: Sequence Derived Features, decision tree.

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Authors: M. R. Aghaebrahimi, S. H. Zahiri, M. Amiri

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In this paper a data miner based on the learning automata is proposed and is called LA-miner. The LA-miner extracts classification rules from data sets automatically. The proposed algorithm is established based on the function optimization using learning automata. The experimental results on three benchmarks indicate that the performance of the proposed LA-miner is comparable with (sometimes better than) the Ant-miner (a data miner algorithm based on the Ant Colony optimization algorithm) and CNZ (a well-known data mining algorithm for classification).

Keywords: Data mining, Learning automata, Classification rules, Knowledge discovery.

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Authors: Bharadwaj Kadiyala, Sunitha V

Abstract:

Most routing protocols (DSR, AODV etc.) that have been designed for wireless adhoc networks incorporate the broadcasting operation in their route discovery scheme. Probabilistic broadcasting techniques have been developed to optimize the broadcast operation which is otherwise very expensive in terms of the redundancy and the traffic it generates. In this paper we have explored percolation theory to gain a different perspective on probabilistic broadcasting schemes which have been actively researched in the recent years. This theory has helped us estimate the value of broadcast probability in a wireless adhoc network as a function of the size of the network. We also show that, operating at those optimal values of broadcast probability there is at least 25-30% reduction in packet regeneration during successful broadcasting.

Keywords: Crossover length, Percolation, Probabilistic broadcast, Wireless adhoc networks

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Authors: Shigeaki Sakurai, Youichi Kitahata, Ryohei Orihara

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This paper proposes a method that discovers sequential patterns corresponding to user-s interests from sequential data. This method expresses the interests as constraint patterns. The constraint patterns can define relationships among attributes of the items composing the data. The method recursively decomposes the constraint patterns into constraint subpatterns. The method evaluates the constraint subpatterns in order to efficiently discover sequential patterns satisfying the constraint patterns. Also, this paper applies the method to the sequential data composed of stock price indexes and verifies its effectiveness through comparing it with a method without using the constraint patterns.

Keywords: Sequential pattern mining, Constraint pattern, Attribute constraint, Stock price indexes

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Authors: Peter Pfeifer, Julian Pfeifer, Niko Pfeifer

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Information processing is at the focus of brain and cognition research. This work has a different perspective, it starts with behaviors. The detailed analysis of behaviors leads to the discovery that a significant proportion of them are based on only five basic drives. These basic drives are combinable, and the combinations result in the diversity of human behavior and thinking. The key elements are drive memories. They collect memories of drive-related situations and feelings. They contain variations of basic drives in numerous areas of life and build combinations with different meanings depending on the area. Human thinking could be explained with variations on these nested combinations of basic drives.

Keywords: Cognitive modeling, psycholinguistics, psychology, psychophysiology of cognition.

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Authors: Agnieszka Danek, Rafał Pokrzywa

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Approximate tandem repeats in a genomic sequence are two or more contiguous, similar copies of a pattern of nucleotides. They are used in DNA mapping, studying molecular evolution mechanisms, forensic analysis and research in diagnosis of inherited diseases. All their functions are still investigated and not well defined, but increasing biological databases together with tools for identification of these repeats may lead to discovery of their specific role or correlation with particular features. This paper presents a new approach for finding approximate tandem repeats in a given sequence, where the similarity between consecutive repeats is measured using the Hamming distance. It is an enhancement of a method for finding exact tandem repeats in DNA sequences based on the Burrows- Wheeler transform.

Keywords: approximate tandem repeats, Burrows-Wheeler transform, Hamming distance, suffix array

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Authors: Faruq A. Al-Omari, Nabeel I. Al-Fayoumi

Abstract:

In this paper, we present a new algorithm for clustering data in large datasets using image processing approaches. First the dataset is mapped into a binary image plane. The synthesized image is then processed utilizing efficient image processing techniques to cluster the data in the dataset. Henceforth, the algorithm avoids exhaustive search to identify clusters. The algorithm considers only a small set of the data that contains critical boundary information sufficient to identify contained clusters. Compared to available data clustering techniques, the proposed algorithm produces similar quality results and outperforms them in execution time and storage requirements.

Keywords: Data clustering, Data mining, Image-mapping, Pattern discovery, Predictive analysis.

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Authors: Paula Verdugo-Hernández, Patricio Cumsille

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We analyze a first-class on the convergence of real number sequences, named hereafter sequences, to foster exploration and discovery of concepts through graphical representations before engaging students in proving. The main goal was to differentiate between sequences and continuous functions-of-a-real-variable and better understand concepts at an initial stage. We applied the analytic frame of Mathematical Working Spaces, which we expect to contribute to extending to sequences since, as far as we know, it has only developed for other objects, and which is relevant to analyze how mathematical work is built systematically by connecting the epistemological and cognitive perspectives, and involving the semiotic, instrumental, and discursive dimensions.

Keywords: Convergence, graphical representations, Mathematical Working Spaces, paradigms of real analysis, real number sequences.

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Authors: Sandeep Chandana, Rene V. Mayorga, Christine W. Chan

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This article outlines conceptualization and implementation of an intelligent system capable of extracting knowledge from databases. Use of hybridized features of both the Rough and Fuzzy Set theory render the developed system flexibility in dealing with discreet as well as continuous datasets. A raw data set provided to the system, is initially transformed in a computer legible format followed by pruning of the data set. The refined data set is then processed through various Rough Set operators which enable discovery of parameter relationships and interdependencies. The discovered knowledge is automatically transformed into a rule base expressed in Fuzzy terms. Two exemplary cancer repository datasets (for Breast and Lung Cancer) have been used to test and implement the proposed framework.

Keywords: Knowledge Extraction, Fuzzy Sets, Rough Sets, Neuro–Fuzzy Systems, Databases

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Authors: Simon B. N. Thompson

Abstract:

Cortisol is essential to the regulation of the immune system and yawning is a pathological symptom of multiple sclerosis (MS). Electromyography activity (EMG) in the jaw muscles typically rises when the muscles are moved and with yawning is highly correlated with cortisol levels in healthy people. Saliva samples from 59 participants were collected at the start and after yawning, or at the end of the presentation of yawning-provoking stimuli, in the absence of a yawn, together with EMG data and questionnaire data: Hospital Anxiety and Depression Scale, Yawning Susceptibility Scale, General Health Questionnaire, demographic, health details. Exclusion criteria: chronic fatigue, diabetes, fibromyalgia, heart condition, high blood pressure, hormone replacement therapy, multiple sclerosis, stroke. Significant differences were found between the saliva cortisol samples for the yawners, t (23) = -4.263, p = 0.000, as compared with the non-yawners between rest and post-stimuli, which was nonsignificant. Significant evidence was found to support the Thompson Cortisol Hypothesis suggesting that rises in cortisol levels are associated with yawning. Further research is exploring the use of cortisol as an early diagnostic tool for MS. Ethics approval granted and professional code of conduct, confidentiality, and safety issues are approved therein.

Keywords: Cortisol, Multiple Sclerosis, Yawning, Thompson’s Cortisol Hypothesis.

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Authors: Amer A. Hasan, Mehri Igci, Ersin Borazan, Rozhgar A. Khailany, Emine Bayraktar, Ahmet Arslan

Abstract:

Gastric Cancer (GC) has high morbidity and fatality rate in various countries. It is still one of the most frequent and deadly diseases. Gastrokine1 (GKN1) and gastrokine2 (GKN2) genes are highly expressed in the normal stomach epithelium and play important roles in maintaining the integrity and homeostasis of stomach mucosal epithelial cells. In this study, 47 paired samples that were grouped according to the types of gastric cancer and the clinical characteristics of the patients, including gender and average of age. They were investigated with gene expression analysis and mutation screening by monitoring RT-PCR, SSCP and nucleotide sequencing techniques. Both GKN1 and GKN2 genes were observed significantly reduced found by (Wilcoxon signed rank test; p<0.05). As a result of gene screening, no mutation (no different genotype) was detected. It is considered that gene mutations are not the cause of gastrokines inactivation. In conclusion, the mRNA expression level of GKN1 and GKN2 genes statistically was decreased regardless the gender, age, or cancer type of patients. Reduced of gastrokine genes seem to occur at the initial steps of gastric cancer development.

Keywords: Diagnostic biomarker, gastric cancer, nucleotide sequencing, semi-quantitative RT-PCR.

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Authors: Pardeep Singh, Sanjay Sharma

Abstract:

With increasing data in medical databases, medical data retrieval is growing in popularity. Some of this analysis including inducing propositional rules from databases using many soft techniques, and then using these rules in an expert system. Diagnostic rules and information on features are extracted from clinical databases on diseases of congenital anomaly. This paper explain the latest soft computing techniques and some of the adaptive techniques encompasses an extensive group of methods that have been applied in the medical domain and that are used for the discovery of data dependencies, importance of features, patterns in sample data, and feature space dimensionality reduction. These approaches pave the way for new and interesting avenues of research in medical imaging and represent an important challenge for researchers.

Keywords: CBIR, GA, Rough sets, CBMIR, SVM.

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Authors: Moon-Tak Oh, Kyung-Min Park, Tae-Eun Yoon, Hoon Choi, Chil-Woo Lee

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This paper is about middleware which enables group-user applications on mobile devices in physical proximity to interact with other devices without intervention of a central server. Requirements of the middleware are identified from service usage scenarios, and the functional architecture of the middleware is specified. These requirements include Group Management, Synchronization, and Resource Management. Group Management needs to provide various capabilities to such applications with respect to managing multiple users (e.g., creation of groups, discovery of group or individual users, member join/leave, election of a group manager and service-group association) using D2D communication technology. We designed the middleware for the above requirements on the Android platform.

Keywords: Group user, middleware, mobile service, physical proximity.

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Authors: S. V. Yendiyarov

Abstract:

Pattern discovery from time series is of fundamental importance. Particularly, when information about the structure of a pattern is not complete, an algorithm to discover specific patterns or shapes automatically from the time series data is necessary. The dynamic time warping is a technique that allows local flexibility in aligning time series. Because of this, it is widely used in many fields such as science, medicine, industry, finance and others. However, a major problem of the dynamic time warping is that it is not able to work with structural changes of a pattern. This problem arises when the structure is influenced by noise, which is a common thing in practice for almost every application. This paper addresses this problem by means of developing a novel technique called adaptive dynamic time warping.

Keywords: Pattern recognition, optimal control, quadratic programming, dynamic programming, dynamic time warping, sintering control.

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Authors: Eiad Yafi, M. A. Alam, Ranjit Biswas

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Knowledge Discovery of Databases (KDD) is the process of extracting previously unknown but useful and significant information from large massive volume of databases. Data Mining is a stage in the entire process of KDD which applies an algorithm to extract interesting patterns. Usually, such algorithms generate huge volume of patterns. These patterns have to be evaluated by using interestingness measures to reflect the user requirements. Interestingness is defined in different ways, (i) Objective measures (ii) Subjective measures. Objective measures such as support and confidence extract meaningful patterns based on the structure of the patterns, while subjective measures such as unexpectedness and novelty reflect the user perspective. In this report, we try to brief the more widely spread and successful subjective measures and propose a new subjective measure of interestingness, i.e. shocking.

Keywords: Shocking rules (SHR).

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