Search results for: sequence alignment problem

Authors: Ernesto Linan, Linda Cruz, Lucero Becerra

Abstract:

In this paper, a new hybridized algorithm based on Chemical Reaction Optimization and Simulated Annealing is proposed to solve the alignment sequence Problem. The Chemical Reaction Optimization is a population-based meta-heuristic algorithm based on the principles of a chemical reaction. Simulated Annealing is applied to solve a large number of combinatorial optimization problems of general-purpose. In this paper, we propose hybridization between Chemical Reaction Optimization algorithm and Simulated Annealing in order to solve the Sequence Alignment Problem. An initial population of molecules is defined at beginning of the proposed algorithm, where each molecule represents a sequence alignment problem. In order to simulate inter-molecule collisions, the process of Chemical Reaction is placed inside the Metropolis Cycle at certain values of temperature. Inside this cycle, change of molecules is done due to collisions; some molecules are accepted by applying Boltzmann probability. The results with the hybrid scheme are better than the results obtained separately.

Keywords: chemical reaction optimization, sequence alignment problem, simulated annealing algorithm, metaheuristics

Procedia PDF Downloads 211

Authors: Muhammad A. Khan, Waseem Shahzad

Abstract:

Analysis of protein sequences is carried out for the purpose to discover their structural and ancestry relationship. Sequence similarity determines similar protein structures, similar function, and homology detection. Biological sequences composed of amino acid residues or nucleotides provide significant information through sequence alignment. In this paper, we present a new similarity/dissimilarity measure to sequence alignment based on the primary structure of a protein. The approach finds the distance between the two given sequences using the novel sequence alignment algorithm and a mathematical model. The algorithm runs at a time complexity of O(n²). A distance matrix is generated to construct a phylogenetic tree of different species. The new similarity/dissimilarity measure outperforms other existing methods.

Keywords: alignment, distance, homology, mathematical model, phylogenetic tree

Procedia PDF Downloads 178

Authors: Lamiche Chaabane

Abstract:

In this study, a new method for solving sequence alignment problem is proposed, which is named ITS (Improved Tabu Search). This algorithm is based on the classical Tabu Search (TS). ITS is implemented in order to obtain results of multiple sequence alignment. Several ideas concerning neighbourhood generation, move selection mechanisms and intensification/diversification strategies for our proposed ITS is investigated. ITS have generated high-quality results in terms of measure of scores in comparison with the classical TS and simple iterative search algorithm.

Keywords: multiple sequence alignment, tabu search, improved tabu search, neighbourhood generation, selection mechanisms

Procedia PDF Downloads 305

Authors: Atef Ibrahim, Hamed Elsimary, Abdullah Aljumah, Fayez Gebali

Abstract:

This paper presents a novel semi-systolic array architecture for an optimized parallel sequence alignment algorithm. This architecture has the advantage that it can be modified to be reused for multiple pass processing in order to increase the number of processing elements that can be packed into a single FPGA and to increase the number of sequences that can be aligned in parallel in a single FPGA. This resolves the potential problem of many FPGA resources left unused for designs that have large values of short read length. When using the previously published conventional hardware design. FPGA implementation results show that, for large values of short read lengths (M>128), the proposed design has a slightly higher speed up and FPGA utilization over the the conventional one.

Keywords: bioinformatics, genome sequence alignment, re-sequencing applications, systolic array

Procedia PDF Downloads 532

Authors: Alireza Dantism

Abstract:

Presently, describing the function of a protein sequence is one of the most common problems in biology. Usually, this problem can be facilitated by studying the three-dimensional structure of proteins. In the absence of a protein structure, comparative modeling often provides a useful three-dimensional model of the protein that is dependent on at least one known protein structure. Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) mainly based on its alignment with one or more proteins of known structure (templates). Comparative modeling consists of four main steps 1. Similarity between the target sequence and at least one known template structure 2. Alignment of target sequence and template(s) 3. Build a model based on alignment with the selected template(s). 4. Prediction of model errors 5. Optimization of the built model There are many computer programs and web servers that automate the comparative modeling process. One of the most important advantages of these servers is that it makes comparative modeling available to both experts and non-experts, and they can easily do their own modeling without the need for programming knowledge, but some other experts prefer using programming knowledge and do their modeling manually because by doing this they can maximize the accuracy of their modeling. In this study, a web-based tool has been designed to predict the tertiary structure of proteins using PHP and Python programming languages. This tool is called EasyModel. EasyModel can receive, according to the user's inputs, the desired unknown sequence (which we know as the target) in this study, the protein sequence file (template), etc., which also has a percentage of similarity with the primary sequence, and its third structure Predict the unknown sequence and present the results in the form of graphs and constructed protein files.

Keywords: structural bioinformatics, protein tertiary structure prediction, modeling, comparative modeling, modeller

Procedia PDF Downloads 98

Authors: Jingyuan Hu, Zhandong Liu

Abstract:

CRISPR genome editing technology has transformed molecular biology by accurately targeting and altering an organism’s DNA. Despite the state-of-art precision of CRISPR genome editing, the imprecise mutation outcome and off-target effects present considerable risk, potentially leading to unintended genetic changes. Targeted deep sequencing, combined with bioinformatics sequence alignment, can detect such unwanted mutations. Nevertheless, the classical method, Needleman-Wunsch (NW) algorithm may produce false alignment outcomes, resulting in inaccurate mutation identification. The key to precisely identifying CRISPR-induced mutations lies in determining optimal parameters for the sequence alignment algorithm. Hidden Markov models (HMM) are ideally suited for this task, offering flexibility across CRISPR systems by leveraging forward-backward algorithms for parameter estimation. In this study, we introduce CRISPR-HMM, a statistical software to precisely call CRISPR-induced mutations. We demonstrate that the software significantly improves precision in identifying CRISPR-induced mutations compared to NW-based alignment, thereby enhancing the overall understanding of the CRISPR gene-editing process.

Keywords: CRISPR, HMM, sequence alignment, gene editing

Procedia PDF Downloads 54

Authors: Ghada Badr, Arwa Alturki

Abstract:

The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: alignment, RNA secondary structure, pairwise, component-based, data mining

Procedia PDF Downloads 459

Authors: Bilal Wajid, Erchin Serpedin

Abstract:

The health industry is aiming towards personalized medicine. If the patient’s genome needs to be sequenced it is important that the entire analysis be completed quickly. This paper explores use of parallel computing to analyze very large sequences. Two cases have been considered. In the first case, the sequence is kept constant and the effect of increasing the number of MPI-based processes is evaluated in terms of execution time, speed and efficiency. In the second case the number of MPI-based processes have been kept constant whereas, the length of the sequence was increased.

Keywords: parallel computing, alignment, genome assembly, alignment

Procedia PDF Downloads 276

Authors: Rema Daher, Theodor Chakhachiro, Daniel Asmar

Abstract:

In the era of autonomous robot mapping, assessing the goodness of the generated maps is important, and is usually performed by aligning them to ground truth. Map alignment is difficult for two reasons: first, the query maps can be significantly distorted from ground truth, and second, establishing what constitutes ground truth for different settings is challenging. Most map alignment techniques to this date have addressed the first problem, while paying too little importance to the second. In this paper, we propose a benchmark dataset, which consists of synthetically transformed maps with their corresponding displacement fields. Furthermore, we propose a new system for comparison, where the displacement field of any map alignment technique can be computed and compared to the ground truth using statistical measures. The local information in displacement fields renders the evaluation system applicable to any alignment technique, whether it is linear or not. In our experiments, the proposed method was applied to different alignment methods from the literature, allowing for a comparative assessment between them all.

Keywords: assessment methods, benchmark, image deformation, map alignment, robot mapping, robot motion

Procedia PDF Downloads 121

Authors: Abdesselem Dakhli, Wajdi Bellil, Chokri Ben Amar

Abstract:

DNA Barcode, a short mitochondrial DNA fragment, made up of three subunits; a phosphate group, sugar and nucleic bases (A, T, C, and G). They provide good sources of information needed to classify living species. Such intuition has been confirmed by many experimental results. Species classification with DNA Barcode sequences has been studied by several researchers. The classification problem assigns unknown species to known ones by analyzing their Barcode. This task has to be supported with reliable methods and algorithms. To analyze species regions or entire genomes, it becomes necessary to use similarity sequence methods. A large set of sequences can be simultaneously compared using Multiple Sequence Alignment which is known to be NP-complete. To make this type of analysis feasible, heuristics, like progressive alignment, have been developed. Another tool for similarity search against a database of sequences is BLAST, which outputs shorter regions of high similarity between a query sequence and matched sequences in the database. However, all these methods are still computationally very expensive and require significant computational infrastructure. Our goal is to build predictive models that are highly accurate and interpretable. This method permits to avoid the complex problem of form and structure in different classes of organisms. On empirical data and their classification performances are compared with other methods. Our system consists of three phases. The first is called transformation, which is composed of three steps; Electron-Ion Interaction Pseudopotential (EIIP) for the codification of DNA Barcodes, Fourier Transform and Power Spectrum Signal Processing. The second is called approximation, which is empowered by the use of Multi Llibrary Wavelet Neural Networks (MLWNN).The third is called the classification of DNA Barcodes, which is realized by applying the algorithm of hierarchical classification.

Keywords: DNA barcode, electron-ion interaction pseudopotential, Multi Library Wavelet Neural Networks (MLWNN)

Procedia PDF Downloads 319

Authors: Joseph Akyeh, Abdul Samed Muntaka, Emmanuel Anin, Dorcas Nuertey

Abstract:

Purpose: This study develops and tests arguments that the relationship between technology alignment and supply chain performance is conditional upon levels of technology championing. Methodology: The proposed relationships are tested on a sample of 217 hospitals in a major sub-Saharan African economy. Findings: Findings from the study indicate that technology alignment has a positive and significant effect on supply chain performance. The study further finds that while technology championing strengthens the direct effects of technology alignment on supply chain performance. Theoretical Contributions: A theoretical contribution from this study is the finding that when technology alignment drives supply chain performance is more complex than previously thought it depends on whether or not technology alignment is first championed by top management. Originality: Though some studies have been conducted on technology alignment and health supply chain performance, to the best of the researcher’s knowledge, no previous study has examined the moderating role of technology championing the link between technology alignment and supply chain performance.

Keywords: technology alignment, supply chain performance, technology championing, structural equation modelling

Procedia PDF Downloads 53

Authors: Jian Shi, Baoguo Yu, Haonan Jia, Meng Liu, Ping Huang

Abstract:

Adapting to the flexibility of war, a large number of guided weapons launch from aircraft. Therefore, the inertial navigation system loaded in the weapon needs to undergo an alignment process in the air. This article proposes the following methods to the problem of inaccurate modeling of the system under large misalignment angles, the accuracy reduction of filtering caused by outliers, and the noise changes in GPS signals: first, considering the large misalignment errors of Strapdown Inertial Navigation System (SINS)/GPS, a more accurate model is made rather than to make a small-angle approximation, and the Unscented Kalman Filter (UKF) algorithms are used to estimate the state; then, taking into account the impact of GPS noise changes on the fine alignment algorithm, the innovation adaptive filtering algorithm is introduced to estimate the GPS’s noise in real-time; at the same time, in order to improve the anti-interference ability of the air fine alignment algorithm, a robust filtering algorithm based on outlier detection is combined with the air fine alignment algorithm to improve the robustness of the algorithm. The algorithm can improve the alignment accuracy and robustness under interference conditions, which is verified by simulation.

Keywords: air alignment, fine alignment, inertial navigation system, integrated navigation system, UKF

Procedia PDF Downloads 171

Authors: S. H. Borghei, E. Teymourian, M. Mobin, G. M. Komaki, S. Sheikh

Abstract:

Imperialist competitive algorithm (ICA) is a recent meta-heuristic method that is inspired by the social evolutions for solving NP-Hard problems. The ICA is a population based algorithm which has achieved a great performance in comparison to other meta-heuristics. This study is about developing enhanced ICA approach to solve the cell formation problem (CFP) using sequence data. In addition to the conventional ICA, an enhanced version of ICA, namely EICA, applies local search techniques to add more intensification aptitude and embed the features of exploration and intensification more successfully. Suitable performance measures are used to compare the proposed algorithms with some other powerful solution approaches in the literature. In the same way, for checking the proficiency of algorithms, forty test problems are presented. Five benchmark problems have sequence data, and other ones are based on 0-1 matrices modified to sequence based problems. Computational results elucidate the efficiency of the EICA in solving CFP problems.

Keywords: cell formation problem, group technology, imperialist competitive algorithm, sequence data

Procedia PDF Downloads 455

Authors: Lely A. Luengas, Pedro R. Vizcaya, Giovanni Sánchez

Abstract:

In this paper, a methodology is presented to obtain the Static Alignment Model for any transtibial amputee person. The proposed methodology starts from experimental data collected on the Hospital Militar Central, Bogotá, Colombia. The effects of transtibial prosthesis malalignment on amputees were measured in terms of joint angles, center of pressure (COP) and weight distribution. Some statistical tools are used to obtain the model parameters. Mathematical predictive models of prosthetic alignment were created. The proposed models are validated in amputees and finding promising results for the prosthesis Static Alignment. Static alignment process is unique to each subject; nevertheless the proposed methodology can be used in each transtibial amputee.

Keywords: information theory, prediction model, prosthetic alignment, transtibial prosthesis

Procedia PDF Downloads 257

Authors: Bouras Zine Eddine, Talai Abdelouaheb

Abstract:

The need to merge software artifacts seems inherent to modern software development. Distribution of development over several teams and breaking tasks into smaller, more manageable pieces are an effective means to deal with the kind of complexity. In each case, the separately developed artifacts need to be assembled as efficiently as possible into a consistent whole in which the parts still function as described. Also, earlier changes are introduced into the life cycle and easier is their management by designers. Interaction-based specifications such as UML sequence diagrams have been found effective in this regard. As a result, sequence diagrams can be used not only for capturing system behaviors but also for merging changes in order to create a new version. The objective of this paper is to suggest a new approach to deal with the problem of software merging at the level of sequence diagrams by using the concept of dependence analysis that captures, formally, all mapping and differences between elements of sequence diagrams and serves as a key concept to create a new version of sequence diagram.

Keywords: system behaviors, sequence diagram merging, dependence analysis, sequence diagram slicing

Procedia PDF Downloads 342

Authors: C. T. Cheung, R. K. P. Ng, T. Y. Lo, Zhou Jinyun

Abstract:

This paper aims at manipulating loop alignment in knitting a three-dimensional (3D) shape by its geometry. Two loop alignment methods are introduced to handle a surface with positive Gaussian curvature. As weft knitting is a two-dimensional (2D) knitting mechanism that the knitting cam carrying the feeders moves in two directions only, left and right, the knitted fabric generated grows in width and length but not in depth. Therefore, a 3D shape is required to be flattened to a 2D plane with surface area preserved for knitting. On this flattened plane, dimensional measurements are taken for loop alignment. The way these measurements being taken derived two different loop alignment methods. In this paper, only plain knitted structure was considered. Each knitted loop was taken as a basic unit for loop alignment in order to achieve the required geometric dimensions, without the inclusion of other stitches which give textural dimensions to the fabric. Two loop alignment methods were experimented and compared. Only one of these two can successfully preserve the dimensions of the shape.

Keywords: 3D knitting, 3D shape, loop alignment, positive Gaussian curvature

Procedia PDF Downloads 345

Authors: Sanjay Kumar Parjapati, Ajai Jain

Abstract:

This paper presents optimization of makespan for ‘n’ jobs and ‘m’ machines flexible job shop scheduling problem with sequence dependent setup time using genetic algorithm (GA) approach. A restart scheme has also been applied to prevent the premature convergence. Two case studies are taken into consideration. Results are obtained by considering crossover probability (pc = 0.85) and mutation probability (pm = 0.15). Five simulation runs for each case study are taken and minimum value among them is taken as optimal makespan. Results indicate that optimal makespan can be achieved with more than one sequence of jobs in a production order.

Keywords: flexible job shop, genetic algorithm, makespan, sequence dependent setup times

Procedia PDF Downloads 333

Authors: Amit Saraswat, Ruchi Tewari

Abstract:

Purpose: The research paper aims at understanding the alignment of business and IT in the Indian context and the business value attached to such an alignment. Methodology: The study is conducted in two stages. Stage one: Bibliographic research was conducted to evolve the parameters for defining alignment. Stage two: Evolving a model for strategic alignment to conduct an empirical study. The model is defined in terms of four fundamental domains of strategic management choice – business strategy, information strategy, organizational structure, and information technology structure. A survey through a questionnaire was conducted across organizations from 4 different industries and Structure Equation Modelling (SEM) technique is used for validating the model. Findings: In the Indian scenario all the subscales of alignment could not be validated. It could be validated that organizational strategy impacts information strategy and information technology structure. Research Limitations: The study is limited to the Indian context. Business IT alignment may be culture dependent so further research is required to validate the model in other cultures. Originality/Value: In the western world several models of alignment of business strategy and information systems is available but they do not measure the extent of alignment which the current study in the Indian context. Findings of the study can be used by managers in strategizing and understanding their business and information systems needs holistically and cohesively leading to efficient use of resources and output.

Keywords: business strategy, information technology (IT), business IT alignment, SEM

Procedia PDF Downloads 388

Authors: Zheng Baichuan, Li Shenghui, Li Bingqian, Zhang Ning, Chen Kai

Abstract:

Entity alignment (EA) tasks in knowledge graphs often play a pivotal role in the integration of knowledge graphs, where structural differences often exist between the source and target graphs, such as the presence or absence of attribute information and the types of attribute information (text, timestamps, images, etc.). However, most current research efforts are focused on improving alignment accuracy, often along with an increased reliance on specific structures -a dependency that inevitably diminishes their practical value and causes difficulties when facing knowledge graph alignment tasks with varying structures. Therefore, we propose a universal knowledge graph alignment approach that only utilizes the common basic structures shared by knowledge graphs. We have demonstrated through experiments that our method achieves state-of-the-art performance in fair comparisons.

Keywords: knowledge graph, entity alignment, transformer, deep learning

Procedia PDF Downloads 47

Authors: Eftah Bte Moh, Hj Abdullah Izazol Binti Idris, Abd. Aziz Bin Abd. Shukor

Abstract:

This study aimed to identify the alignment of understanding and assessment practices among secondary school teachers. The study was carried out using quantitative descriptive study. The sample consisted of 164 teachers who taught Form 1 and 2 from 11 secondary schools in the district of North Kinta, Perak, Malaysia. Data were obtained from 164 respondents who answered Expectation Alignment Understanding and Practices of School Assessment (PEKDAPS) questionnaire. The data were analysed using SPSS 17.0 +. The Cronbach alpha value obtained through PEKDAPS questionnaire pilot study was 0.86. The results showed that teachers' performance in PEKDAPS based on the mean value was less than 3, which means that perfect alignment does not occur between the understanding and practices of school assessment. Two major PEKDAPS sub-constructs of articulation across grade and age and usability of the system were higher than the moderate alignment of the understanding and practices of school assessment (Min=2.0). The content was focused on PEKDAPs sub-constructs which showed lower than the moderate alignment of the understanding and practices of school assessment (Min=2.0). Another two PEKDAPS sub-constructs of transparency and fairness and the pedagogical implications showed moderate alignment (2.0). The implications of the study is that teachers need to fully understand the importance of alignment among components of assessment, learning and teaching and learning objectives as strategies to achieve quality assessment process.

Keywords: school based assessment, alignment, understanding, assessment practices

Procedia PDF Downloads 461

Authors: Seyyd Hossein Jafari-Petroudi, Maryam Pirouz

Abstract:

This note is devoted to (k; h)-Jacobsthal sequence as a general term of particular series. More formulas for nth term and sum of the first n terms of series that their general terms are (k; h)-Jacobsthal sequence and (k; h)-Jacobsthal-Petroudi sequence are derived. Finally other properties of these sequences are represented.

Keywords: (k, h)-Jacobsthal sequence, (k, h)-Jacobsthal Petroudisequence, recursive relation, sum

Procedia PDF Downloads 394

Authors: Duc Dong Do, Ngoc Ha Tran, Thanh Hai Dang, Cao Cuong Dang, Xuan Huan Hoang

Abstract:

Global aligning two protein-protein interaction networks is an essentially important task in bioinformatics/computational biology field of study. It is a challenging and widely studied research topic in recent years. Accurately aligned networks allow us to identify functional modules of proteins and/ororthologous proteins from which unknown functions of a protein can be inferred. We here introduce a novel efficient heuristic global network alignment algorithm called FASTAn, including two phases: the first to construct an initial alignment and the second to improve such alignment by exerting a local optimization repeated procedure. The experimental results demonstrated that FASTAn outperformed the state-of-the-art global network alignment algorithm namely SPINAL in terms of both commonly used objective scores and the run-time.

Keywords: FASTAn, Heuristic algorithm, biological network alignment, protein-protein interaction networks

Procedia PDF Downloads 605

Authors: Xu LiYun, Briand Florent, Fan GuoLiang

Abstract:

The loop-layout design problem (LLDP) aims at optimizing the sequence of positioning of the machines around the cyclic production line. Traffic congestion is the usual criteria to minimize in this type of problem, i.e. the number of additional cycles spent by each part in the network until the completion of its required routing sequence of machines. This paper aims at applying several improvements mechanisms such as a positioned-based crossover operator for the Genetic Algorithm (GA) called a Two Points Crossover (TPC) and an offspring selection process. The performance of the improved GA is measured using well-known examples from literature and compared to other evolutionary algorithms. Good results show that GA can still be competitive for this type of problem against more recent evolutionary algorithms.

Keywords: crossover, genetic algorithm, layout design problem, loop-layout, manufacturing optimization

Procedia PDF Downloads 281

Authors: Gaylord K. Booto, Marinelli Giuseppe, Helge Brattebø, Rolf A. Bohne

Abstract:

Emissions reduction has emerged among the principal targets in the process of planning and designing road alignments today. Intelligent road design methods that can result in optimized alignment constitute concrete and innovative responses towards better alternatives and more sustainable road infrastructures. As the largest amount of emissions of road infrastructures occur in the operation stage, it becomes very important to consider traffic weight and distribution in alignment design process. This study analyzes the effects of four traffic factors (i.e. operating speed, vehicle category, technology and fuel type) on adjusting the vertical alignment of a given road, using optimization techniques. Further, factors’ effects are assessed qualitatively and quantitatively, and the emission profiles of resulting alignment alternatives are compared.

Keywords: alignment adjustment, emissions reduction, optimization, traffic-oriented

Procedia PDF Downloads 370

Authors: Angela U. Makolo

Abstract:

Protein-coding and Non-coding regions determine the biology of a sequenced transcriptome. Research advances have shown that Non-coding regions are important in disease progression and clinical diagnosis. Existing bioinformatics tools have been targeted towards Protein-coding regions alone. Therefore, there are challenges associated with gaining biological insights from transcriptome sequence data. These tools are also limited to computationally intensive sequence alignment, which is inadequate and less accurate to identify both Protein-coding and Non-coding regions. Alignment-free techniques can overcome the limitation of identifying both regions. Therefore, this study was designed to develop an efficient sequence alignment-free model for identifying both Protein-coding and Non-coding regions in sequenced transcriptomes. Feature grouping and randomization procedures were applied to the input transcriptomes (37,503 data points). Successive iterations were carried out to compute the gradient vector that converged the developed Protein-coding and Non-coding Region Identifier (PNRI) model to the approximate coefficient vector. The logistic regression algorithm was used with a sigmoid activation function. A parameter vector was estimated for every sample in 37,503 data points in a bid to reduce the generalization error and cost. Maximum Likelihood Estimation (MLE) was used for parameter estimation by taking the log-likelihood of six features and combining them into a summation function. Dynamic thresholding was used to classify the Protein-coding and Non-coding regions, and the Receiver Operating Characteristic (ROC) curve was determined. The generalization performance of PNRI was determined in terms of F1 score, accuracy, sensitivity, and specificity. The average generalization performance of PNRI was determined using a benchmark of multi-species organisms. The generalization error for identifying Protein-coding and Non-coding regions decreased from 0.514 to 0.508 and to 0.378, respectively, after three iterations. The cost (difference between the predicted and the actual outcome) also decreased from 1.446 to 0.842 and to 0.718, respectively, for the first, second and third iterations. The iterations terminated at the 390th epoch, having an error of 0.036 and a cost of 0.316. The computed elements of the parameter vector that maximized the objective function were 0.043, 0.519, 0.715, 0.878, 1.157, and 2.575. The PNRI gave an ROC of 0.97, indicating an improved predictive ability. The PNRI identified both Protein-coding and Non-coding regions with an F1 score of 0.970, accuracy (0.969), sensitivity (0.966), and specificity of 0.973. Using 13 non-human multi-species model organisms, the average generalization performance of the traditional method was 74.4%, while that of the developed model was 85.2%, thereby making the developed model better in the identification of Protein-coding and Non-coding regions in transcriptomes. The developed Protein-coding and Non-coding region identifier model efficiently identified the Protein-coding and Non-coding transcriptomic regions. It could be used in genome annotation and in the analysis of transcriptomes.

Keywords: sequence alignment-free model, dynamic thresholding classification, input randomization, genome annotation

Procedia PDF Downloads 68

Authors: Didem Can

Abstract:

Scheduling problems are one of the most fundamental issues of production systems. Many different approaches and models have been developed according to the production processes of the parts and the main purpose of the problem. In this study, one of the bottleneck stations of a company serving in the aerospace industry is analyzed and considered as a single machine scheduling problem with sequence-dependent setup times. The objective of the problem is assigning a large number of similar parts to the same shift -to reduce chemical waste- while minimizing the number of tardy jobs. The goal programming method will be used to achieve two different objectives simultaneously. The assignment of parts to the shift will be expressed using the integer programming method. Finally, the constraint programming method will be used as it provides a way to find a result in a short time by avoiding worse resulting feasible solutions with the defined variables set. The model to be established will be tested and evaluated with real data in the application part.

Keywords: constraint programming, goal programming, integer programming, sequence-dependent setup, single machine scheduling

Procedia PDF Downloads 238

Authors: Wartika Memed Purawinata, Kridanto Surendro, Husni Sastramiharja, Iping Supriana S.

Abstract:

The information system is one of the contributors to environmental degradation and pollution are known to be released, such as the increasing of use of IT equipment and energy consumption , life cycles of IT equipment are getting shorter, IT equipment waste disposal and so on, therefore the information system should have a role in related environmental issues. Organization need to develop the ability of green to minimize negative impacts on the environment. Although the green information system is an important topic, many organizations fail to manage the environment in a way that is adequate because they ignore aspect of strategy. Alignment strategy is very important to ensure that all people do the activities of the organization headed in the same direction. Alignment strategy helps organization, determine which is more important for organization, and then make road mad to achieve the organization goal. Therefore, this paper discusses the review of the alignment, information systems strategy, and IS green strategy. With this discussion is expected there is an understanding about the alignment of information systems strategy and strategy of green IS, and its relationship with the achievement of business goals that have commitment to reduce the negative impact of information systems on the environment.

Keywords: alignment, strategy, information system, green

Procedia PDF Downloads 457

Authors: A. Bouabid, B. Bielenberg, S. Ainane, N. Pasha

Abstract:

In this paper, a team of faculty members of the Petroleum Institute in Abu Dhabi, UAE representing six different courses across General Engineering (ENGR), Communication (COMM), and Design (STPS) worked together to establish a clear developmental progression of learning outcomes and performance indicators for targeted knowledge, areas of competency, and skills for the first three semesters of the Bachelor of Sciences in Engineering curriculum. The sequences of courses studied in this project were ENGR/COMM, COMM/STPS, and ENGR/STPS. For each course’s nine areas of knowledge, competency, and skills, the research team reviewed the existing learning outcomes and related performance indicators with a focus on identifying linkages across disciplines as well as within the courses of a discipline. The team reviewed existing performance indicators for developmental progression from semester to semester for same discipline related courses (vertical alignment) and for different discipline courses within the same semester (horizontal alignment). The results of this work have led to recommendations for modifications of the initial indicators when incoherence was identified, and/or for new indicators based on best practices (identified through literature searches) when gaps were identified. It also led to recommendations for modifications of the level of emphasis within each course to ensure developmental progression. The exercise has led to a revised Sequence Performance Indicator Mapping for the knowledge, skills, and competencies across the six core courses.

Keywords: curriculum alignment, horizontal and vertical progression, performance indicators, skill level

Procedia PDF Downloads 223

Authors: Yuri Bizzoni, Marianne Reboul

Abstract:

Our program compares French and Italian translations of Homer’s Odyssey, from the XVIth to the XXth century. We focus on the third point, showing how distributional semantics systems can be used both to improve alignment between different French translations as well as between the Greek text and a French translation. Although we focus on French examples, the techniques we display are completely language independent.

Keywords: classical receptions, computational linguistics, distributional semantics, Homeric poems, machine translation, translation studies, text alignment

Procedia PDF Downloads 435

Authors: Khaled Jaber

Abstract:

The estimation of effort in software development is a complex task. The traditional Waterfall approach used to develop software systems requires a lot of time to estimate the effort needed to implement user requirements. Agile manifesto, however, is currently more used in the industry than the Waterfall to develop software systems. In Agile, the user requirement is referred to as a user story. Agile teams mostly use the Fibonacci sequence 1, 2, 3, 5, 8, 11, etc. in estimating the effort needed to implement the user story. This work shows through analysis that the Arithmetic sequence, e.g., 3, 6, 9, 12, etc., is more effective than the Fibonacci sequence in estimating the user stories. This paper mathematically and visually proves the effectiveness of the Arithmetic sequence over the FB sequence.

Keywords: agie, scrum, estimation, fibonacci sequence

Procedia PDF Downloads 207