Using Grammatical Evolution Decision Trees for Detecting Gene-Gene Interactions in Genetic Epidemiology
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Date
2009-11-30
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Abstract
A major goal of human genetics is the discovery and validation of genetic polymorphisms that predict common, complex diseases. It is hypothesized that complex diseases are due to a myriad of factors including environmental exposures and complex genetic models. This etiological complexity, coupled with rapid advances in genotyping technology present enormous theoretical and practical concerns for statistical and computational analysis. Specifically, the challenge presented by epistasis, or gene-gene interactions, has sparked the development of a multitude of statistical techniques over the years. Subsequently, pattern matching and machine learning approaches have been explored to overcome the limitations of traditional computational methods. Grammatical Evolution Neural Networks (GENN) uses grammatical evolution to optimize neural network architectures and better detect and analyze gene-gene interactions. Motivated by good results shown by GENN to identify epistasis in complex datasets, we have developed a new method of Grammatical Evolution Decision Trees (GEDT). GEDT replaces the black-box approach of neural networks with the white-box approach of decision trees improving understandability and interpretability. We provide a detailed technical understanding of coupling Grammatical Evolution with Decision Tress using Backus Naur Form (BNF) grammar. Further, the GEDT system has been analyzed for power results on simulated datasets. Finally, we show the results of using GEDT on two different epistatis models and discuss the direction it would take in the future.
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Genetic Epidemiology, Machine Learning, Gene-Gene Interactions, Epistasis, Decision Trees, Grammatical Evolution
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Degree
MS
Discipline
Computer Science
