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Master's Dissertation
DOI
https://doi.org/10.11606/D.3.2012.tde-11062013-102421
Document
Author
Full name
Ricardo Henrique Gracini Guiraldelli
E-mail
Institute/School/College
Knowledge Area
Date of Defense
Published
São Paulo, 2012
Supervisor
Committee
Rocha, Ricardo Luis de Azevedo da (President)
Miyaki, Cristina Yumi
Saraiva, Antonio Mauro
Title in Portuguese
Algoritmo de unificação de grafos e simulação para redes haplotípicas.
Keywords in Portuguese
Bioinformática
Computação adaptativa
Filogenética
Genética de populações
Simulação de sistemas
Teoria dos grafos
Abstract in Portuguese
Esta pesquisa lidou com a unificação de grafos aplicada ao problema das redes haplotípicas. A partir da baixa confiabilidade encontrada nas redes geradas pelos algoritmos tradicionais, foi necessário introduzir uma nova proposição para melhorar o resultado obtido. Para esta avaliar o resultado obtido pelo novo algoritmo, desenvolveu-se um arcabouço teórico-formal possibilitando a generalização de soluções relativas a redes haplotípicas através de aplicação de funções parametrizáveis, facilmente representadas através de linguagens funcionais no estilo LISP. Para aplicação em problemas reais, desenvolveu-se estrutura de simulação e testes que constrói cadeias genéticas de maneira aleatória ou ainda parametrizável. Os testes gerados permitiram observar a melhoria esperada no algoritmo, especialmente para os casos de baixa mutação. O arcabouço de simulação e testes mostrou-se extremamente propício e de fácil utilização, o que o torna, em si mesmo, uma ferramenta a ser disponibilizada para a comunidade acadêmica da área de Biologia.
Title in English
Algorithmic graph unification and simulations for haplotype networks.
Keywords in English
Adaptative computation
Bioinformatics
Graph theory
Phylogenetics
Population genetics
Systems simulation
Abstract in English
This research dealt with the unification of graphs applied to the problem of haplotype networks. From the low reliability found in networks generated by the traditional algorithms, it was necessary to introduce a new proposition to improve the outcome. For proper evaluation of the results obtained by the new algorithm, a formal-theoretical framework for generalization of haplotype networks related solutions, making use of parameterized functions easily represented through LISP-like functional languages. Seeking for real case application of the theory developed, a structure of simulation and testing were developed to build genetic code strings randomly or even parameterized. The generated tests have allowed to observe the expected improvement in the algorithm, especially for cases of low mutation. The framework for simulation and testing was extremely useful and easy to use, making itself a product to be distributed to the academic Biology community.
 
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Publishing Date
2013-06-14
 
WARNING: The material described below relates to works resulting from this thesis or dissertation. The contents of these works are the author's responsibility.
  • GUIRALDELLI, R. H. G., e ROCHA, R. L. A. Adaptive Unification Of Graphs Applied To Haplotype Networks. Revista IEEE América Latina, 2011, vol. 9, p. 950-955.
  • SILVA FILHO, R. I., ROCHA, R. L. A., and GUIRALDELLI, R. H. G. Learning in the Limit: a mutational and adaptive approach. In Solomonoff 85th Memorial Conference, Melbourne, 2013. Algorithmic Probability and Friends. Bayesian Prediction and Artificial Intelligence - LNCS/LNAI.Heidelberg : Springer-Verlag, 2013. Available from: http://link.springer.com/chapter/10.1007/978-3-642-44958-1_8.
  • GUIRALDELLI, R. H. G., e ROCHA, R. L. A. Um Algoritmo Adaptativivo de Unificação de Redes Haplotípicas. In Quinto Workshop de Tecnologia Adaptativa - WTA 2011, São Paulo, 2011. Memórias do WTA 2011 - Quinto Workshop de Tecnologia Adaptativa.São Paulo : Escola Politécnica da USP, 2011.
  • GUIRALDELLI, R. H. G., and ROCHA, R. L. A. Adaptive NIBP Low-pulse detection. In BIODEVICES 2010, Valência, 2010. Proceedings of the Third International Conference on Biomedical Electronics and Devices.Lisboa : Institute for Systems and Technologies of Information, Control and Communication, 2010. Available from: http://www.scitepress.org/DigitalLibrary/Default.aspx.
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