Search results for: gene name recognition

Authors: Chyn Liaw, Chun-Wei Tung, Shinn-Jang Ho, Shinn-Ying Ho

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The γ-turns play important roles in protein folding and molecular recognition. The prediction and analysis of γ-turn types are important for both protein structure predictions and better understanding the characteristics of different γ-turn types. This study proposed a physicochemical property-based decision tree (PPDT) method to interpretably predict γ-turn types. In addition to the good prediction performance of PPDT, three simple and human interpretable IF-THEN rules are extracted from the decision tree constructed by PPDT. The identified informative physicochemical properties and concise rules provide a simple way for discriminating and understanding γ-turn types.

Keywords: Classification and regression tree (CART), γ-turn, Physicochemical properties, Protein secondary structure.

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Authors: Brigitte Rafael, Stefan M. Oertl

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Music segmentation is a key issue in music information retrieval (MIR) as it provides an insight into the internal structure of a composition. Structural information about a composition can improve several tasks related to MIR such as searching and browsing large music collections, visualizing musical structure, lyric alignment, and music summarization. The authors of this paper present the MTSSM framework, a twolayer framework for the multi-track segmentation of symbolic music. The strength of this framework lies in the combination of existing methods for local track segmentation and the application of global structure information spanning via multiple tracks. The first layer of the MTSSM uses various string matching techniques to detect the best candidate segmentations for each track of a multi-track composition independently. The second layer combines all single track results and determines the best segmentation for each track in respect to the global structure of the composition.

Keywords: Pattern Recognition, Music Information Retrieval, Machine Learning.

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Authors: Waqar Shahid Qureshi, Abu-Baqar Nisar Alvi

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Vision based tracking problem is solved through a combination of optical flow, MACH filter and log r-θ mapping. Optical flow is used for detecting regions of movement in video frames acquired under variable lighting conditions. The region of movement is segmented and then searched for the target. A template is used for target recognition on the segmented regions for detecting the region of interest. The template is trained offline on a sequence of target images that are created using the MACH filter and log r-θ mapping. The template is applied on areas of movement in successive frames and strong correlation is seen for in-class targets. Correlation peaks above a certain threshold indicate the presence of target and the target is tracked over successive frames.

Keywords: Correlation filters, optical flow, log r-θ mapping.

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Authors: Ahmet Denker, Tuğrul Adıgüzel

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In this paper, a solution is presented for a robotic manipulation problem in industrial settings. The problem is sensing objects on a conveyor belt, identifying the target, planning and tracking an interception trajectory between end effector and the target. Such a problem could be formulated as combining object recognition, tracking and interception. For this purpose, we integrated a vision system to the manipulation system and employed tracking algorithms. The control approach is implemented on a real industrial manipulation setting, which consists of a conveyor belt, objects moving on it, a robotic manipulator, and a visual sensor above the conveyor. The trjectory for robotic interception at a rendezvous point on the conveyor belt is analytically calculated. Test results show that tracking the raget along this trajectory results in interception and grabbing of the target object.

Keywords: robotics, robot vision, rendezvous planning, self organizingmaps.

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Authors: Sergio Pissanetzky

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The ability of the brain to organize information and generate the functional structures we use to act, think and communicate, is a common and easily observable natural phenomenon. In object-oriented analysis, these structures are represented by objects. Objects have been extensively studied and documented, but the process that creates them is not understood. In this work, a new class of discrete, deterministic, dissipative, host-guest dynamical systems is introduced. The new systems have extraordinary self-organizing properties. They can host information representing other physical systems and generate the same functional structures as the brain does. A simple mathematical model is proposed. The new systems are easy to simulate by computer, and measurements needed to confirm the assumptions are abundant and readily available. Experimental results presented here confirm the findings. Applications are many, but among the most immediate are object-oriented engineering, image and voice recognition, search engines, and Neuroscience.

Keywords: AI, artificial intelligence, complex system, object oriented, OO, refactoring.

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Authors: Hanina M. N., Hairul Shahril M., Ismatul Nurul Asyikin I., Abdul Jalil A. K., Salina M. R., Maryam M. R., Rosfarizan M.

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The extracellular proteins secreted by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was carried out to determine the effect of Streptomycin Sulfate in regulating extracellular proteins secreted by Bacillus subtilis ATCC21332. Results of Microdilution assay showed that the Minimum Inhibition Concentration (MIC) of Streptomycin Sulfate on B. subtilis ATCC21332 was 2.5 mg/ml. The bacteria cells were then exposed to Streptomycin Sulfate at concentration of 0.01 MIC before being further incubated for 48h to 72 h. The extracellular proteins secreted were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins profile revealed that three additional bands with approximate sizes of 30 kDa, 22 kDa and 23 kDa were appeared for the treated bacteria with Streptomycin Sulfate. Thus, B. subtilis ATCC21332 in stressful condition with the presence of Streptomycin Sulfate at low concentration could induce the extracellular proteins secretion.

Keywords: Bacillus subtilis ATCC21332, Streptomycin Sulfate, extracellular proteins.

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Authors: Dinh Ha, Tran, Chung - Ruey Yen

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This study explored the morphological characteristics and effects of pollination methods on fruit set and characteristics in 4 red pitaya (Hylocereus spp.) clones. The distinctive morphological recognition and classification among pitaya clones were confirmed by the stem, flower and fruit features. The fruit production season was indicated from the beginning of May to the end of August – the beginning of September with 6-7 flowering cycles per year. The floral stage took from 15-19 days and fruit duration spent 30–32 days. VN White, fully self-compatible, obtained high fruit set rates (80.0–90.5%) in all pollination treatments and the maximum fruit weight (402.6g) in hand self- and (403.4g) in open-pollination. Chaozhou 5 was partially self-compatible while Orejona and F₁₁ were completely self-incompatible. Hand cross-pollination increased significantly fruit set (95.8; 88.4 and 90.2%) and fruit weight (374.2; 281.8 and 416.3 g) in Chaozhou 5, Orejona, and F₁₁, respectively. TSS contents were not much influenced by pollination methods.

Keywords: Hylocereus spp., morphology, floral phenology, pollination requirement.

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Authors: Dinh - Ha Tran, Chung - Ruey Yen

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This study explored the morphological characteristics and effects of pollination methods on fruit set and characteristics in 4 red pitaya (Hylocereus spp.) clones. The distinctive morphological recognition and classification among pitaya clones were confirmed by the stem, flower and fruit features. The fruit production season was indicated from the beginning of May to the end of August – the beginning of September with 6-7 flowering cycles per year. The floral stage took from 15-19 days and fruit duration spent 30–32 days. VN White, fully self-compatible, obtained high fruit set rates (80.0–90.5%) in all pollination treatments and the maximum fruit weight (402.6g) in hand self- and (403.4g) in open-pollination. Chaozhou 5 was partially self-compatible while Orejona and F₁₁ were completely self-incompatible. Hand cross-pollination increased significantly fruit set (95.8; 88.4 and 90.2%) and fruit weight (374.2; 281.8 and 416.3g) in Chaozhou 5, Orejona and F₁₁, respectively. TSS contents were not much influcenced by pollination methods.

Keywords: Hylocereus spp., morphology, floral phenology, pollination requirement.

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Authors: Ying Zhao

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Keystroke authentication is a new access control system to identify legitimate users via their typing behavior. In this paper, machine learning techniques are adapted for keystroke authentication. Seven learning methods are used to build models to differentiate user keystroke patterns. The selected classification methods are Decision Tree, Naive Bayesian, Instance Based Learning, Decision Table, One Rule, Random Tree and K-star. Among these methods, three of them are studied in more details. The results show that machine learning is a feasible alternative for keystroke authentication. Compared to the conventional Nearest Neighbour method in the recent research, learning methods especially Decision Tree can be more accurate. In addition, the experiment results reveal that 3-Grams is more accurate than 2-Grams and 4-Grams for feature extraction. Also, combination of attributes tend to result higher accuracy.

Keywords: Keystroke Authentication, Pattern recognition, MachineLearning, Instance-based Learning, Bayesian, Decision Tree.

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Authors: Musammat F. Nahar, Anna Roujeinikova

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Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.

Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.

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Authors: Jafar Ahmadi, Alireza Pour-Aboughadareh

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Wheat is the first and the most important grain of the world and its bakery property is due to glutenin and gliadin qualities. Wheat seed proteins were divided into four groups according to solubility including albumin, globulin, glutenin and prolamin or gliadin. Gliadins are major components of the storage proteins in wheat endosperm. It seems that little information is available about gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this study was the evaluation of the wheat wild relatives collected from different origins of Zagros Mountains in Iran, in terms of coding gliadin genes using specific primers. For this, forty accessions of Triticum boeoticum and Triticum urartu were selected for this study. For each accession, genomic DNA was extracted and PCRs were performed in total volumes of 15 μl. The amplification products were separated on 1.5% agarose gels. In results, for Gli-2A locus three allelic variants were detected by Gli-2As primer pairs. The sizes of PCR products for these alleles were 210, 490 and 700 bp. Only five (13%) and two accessions (5%) produced 700 and 490 bp fragments when their DNA was amplified with the Gli.As.2 primer pairs. However, 93% of the accessions carried allele 210 bp, and only 8% did not any product for this marker. Therefore, these germplasm could be used as rich gene pool to broaden the genetic base of bread wheat.

Keywords: Diploied wheat, gliadin, Triticum boeoticum, Triticum urartu.

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Authors: D. Beziakina, E. Bulgakova

Abstract:

The paper deals with cross-gender and cross-linguistic comparison of pitch characteristics for Tuvinian with two other Turkic languages - Uzbek and Azerbaijani, based on the results of statistical analysis of pitch parameter values and intonation patterns used by male and female speakers.

The main goal of our work is to obtain the ranges of pitch parameter values typical for Tuvinian speakers for the purpose of automatic language identification. We also propose a cross-gender analysis of declarative intonation in the poorly studied Tuvinian language.

The ranges of pitch parameter values were obtained by means of specially developed software that deals with the distribution of pitch values and allows us to obtain statistical language-specific pitch intervals.

Keywords: Speech analysis, Statistical analysis, Speaker recognition, Identification of person.

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Authors: Ramin Javadzadeh., Zahra Afsahi, MohammadReza Meybodi

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The Artificial immune systems algorithms are Meta heuristic optimization method, which are used for clustering and pattern recognition applications are abundantly. These algorithms in multimodal optimization problems are more efficient than genetic algorithms. A major drawback in these algorithms is their slow convergence to global optimum and their weak stability can be considered in various running of these algorithms. In this paper, improved Artificial Immune System Algorithm is introduced for the first time to overcome its problems of artificial immune system. That use of the small size of a local search around the memory antibodies is used for improving the algorithm efficiently. The credibility of the proposed approach is evaluated by simulations, and it is shown that the proposed approach achieves better results can be achieved compared to the standard artificial immune system algorithms

Keywords: Artificial immune system, Cellular Automata, Cellular learning automata, Cellular learning automata, , Local search, Optimization.

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Authors: Silva, Fátima, Fernandes, Paula Odete

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The future of Higher Education Institutions (HEI) depend on their ability to attract and retain students, increase recognition and prestige. In order to respond to the 'customers' increasingly demanding, HEI need to identify the key factors that influence the satisfaction of a 'customers', thereby creating competitive advantages. These determinants of satisfaction are important elements that guide the strategy of an institution and allow the successful achievement of strategic plans, both teaching and administrative, to offer their ‘costumers’ services and products with higher quality. Following this way of thinking, the purpose of this study was to evaluate the satisfaction with the service quality of the School of Technology and Management of Bragança (ESTiG), of the Polytechnic Institute of Bragança, identifying, thus, the dimensions related to the quality of services that might influence students' satisfaction. The results showed that, in general, the students are satisfied with the performance of ESTiG.

Keywords: Customer Satisfaction, Higher Education Institutions, Importance-Satisfaction Model.

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Authors: Anastasia Rita Widiarti

Abstract:

This paper compares Hilditch, Rosenfeld, Zhang- Suen, dan Nagendraprasad Wang Gupta (NWG) thinning algorithms for Javanese character image recognition. Thinning is an effective process when the focus in not on the size of the pattern, but rather on the relative position of the strokes in the pattern. The research analyzes the thinning of 60 Javanese characters. Time-wise, Zhang-Suen algorithm gives the best results with the average process time being 0.00455188 seconds. But if we look at the percentage of pixels that meet one-pixel thickness, Rosenfelt algorithm gives the best results, with a 99.98% success rate. From the number of pixels that are erased, NWG algorithm gives the best results with the average number of pixels erased being 84.12%. It can be concluded that the Hilditch algorithm performs least successfully compared to the other three algorithms.

Keywords: Hilditch algorithm, Nagendraprasad-Wang-Guptaalgorithm, Rosenfeld algorithm, Thinning, Zhang-suen algorithm

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Authors: Fabio Fabris, Alex A. Freitas

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Hierarchical classification is a special type of classification task where the class labels are organised into a hierarchy, with more generic class labels being ancestors of more specific ones. Meta-learning for classification-algorithm recommendation consists of recommending to the user a classification algorithm, from a pool of candidate algorithms, for a dataset, based on the past performance of the candidate algorithms in other datasets. Meta-learning is normally used in conventional, non-hierarchical classification. By contrast, this paper proposes a meta-learning approach for more challenging task of hierarchical classification, and evaluates it in a large number of bioinformatics datasets. Hierarchical classification is especially relevant for bioinformatics problems, as protein and gene functions tend to be organised into a hierarchy of class labels. This work proposes meta-learning approach for recommending the best hierarchical classification algorithm to a hierarchical classification dataset. This work’s contributions are: 1) proposing an algorithm for splitting hierarchical datasets into new datasets to increase the number of meta-instances, 2) proposing meta-features for hierarchical classification, and 3) interpreting decision-tree meta-models for hierarchical classification algorithm recommendation.

Keywords: Algorithm recommendation, meta-learning, bioinformatics, hierarchical classification.

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Authors: Alexander L. Dmitriev, Sophia A. Bulgakova

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Temperature dependence of force of gravitation is one of the fundamental problems of physics. This problem has got special value in connection with that the general theory of relativity, supposing the weakest positive influence of a body temperature on its weight, actually rejects an opportunity of measurement of negative influence of temperature on gravity in laboratory conditions. Really, the recognition of negative temperature dependence of gravitation, for example, means basic impossibility of achievement of a singularity («a black hole») at a gravitational collapse. Laboratory experiments with exact weighing the heated up metal samples, indicating negative influence temperatures of bodies on their physical weight are described. Influence of mistakes of measurements is analyzed. Calculations of distribution of temperature in volume of the bar, agreed with experimental data of time dependence of weight of samples are executed. The physical substantiation of negative temperature dependence of weight of the bodies, based on correlation of acceleration at thermal movement of micro-particles of a body and its absolute temperature, are given.

Keywords: Gravitation, temperature, weight.

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Authors: Yanhui Zhang, Wenyu Yang

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One of the difficulties of the vibration-based damage identification methods is the nonuniqueness of the results of damage identification. The different damage locations and severity may cause the identical response signal, which is even more severe for detection of the multiple damage. This paper proposes a new strategy for damage detection to avoid this nonuniqueness. This strategy firstly determines the approximates damage area based on the statistical pattern recognition method using the dynamic strain signal measured by the distributed fiber Bragg grating, and then accurately evaluates the damage information based on the Bayesian model updating method using the experimental modal data. The stochastic simulation method is then used to compute the high-dimensional integral in the Bayesian problem. Finally, an experiment of the plate structure, simulating one part of mechanical structure, is used to verify the effectiveness of this approach.

Keywords: Bayesian method, damage detection, fiber Bragg grating, structural health monitoring.

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Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

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In April 2009, a new variant of Influenza A virus subtype H1N1 emerged in Mexico and spread all over the world. The influenza has three subtypes in human (H1N1, H1N2 and H3N2) Types B and C influenza tend to be associated with local or regional epidemics. Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. Nucleotide sequence analysis of the Haemagglutinin (HA) and Neuraminidase (NA) are similar to each other and the majority of their genes of swine influenza viruses, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza. Sequence similarity between the 2009 A (H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Nucleic acid sequence Maximum Likelihood (MCL) and DNA Empirical base frequencies, Phylogenetic relationship amongst the HA genes of H1N1 virus isolated in Genbank having high nucleotide sequence homology. In this paper we used 16 HA nucleotide sequences from NCBI for computing sequence relationships similarity of swine influenza A virus using the following method MCL the result is 28%, 36.64% for Optimal tree with the sum of branch length, 35.62% for Interior branch phylogeny Neighber – Join Tree, 1.85% for the overall transition/transversion, and 8.28% for Overall mean distance.

Keywords: Sequence DNA, Relationship of swine, Swineinfluenza, Sequence Similarity

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Authors: Leena N. Fukey, Surya S. Issac

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This review paper aims at understanding the importance of implementing sustainable green practices in the current hotel industry and the perception of the same from the point of view of the customers as well as the industry experts. Many hotels have benefited from green management such as enhanced reputation of the firm and more worth customers. For the business standing, it reduces business’s cost for posting advertisements and the clear hotel’s orientation shows hotels’ positive image which might increase employees’ recognition toward the business. Sustainability in business is the growth in lively processes which enable people to understand the potential to protect the Earth’s existent support systems. Well, looking to the future today’s green concerns will definitely become facet of more synchronized business environment, perhaps the concerns discussed in this study, may exchange a few words which hotels may consider in near future to widen awareness and improve business model.

Keywords: Environmental Protection, Green Hotel Concept, Hotel Industry, Sustainability.

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Authors: Jieh-Haur Chen, Pei-Fen Huang

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This paper presents an integrated model that automatically measures the change of rivers, damage area of bridge surroundings, and change of vegetation. The proposed model is on the basis of a neurofuzzy mechanism enhanced by SOM optimization algorithm, and also includes three functions to deal with river imagery. High resolution imagery from FORMOSAT-2 satellite taken before and after the invasion period is adopted. By randomly selecting a bridge out of 129 destroyed bridges, the recognition results show that the average width has increased 66%. The ruined segment of the bridge is located exactly at the most scour region. The vegetation coverage has also reduced to nearly 90% of the original. The results yielded from the proposed model demonstrate a pinpoint accuracy rate at 99.94%. This study brings up a successful tool not only for large-scale damage assessment but for precise measurement to disasters.

Keywords: remote sensing image, damage assessment, typhoon disaster, bridge, ANN, fuzzy, SOM, optimization.

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Authors: Oi Mean Foong, Tan Jung Low, Satrio Wibowo

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Hand gesture is one of the typical methods used in sign language for non-verbal communication. It is most commonly used by people who have hearing or speech problems to communicate among themselves or with normal people. Various sign language systems have been developed by manufacturers around the globe but they are neither flexible nor cost-effective for the end users. This paper presents a system prototype that is able to automatically recognize sign language to help normal people to communicate more effectively with the hearing or speech impaired people. The Sign to Voice system prototype, S2V, was developed using Feed Forward Neural Network for two-sequence signs detection. Different sets of universal hand gestures were captured from video camera and utilized to train the neural network for classification purpose. The experimental results have shown that neural network has achieved satisfactory result for sign-to-voice translation.

Keywords: Hand gesture detection, neural network, signlanguage, sequence detection.

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Authors: Jun Wan, Zehua Chen, Yingwu Chen, Zhidong Bai

Abstract:

Classification is an interesting problem in functional data analysis (FDA), because many science and application problems end up with classification problems, such as recognition, prediction, control, decision making, management, etc. As the high dimension and high correlation in functional data (FD), it is a key problem to extract features from FD whereas keeping its global characters, which relates to the classification efficiency and precision to heavens. In this paper, a novel automatic method which combined Genetic Algorithm (GA) and classification algorithm to extract classification features is proposed. In this method, the optimal features and classification model are approached via evolutional study step by step. It is proved by theory analysis and experiment test that this method has advantages in improving classification efficiency, precision and robustness whereas using less features and the dimension of extracted classification features can be controlled.

Keywords: Classification, functional data, feature extraction, genetic algorithm, wavelet.

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Authors: Besa Muslimi, Miriam A. M. Capretz, Jagath Samarabandu

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Artificial neural networks (ANN) have the ability to model input-output relationships from processing raw data. This characteristic makes them invaluable in industry domains where such knowledge is scarce at best. In the recent decades, in order to overcome the black-box characteristic of ANNs, researchers have attempted to extract the knowledge embedded within ANNs in the form of rules that can be used in inference systems. This paper presents a new technique that is able to extract a small set of rules from a two-layer ANN. The extracted rules yield high classification accuracy when implemented within a fuzzy inference system. The technique targets industry domains that possess less complex problems for which no expert knowledge exists and for which a simpler solution is preferred to a complex one. The proposed technique is more efficient, simple, and applicable than most of the previously proposed techniques.

Keywords: fuzzy rule extraction, fuzzy systems, knowledgeacquisition, pattern recognition, artificial neural networks.

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Authors: Carlos Machado, José A. Mendes

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Home Automation is a field that, among other subjects, is concerned with the comfort, security and energy requirements of private homes. The configuration of automatic functions in this type of houses is not always simple to its inhabitants requiring the initial setup and regular adjustments. In this work, the ubiquitous computing system vision is used, where the users- action patterns are captured, recorded and used to create the contextawareness that allows the self-configuration of the home automation system. The system will try to free the users from setup adjustments as the home tries to adapt to its inhabitants- real habits. In this paper it is described a completely automated process to determine the light state and act on them, taking in account the users- daily habits. Artificial Neural Network (ANN) is used as a pattern recognition method, classifying for each moment the light state. The work presented uses data from a real house where a family is actually living.

Keywords: ANN, Home Automation, Neural Systems, PatternRecognition, Ubiquitous Computing.

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Authors: Monika Jain, Shikhar Puri, Shivali Unishree

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This paper presents the ‘Eye Ball Motion Controlled Wheelchair using IR Sensors’ for the elderly and differently abled people. In this eye tracking based technology, three Proximity Infrared (IR) sensor modules are mounted on an eye frame to trace the movement of the iris. Since, IR sensors detect only white objects; a unique sequence of digital bits is generated corresponding to each eye movement. These signals are then processed via a micro controller IC (PIC18F452) to control the motors of the wheelchair. The potential and efficiency of previously developed rehabilitation systems that use head motion, chin control, sip-n-puff control, voice recognition, and EEG signals variedly have also been explored in detail. They were found to be inconvenient as they served either limited usability or non-affordability. After multiple regression analyses, the proposed design was developed as a cost-effective, flexible and stream-lined alternative for people who have trouble adopting conventional assistive technologies.

Keywords: Eye tracking technology, Intelligent wheelchair, IR module, rehabilitation technology.

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Authors: N. Tsvetkova, R. Harizanov A. Ivanova, I. Rainova, N. Yancheva-Petrova, D. Strashimirov, R. Enikova, M. Videnova, E. Kaneva, I. Kaftandjiev, V. Levterova, I. Simeonovski, N. Yanev, G. Hinkov

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The Pneumocystis jirovecii (P. jirovecii) and protozoan of the genera Acanthamoeba, Cryptosporidium, and Toxoplasma gondii are opportunistic pathogens that can cause life-threatening infections in immunocompromised patients. Aim of the study was to evaluate the coinfection rate with opportunistic protozoal agents among Bulgarian patients diagnosed with P. jirovecii pneumonia. 38 pulmonary samples were collected from 38 patients (28 HIV-infected) with P. jirovecii infection. P. jirovecii DNA was detected by real-time PCR targeting the large mitochondrial subunit ribosomal RNA gene. Acanthamoeba was determined by genus-specific conventional PCR assay. Real-time PCR for the detection of a Toxoplasma gondii and Cryptosporidium DNA fragment was used. Pneumocystis DNA was detected in all 38 specimens; 28 (73.7%) were from HIV-infected patients. Three (10,7%) of them were coinfected with T. gondii and 1 (3.6%) with Cryptosporidium. In the group of non-HIV-infected (n = 10), Cryptosporidium DNA was detected in an infant (10%). Acanthamoeba DNA was not found in the tested samples. The current study showed a relatively low rate of coinfections of Cryptosporidium spp./T. gondii and P. jirovecii in the Bulgarian patients studied.

Keywords: Coinfection, opportunistic protozoal agents, Pneumocystis jirovecii, pulmonary infections.

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Authors: Guyue Zhu, Liangping Hong

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Chinese overall urban design faces a large number of problems such as the neglect of urban characteristics, generalization of content, and difficulty in implementation. Focusing on these issues, this paper proposes the main points of shaping urban characteristics in overall urban design: focuses on core problems in city function and scale, landscape pattern, historical culture, social resources and modern city style and digs the urban characteristic genes. Then, we put forward “core problem location and characteristic gene enhancement” as a kind of overall urban design technical method. Firstly, based on the main problems in urban space as a whole, for the operability goal, the method extracts the key genes and integrates into the multi-dimension system in a targeted manner. Secondly, hierarchical management and guidance system is established which may be in line with administrative management. Finally, by converting the results, action plan is drawn up that can be dynamically implemented. Based on the above idea and method, a practical exploration has been performed in the case of Xiangyang central city.

Keywords: City characteristics, overall urban design, planning implementation, Xiangyang central city.

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Authors: Zelmina Lubovac, Björn Olsson, Jonas Gamalielsson

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This paper describes a novel approach for deriving modules from protein-protein interaction networks, which combines functional information with topological properties of the network. This approach is based on weighted clustering coefficient, which uses weights representing the functional similarities between the proteins. These weights are calculated according to the semantic similarity between the proteins, which is based on their Gene Ontology terms. We recently proposed an algorithm for identification of functional modules, called SWEMODE (Semantic WEights for MODule Elucidation), that identifies dense sub-graphs containing functionally similar proteins. The rational underlying this approach is that each module can be reduced to a set of triangles (protein triplets connected to each other). Here, we propose considering semantic similarity weights of all triangle-forming edges between proteins. We also apply varying semantic similarity thresholds between neighbours of each node that are not neighbours to each other (and hereby do not form a triangle), to derive new potential triangles to include in module-defining procedure. The results show an improvement of pure topological approach, in terms of number of predicted modules that match known complexes.

Keywords: Modules, systems biology, protein interactionnetworks, yeast.

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Authors: Julio Molleda, Daniel F. García, Juan C. Granda, Francisco J. Suárez

Abstract:

One of the main trouble in a steel strip manufacturing line is the breakage of whatever weld carried out between steel coils, that are used to produce the continuous strip to be processed. A weld breakage results in a several hours stop of the manufacturing line. In this process the damages caused by the breakage must be repaired. After the reparation and in order to go on with the production it will be necessary a restarting process of the line. For minimizing this problem, a human operator must inspect visually and manually each weld in order to avoid its breakage during the manufacturing process. The work presented in this paper is based on the Bayesian decision theory and it presents an approach to detect, on real-time, steel strip defective welds. This approach is based on quantifying the tradeoffs between various classification decisions using probability and the costs that accompany such decisions.

Keywords: Classification, Pattern Recognition, ProbabilisticReasoning, Statistical Data Analysis.

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