Search results for: Categorical data sequences

Authors: Huaizhong Li, C.Peng Lam

Abstract:

State-based testing is frequently used in software testing. Test data generation is one of the key issues in software testing. A properly generated test suite may not only locate the errors in a software system, but also help in reducing the high cost associated with software testing. It is often desired that test data in the form of test sequences within a test suite can be automatically generated to achieve required test coverage. This paper proposes an Ant Colony Optimization approach to test data generation for the state-based software testing.

Keywords: Software testing, ant colony optimization, UML.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3398

Authors: G.K.Panda, S.S.Rout

Abstract:

The balancing numbers are natural numbers n satisfying the Diophantine equation 1 + 2 + 3 + · · · + (n - 1) = (n + 1) + (n + 2) + · · · + (n + r); r is the balancer corresponding to the balancing number n.The nth balancing number is denoted by Bn and the sequence {Bn}1 n=1 satisfies the recurrence relation Bn+1 = 6Bn-Bn-1. The balancing numbers posses some curious properties, some like Fibonacci numbers and some others are more interesting. This paper is a study of recurrent sequence {xn}1 n=1 satisfying the recurrence relation xn+1 = Axn - Bxn-1 and possessing some curious properties like the balancing numbers.

Keywords: Recurrent sequences, Balancing numbers, Lucas balancing numbers, Binet form.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1453

Authors: Mohamed Gouskir, Belaid Bouikhalene, Hicham Aissaoui, Benachir Elhadadi

Abstract:

In this paper, we present an application of Riemannian geometry for processing non-Euclidean image data. We consider the image as residing in a Riemannian manifold, for developing a new method to brain edge detection and brain extraction. Automating this process is a challenge due to the high diversity in appearance brain tissue, among different patients and sequences. The main contribution, in this paper, is the use of an edge-based anisotropic diffusion tensor for the segmentation task by integrating both image edge geometry and Riemannian manifold (geodesic, metric tensor) to regularize the convergence contour and extract complex anatomical structures. We check the accuracy of the segmentation results on simulated brain MRI scans of single T1-weighted, T2-weighted and Proton Density sequences. We validate our approach using two different databases: BrainWeb database, and MRI Multiple sclerosis Database (MRI MS DB). We have compared, qualitatively and quantitatively, our approach with the well-known brain extraction algorithms. We show that using a Riemannian manifolds to medical image analysis improves the efficient results to brain extraction, in real time, outperforming the results of the standard techniques.

Keywords: Riemannian manifolds, Riemannian Tensor, Brain Segmentation, Non-Euclidean data, Brain Extraction.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1622

Authors: Mahmoud Elmezain, Ayoub Al-Hamadi, Robert Niese, Bernd Michaelis

Abstract:

Real-time hand tracking is a challenging task in many computer vision applications such as gesture recognition. This paper proposes a robust method for hand tracking in a complex environment using Mean-shift analysis and Kalman filter in conjunction with 3D depth map. The depth information solve the overlapping problem between hands and face, which is obtained by passive stereo measuring based on cross correlation and the known calibration data of the cameras. Mean-shift analysis uses the gradient of Bhattacharyya coefficient as a similarity function to derive the candidate of the hand that is most similar to a given hand target model. And then, Kalman filter is used to estimate the position of the hand target. The results of hand tracking, tested on various video sequences, are robust to changes in shape as well as partial occlusion.

Keywords: Computer Vision and Image Analysis, Object Tracking, Gesture Recognition.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2862

Authors: Nerguè Kassahan Kone, Souleymane Oumtanaga

Abstract:

The third generation (3G) of cellular system adopted the spread spectrum as solution for the transmission of the data in the physical layer. Contrary to systems IS-95 or CDMAOne (systems with spread spectrum of the preceding generation), the new standard, called Universal Mobil Telecommunications System (UMTS), uses long codes in the down link. The system is conceived for the vocal communication and the transmission of the data. In particular, the down link is very important, because of the asymmetrical request of the data, i.e., more remote loading towards the mobiles than towards the basic station. Moreover, the UMTS uses for the down link an orthogonal spreading out with a variable factor of spreading out (OVSF for Orthogonal Variable Spreading Factor). This characteristic makes it possible to increase the flow of data of one or more users by reducing their factor of spreading out without changing the factor of spreading out of other users. In the current standard of the UMTS, two techniques to increase the performances of the down link were proposed, the diversity of sending antenna and the codes space-time. These two techniques fight only fainding. The receiver proposed for the mobil station is the RAKE, but one can imagine a receiver more sophisticated, able to reduce the interference between users and the impact of the coloured noise and interferences to narrow band. In this context, where the users have long codes synchronized with variable factor of spreading out and ignorance by the mobile of the other active codes/users, the use of the sequences of code pseudo-noises different lengths is presented in the form of one of the most appropriate solutions.

Keywords: DS-CDMA, multiple access interference, ratio Signal / interference + Noise.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1311

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

Abstract:

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.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2049

Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

Abstract:

Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence, and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, Brassinosteroids, Phylogenetic analysis, Transcription factor.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2209

Authors: S. Sarumathi, N. Shanthi, M. Sharmila

Abstract:

Over the past epoch a rampant amount of work has been done in the data clustering research under the unsupervised learning technique in Data mining. Furthermore several algorithms and methods have been proposed focusing on clustering different data types, representation of cluster models, and accuracy rates of the clusters. However no single clustering algorithm proves to be the most efficient in providing best results. Accordingly in order to find the solution to this issue a new technique, called Cluster ensemble method was bloomed. This cluster ensemble is a good alternative approach for facing the cluster analysis problem. The main hope of the cluster ensemble is to merge different clustering solutions in such a way to achieve accuracy and to improve the quality of individual data clustering. Due to the substantial and unremitting development of new methods in the sphere of data mining and also the incessant interest in inventing new algorithms, makes obligatory to scrutinize a critical analysis of the existing techniques and the future novelty. This paper exposes the comparative study of different cluster ensemble methods along with their features, systematic working process and the average accuracy and error rates of each ensemble methods. Consequently this speculative and comprehensive analysis will be very useful for the community of clustering practitioners and also helps in deciding the most suitable one to rectify the problem in hand.

Keywords: Clustering, Cluster Ensemble methods, Co-association matrix, Consensus function, Median partition.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2554

Authors: J. Trarbach, S. Schosser, B. Vogt

Abstract:

Decision-makers tend to prefer the first alternative over subsequent alternatives which is called the primacy effect. To reliably measure this effect, we conducted an experiment with real consequences for preference statements. Therefore, we elicit preferences of subjects using a rating scale, i.e. hypothetical preferences, and willingness to pay, i.e. real preferences, for two sequences of pain. Within these sequences, both overall intensity and duration of pain are identical. Hence, a rational decision-maker should be indifferent, whereas the primacy effect predicts a stronger preference for the first sequence. What we see is a primacy effect only for hypothetical preferences. This effect vanishes for real preferences.

Keywords: Decision making, primacy effect, real incentives, willingness to pay.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 827

Authors: Mohammad Shoyaib, M. Abdullah-Al-Wadud, Oksam Chae

Abstract:

Proteomics is one of the largest areas of research for bioinformatics and medical science. An ambitious goal of proteomics is to elucidate the structure, interactions and functions of all proteins within cells and organisms. Predicting Protein-Protein Interaction (PPI) is one of the crucial and decisive problems in current research. Genomic data offer a great opportunity and at the same time a lot of challenges for the identification of these interactions. Many methods have already been proposed in this regard. In case of in-silico identification, most of the methods require both positive and negative examples of protein interaction and the perfection of these examples are very much crucial for the final prediction accuracy. Positive examples are relatively easy to obtain from well known databases. But the generation of negative examples is not a trivial task. Current PPI identification methods generate negative examples based on some assumptions, which are likely to affect their prediction accuracy. Hence, if more reliable negative examples are used, the PPI prediction methods may achieve even more accuracy. Focusing on this issue, a graph based negative example generation method is proposed, which is simple and more accurate than the existing approaches. An interaction graph of the protein sequences is created. The basic assumption is that the longer the shortest path between two protein-sequences in the interaction graph, the less is the possibility of their interaction. A well established PPI detection algorithm is employed with our negative examples and in most cases it increases the accuracy more than 10% in comparison with the negative pair selection method in that paper.

Keywords: Interaction graph, Negative training data, Protein-Protein interaction, Support vector machine.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1658

Authors: Nora A. Naguib, Ahmed E. Hussein, Hesham A. Keshk, Mohamed I. El-Adawy

Abstract:

Classification of video sequences based on their contents is a vital process for adaptation techniques. It helps decide which adaptation technique best fits the resource reduction requested by the client. In this paper we used the principal feature analysis algorithm to select a reduced subset of video features. The main idea is to select only one feature from each class based on the similarities between the features within that class. Our results showed that using this feature reduction technique the source video features can be completely omitted from future classification of video sequences.

Keywords: Adaptation, feature selection, H.264, Principal Feature Analysis (PFA)

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1561

Authors: A. Roukouni, S. Basbas, M. Giannopoulou

Abstract:

Transport and land use are two systems that are mutually influenced. Their interaction is a complex process associated with continuous feedback. The paper examines the existing land use around an under construction metro station of the new metro network of Thessaloniki, Greece, through the use of field investigations, around the station-s predefined location. Moreover, except from the analytical land use recording, a sampling questionnaire survey is addressed to several selected enterprises of the study area. The survey aims to specify the characteristics of the enterprises, the trip patterns of their employees and clients, as well as the stated preferences towards the changes the new metro station is considered to bring to the area. The interpretation of the interrelationships among selected data from the questionnaire survey takes place using the method of Principal Components Analysis for Categorical Data. The followed methodology and the survey-s results contribute to the enrichment of the relevant bibliography concerning the way the creation of a new metro station can have an impact on the land use pattern of an area, by examining the situation before the operation of the station.

Keywords: land use, metro station, questionnaire survey

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3044

Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3087

Authors: Jung Ho Yang, Yong Soo Kim

Abstract:

Electrical units are operated by electrical and electronic components. An environmental test sequence is useful for testing electrical units to reduce reliability issues. This study introduces test sequence guidelines based on relevant principles and considerations for electronic testing according to International Standard IEC-60068-1 and the United States Military Standard MIL-STD-810G. Test sequences were then proposed based on the descriptions for each test. Finally, General Motors (GM) specification GMW3172 was interpreted and compared to IEC-60068-1 and MIL-STD-810G.

Keywords: Reliability, Environmental test sequence, Electrical units, IEC 60068-1, MIL-STD-810G.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 4264

Authors: G. Nur

Abstract:

Monitored 3-Dimensional (3D) video experience can be utilized as “feedback information” to fine tune the service parameters for providing a better service to the demanding 3D service customers. The 3D video experience which includes both video quality and depth perception is influenced by several contextual and content related factors (e.g., ambient illumination condition, content characteristics, etc) due to the complex nature of the 3D video. Therefore, effective factors on this experience should be utilized while assessing it. In this paper, structural information of the depth map sequences of the 3D video is considered as content related factor effective on the depth perception assessment. Cartoon-like filter is utilized to abstract the significant depth levels in the depth map sequences to determine the structural information. Moreover, subjective experiments are conducted using 3D videos associated with cartoon-like depth map sequences to investigate the effectiveness of ambient illumination condition, which is a contextual factor, on depth perception. Using the knowledge gained through this study, 3D video experience metrics can be developed to deliver better service to the 3D video service users. 

Keywords: 3D Video, Ambient Illumination, Cartoon Effect, Depth Perception.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1684

Authors: Robersy Sánchez, Ricardo Grau

Abstract:

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represent one or more hypothetical bases with unspecific pairing. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvements of a primitive DNA repair system could make possible the transition from the ancient to the modern genetic code. Our results suggest that the Watson-Crick base pairing and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as the transition from the former to the later. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences.

Keywords: Genetic code vector space, primeval genetic code, power spectrum.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2330

Authors: Minsoo Lee, Yun-mi Kim, Yearn Jeong Kim, Yoon-kyung Lee, Hyejung Yoon

Abstract:

Biological data has several characteristics that strongly differentiate it from typical business data. It is much more complex, usually large in size, and continuously changes. Until recently business data has been the main target for discovering trends, patterns or future expectations. However, with the recent rise in biotechnology, the powerful technology that was used for analyzing business data is now being applied to biological data. With the advanced technology at hand, the main trend in biological research is rapidly changing from structural DNA analysis to understanding cellular functions of the DNA sequences. DNA chips are now being used to perform experiments and DNA analysis processes are being used by researchers. Clustering is one of the important processes used for grouping together similar entities. There are many clustering algorithms such as hierarchical clustering, self-organizing maps, K-means clustering and so on. In this paper, we propose a clustering algorithm that imitates the ecosystem taking into account the features of biological data. We implemented the system using an Ant-Colony clustering algorithm. The system decides the number of clusters automatically. The system processes the input biological data, runs the Ant-Colony algorithm, draws the Topic Map, assigns clusters to the genes and displays the output. We tested the algorithm with a test data of 100 to1000 genes and 24 samples and show promising results for applying this algorithm to clustering DNA chip data.

Keywords: Ant colony system, biological data, clustering, DNA chip.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1930

Authors: Kazuki Murakami, Takashige Nakamura, Noriko Sakamoto, Kunio Aizawa

Abstract:

A Watson-Crick automaton is recently introduced as a computational model of DNA computing framework. It works on tapes consisting of double stranded sequences of symbols. Symbols placed on the corresponding cells of the double-stranded sequences are related by a complimentary relation. In this paper, we investigate a variation of Watson-Crick automata in which both heads read the tape in reverse directions. They are called reverse Watson-Crick finite automata (RWKFA). We show that all of following four classes, i.e., simple, 1-limited, all-final, all-final and simple, are equal to non-restricted version of RWKFA.

Keywords: automaton, DNA computing, formal languages, Watson-Crick automaton

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1466

Authors: Shigeaki Sakurai, Ken Ueno, Ryohei Orihara

Abstract:

This paper proposes a method that discovers time series event patterns from textual data with time information. The patterns are composed of sequences of events and each event is extracted from the textual data, where an event is characteristic content included in the textual data such as a company name, an action, and an impression of a customer. The method introduces 7 types of time constraints based on the analysis of the textual data. The method also evaluates these constraints when the frequency of a time series event pattern is calculated. We can flexibly define the time constraints for interesting combinations of events and can discover valid time series event patterns which satisfy these conditions. The paper applies the method to daily business reports collected by a sales force automation system and verifies its effectiveness through numerical experiments.

Keywords: Text mining, sequential mining, time constraints, daily business reports.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1440

Authors: Layal Al Ait, Eduardo Corel, Kifah Tout, Burkhard Morgenstern

Abstract:

Background: Dialign is a DNA/Protein alignment tool for performing pairwise and multiple pairwise alignments through the comparison of gap-free segments (fragments) between sequence pairs. An alignment of two sequences is a chain of fragments, i.e local gap-free pairwise alignments, with the highest total score. METHOD: A new approach is defined in this article which relies on the concept of using three-dimensional fragments – i.e. local threeway alignments -- in the alignment process instead of twodimensional ones. These three-dimensional fragments are gap-free alignments constituting of equal-length segments belonging to three distinct sequences. RESULTS: The obtained results showed good improvments over the performance of DIALIGN.

Keywords: DIALIGN, Multiple sequence alignment, Threedimensional fragments.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1494

Authors: Reena Murali, David Peter S.

Abstract:

The small interfering RNA (siRNA) alters the regulatory role of mRNA during gene expression by translational inhibition. Recent studies show that upregulation of mRNA because serious diseases like cancer. So designing effective siRNA with good knockdown effects plays an important role in gene silencing. Various siRNA design tools had been developed earlier. In this work, we are trying to analyze the existing good scoring second generation siRNA predicting tools and to optimize the efficiency of siRNA prediction by designing a computational model using Artificial Neural Network and whole stacking energy (%G), which may help in gene silencing and drug design in cancer therapy. Our model is trained and tested against a large data set of siRNA sequences. Validation of our results is done by finding correlation coefficient of experimental versus observed inhibition efficacy of siRNA. We achieved a correlation coefficient of 0.727 in our previous computational model and we could improve the correlation coefficient up to 0.753 when the threshold of whole tacking energy is greater than or equal to -32.5 kcal/mol.

Keywords: Artificial Neural Network, Double Stranded RNA, RNA Interference, Short Interfering RNA.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2612

Authors: Sang Hyun Kim

Abstract:

In this paper, a fast motion compensation algorithm is proposed that improves coding efficiency for video sequences with brightness variations. We also propose a cross entropy measure between histograms of two frames to detect brightness variations. The framewise brightness variation parameters, a multiplier and an offset field for image intensity, are estimated and compensated. Simulation results show that the proposed method yields a higher peak signal to noise ratio (PSNR) compared with the conventional method, with a greatly reduced computational load, when the video scene contains illumination changes.

Keywords: Motion estimation, Fast motion compensation, Brightness variation compensation, Brightness change detection, Cross entropy.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1722

Authors: Jaime R. S. Fonseca

Abstract:

Nevertheless the widespread application of finite mixture models in segmentation, finite mixture model selection is still an important issue. In fact, the selection of an adequate number of segments is a key issue in deriving latent segments structures and it is desirable that the selection criteria used for this end are effective. In order to select among several information criteria, which may support the selection of the correct number of segments we conduct a simulation study. In particular, this study is intended to determine which information criteria are more appropriate for mixture model selection when considering data sets with only categorical segmentation base variables. The generation of mixtures of multinomial data supports the proposed analysis. As a result, we establish a relationship between the level of measurement of segmentation variables and some (eleven) information criteria-s performance. The criterion AIC3 shows better performance (it indicates the correct number of the simulated segments- structure more often) when referring to mixtures of multinomial segmentation base variables.

Keywords: Quantitative Methods, Multivariate Data Analysis, Clustering, Finite Mixture Models, Information Theoretical Criteria, Simulation experiments.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1476

Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

Abstract:

A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: Bacteria chromosome, bacterial identification, sequence, primer generation.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 994

Authors: Alisha Khanal, Gokhan Saygili

Abstract:

It is commonly observed that aftershocks follow the mainshock. Aftershocks continue over a period of time with a decreasing frequency and typically there is not sufficient time for repair and retrofit between a mainshock–aftershock sequence. Usually, aftershocks are smaller in magnitude; however, aftershock ground motion characteristics such as the intensity and duration can be greater than the mainshock due to the changes in the earthquake mechanism and location with respect to the site. The seismic performance of slopes is typically evaluated based on the sliding displacement predicted to occur along a critical sliding surface. Various empirical models are available that predict sliding displacement as a function of seismic loading parameters, ground motion parameters, and site parameters but these models do not include the aftershocks. The seismic risks associated with the post-mainshock slopes ('damaged slopes') subjected to aftershocks is significant. This paper extends the empirical sliding displacement models for flexible slopes subjected to earthquake mainshock-aftershock sequences (a multi hazard approach). A dataset was developed using 144 pairs of as-recorded mainshock-aftershock sequences using the Pacific Earthquake Engineering Research Center (PEER) database. The results reveal that the combination of mainshock and aftershock increases the seismic demand on slopes relative to the mainshock alone; thus, seismic risks are underestimated if aftershocks are neglected.

Keywords: Seismic slope stability, sliding displacement, mainshock, aftershock, landslide, earthquake.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 837

Authors: Sean Paulsen, Michael Casey

Abstract:

In this work, we present a self-supervised pretraining framework for transformers on functional Magnetic Resonance Imaging (fMRI) data. First, we pretrain our architecture on two self-supervised tasks simultaneously to teach the model a general understanding of the temporal and spatial dynamics of human auditory cortex during music listening. Our pretraining results are the first to suggest a synergistic effect of multitask training on fMRI data. Second, we finetune the pretrained models and train additional fresh models on a supervised fMRI classification task. We observe significantly improved accuracy on held-out runs with the finetuned models, which demonstrates the ability of our pretraining tasks to facilitate transfer learning. This work contributes to the growing body of literature on transformer architectures for pretraining and transfer learning with fMRI data, and serves as a proof of concept for our pretraining tasks and multitask pretraining on fMRI data.

Keywords: Transfer learning, fMRI, self-supervised, brain decoding, transformer, multitask training.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 56

Authors: Victor Breux, Jérôme Boutet, Alain Goret, Viviane Cattin

Abstract:

Early detection of anomalies in data centers is important to reduce downtimes and the costs of periodic maintenance. However, there is little research on this topic and even fewer on the fusion of sensor data for the detection of abnormal events. The goal of this paper is to propose a method for anomaly detection in data centers by combining sensor data (temperature, humidity, power) and deep learning models. The model described in the paper uses one autoencoder per sensor to reconstruct the inputs. The auto-encoders contain Long-Short Term Memory (LSTM) layers and are trained using the normal samples of the relevant sensors selected by correlation analysis. The difference signal between the input and its reconstruction is then used to classify the samples using feature extraction and a random forest classifier. The data measured by the sensors of a data center between January 2019 and May 2020 are used to train the model, while the data between June 2020 and May 2021 are used to assess it. Performances of the model are assessed a posteriori through F1-score by comparing detected anomalies with the data center’s history. The proposed model outperforms the state-of-the-art reconstruction method, which uses only one autoencoder taking multivariate sequences and detects an anomaly with a threshold on the reconstruction error, with an F1-score of 83.60% compared to 24.16%.

Keywords: Anomaly detection, autoencoder, data centers, deep learning.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 667

Authors: Bezuidt O., Lima-Mendez G., Reva O. N.

Abstract:

SeqWord Gene Island Sniffer, a new program for the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial genomes and further analyzed by sequence similarity and the functionality of encoded proteins. The results of this study are stored in an open database http://anjie.bi.up.ac.za/geidb/geidbhome. php). The developed computer program and the database provide the information valuable for further investigation of the distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.

Keywords: mobile genetic elements, virulence, bacterial genomes

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1696

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

Abstract:

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

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

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2301

Authors: Yan Ren, Jun Qiao, Xianxia Liu, Pengyan Wang, Qiang Fu, Huijun Shi, Fei Guo, Yuanzhi Wang, Hui Zhang, Jinliang Sheng, Xinli Gu, Xiao-Jun Liu, Chuangfu Chen

Abstract:

As part of national epidemiological survey on bovine viral diarrhea virus (BVDV), a total of 274 dejecta samples were collected from 14 cattle farms in 8 areas of Xinjiang Uygur Autonomous Region in northwestern China. Total RNA was extracted from each sample, and 5--untranslated region (UTR) of BVDV genome was amplified by using two-step reverse transcriptase-polymerase chain reaction (RT-PCR). The PCR products were subsequently sequenced to study the genetic variations of BVDV in these areas. Among the 274 samples, 33 samples were found virus-positive. According to sequence analysis of the PCR products, the 33 samples could be arranged into 16 groups. All the sequences, however, were highly conserved with BVDV Osloss strains. The virus possessed theses sequences belonged to BVDV-1b subtype by phylogenetic analysis. Based on these data, we established a typing tree for BVDV in these areas. Our results suggested that BVDV-1b was a predominant subgenotype in northwestern China and no correlation between the genetic and geographical distances could be observed above the farm level.

Keywords: bovine viral diarrhea virus, molecular epidemiology, phylogenetic analysis.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2439