Pub Date : 2018-11-28DOI: 10.21533/SCJOURNAL.V7I2.159
A. Selimi, M. Saračević
Computational geometry is an integral part of mathematics and computer science deals with the algorithmic solution of geometry problems. From the beginning to today, computer geometry links different areas of science and techniques, such as the theory of algorithms, combinatorial and Euclidean geometry, but including data structures and optimization. Today, computational geometry has a great deal of application in computer graphics, geometric modeling, computer vision, and geodesic path, motion planning and parallel computing. The complex calculations and theories in the field of geometry are long time studied and developed, but from the aspect of application in modern information technologies they still are in the beginning. In this research is given the applications of computational geometry in polygon triangulation, manufacturing of objects with molds, point location, and robot motion planning.
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Pub Date : 2018-11-28DOI: 10.21533/SCJOURNAL.V7I2.165
A. Abidi
Experimental methods used for characterizing epitopes that play a vital role in the development of peptide vaccines, in diagnosis of diseases, and also for allergy research are time consuming and need huge resources. There are many online epitope prediction tools are available that can help scientists in short listing the candidate peptides. To predict B-cell epitopes in an antigenic sequence, Jordan recurrent neural network (BIRUNI) is found to besuccessful. To train and test neural networks, 262.583 B epitopes are retrieved from IEDB database. 99.9% of these epitopes have lengths in the interval 6-25 amino acids. For each of these lengths, committees of 11 expert recurrent neural networks are trained. To train these experts alongside epitopes, non-epitopes are needed. Non-epitopes are created as random sequences of amino acids of the same length followed by a filtering process. To distinguish epitopes and non-epitopes, the votes of eleven experts are aggregated by majority vote. An overall accuracy of 97.23% is achieved. Then these experts are used to predict the Linear Bepitopes of five antigens, Plasmodium Falciparum, Human Polio Virus Sabin Strain, Meningitis, Plasmodium Vivax and Mycobacterium Tuberculosis. The success of BIRUNU is compared with the five online prediction tools ABCPRED, BCPRED, K&T, BEPIPRED, and AAP.It is seen that BIRUNI outperforms all of them in the average.
{"title":"A Recurrent Neural Network Linear B-Epitope Predictor: BIRUNI","authors":"A. Abidi","doi":"10.21533/SCJOURNAL.V7I2.165","DOIUrl":"https://doi.org/10.21533/SCJOURNAL.V7I2.165","url":null,"abstract":"Experimental methods used for characterizing epitopes that play a vital role in the development of peptide vaccines, in diagnosis of diseases, and also for allergy research are time consuming and need huge resources. There are many online epitope prediction tools are available that can help scientists in short listing the candidate peptides. To predict B-cell epitopes in an antigenic sequence, Jordan recurrent neural network (BIRUNI) is found to besuccessful. To train and test neural networks, 262.583 B epitopes are retrieved from IEDB database. 99.9% of these epitopes have lengths in the interval 6-25 amino acids. For each of these lengths, committees of 11 expert recurrent neural networks are trained. To train these experts alongside epitopes, non-epitopes are needed. Non-epitopes are created as random sequences of amino acids of the same length followed by a filtering process. To distinguish epitopes and non-epitopes, the votes of eleven experts are aggregated by majority vote. An overall accuracy of 97.23% is achieved. Then these experts are used to predict the Linear Bepitopes of five antigens, Plasmodium Falciparum, Human Polio Virus Sabin Strain, Meningitis, Plasmodium Vivax and Mycobacterium Tuberculosis. The success of BIRUNU is compared with the five online prediction tools ABCPRED, BCPRED, K&T, BEPIPRED, and AAP.It is seen that BIRUNI outperforms all of them in the average.","PeriodicalId":243185,"journal":{"name":"Southeast Europe Journal of Soft Computing","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126882441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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