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Access Type

WSU Access

Date of Award


Degree Type


Degree Name



Computer Science

First Advisor

Farshad Fotouhi


There are many needs to populate bioinformatics databases for its professional purposes to build a valuable view of various genomic databases over the Internet. One of these studies is to testify a way to build an organism-specific protein interaction database. The multilayered architecture of the designed system has wrapper, mediator, relational database, and user interface components. Even though neural network has been proven a good approach in machine learning, it has not been popular in proteomic studies because of categorical data description and data size in those applications. In order to avoid these problems, this study adopts decimal-to-binary coding scheme and class decomposition in data analysis. Each decomposed subproblem constructs a modular neural network to predict functions of proteins without known function. The experiments show that this modular neural network approach benefits of fast learning and high accuracy. Another study for predictive model of protein function is based on instance-based learning. The studied method fully uses the concept of "guilt-by-interaction" in assigning functions to proteins without known function. The mechanism to choose reliable interactions is embedded in the proposed method. In experiments, the accuracy of a modular neural network can be improved through an ensemble methodology with an instance-based learning.

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