Forty-six genomic gene expression studies of free living soil nematode C. eleganshave been published. To facilitate exploratory analysis of those studies, we constructed adatabase containing all the published C. elegans expression datasets. A Perl CGIprogram, called Microarray Analysis Display (MAdisplay), allows gene expressionclustergrams of any combination of entered genes and datasets to be viewed(http://elegans.uky.edu/gl/madisplay). Perl programs were used to preprocess the rawdata from different sources into a common format and to transform the data to displaythe expression changes relative to each experiment's controls. Three hundred lists ofgenes from figures and tables were extracted from the publications and made available inthe GeneLists database, which also contains Gene Ontology and KEGG gene lists. Weused these tools to examine in a systematic fashion the mean expression of gene lists inthe set of microarray and SAGE experiments. Seventy-nine percent of publicationderived gene lists show a strong expression change (p-value andlt;0.001) in more than oneexperiment with the median being fourteen out of the 127 experiments that are derivedfrom the forty-six publications. This indicates that groups of genes identified in onepublication typically show an expression effect in many other experiments.

Genome scale protein-protein interactions (PPIs) are interpreted as networks or graphs with thousands of nodes from the perspective of computer science. PPI networks represent various types of possible interactions among proteins or genes of a genome. PPI data is vital in protein function prediction since functions of the cells are performed by groups of proteins interacting with each other and main complexes of the cell are made of proteins interacting with each other. Recent increase in protein interaction prediction techniques have made great amount of protein-protein interaction data available for genomes. As a consequence, a systematic visualization and analysis technique has become crucial. To the best of our knowledge, no PPI visualization tool consider multi-resolution viewing of PPI network. In this thesis, we implemented a new approach for PPI network visualization which supports multi-resolution viewing of compound graphs. We construct compound nodes and label them by using gene set enrichment methods based on Gene Ontology annotations. This thesis further suggests new methods for PPI network visualization.

Many e-commerce web sites such as online book retailers or specialized information hubs such as online movie databases make use of recommendation systems where users are directed to items of interests based on past user interactions. Keyword-based approaches, collaborative and content filtering techniques have been tried and used over the years each having their own shortcomings. While keyword based approaches are naive and do not take content or context into account collaborative and content filtering techniques suffer from biased ratings, first item and first-rater problems. Recent approaches try to incorporate underlying semantic properties of data by employing ontology based usage mining. This thesis aims to design a recommendation system based on ontological data where web pages are seen as objects with attributes and relations. Instead of relying on users&rsquo / content ratings, user sessions are clustered on a iv semantic level to capture different behavioral groups. Since semantic information is used for the clustering distance function, each cluster represents a behavior group instead of simpler data groups. New users are then assigned to individual clusters that best represent their behavior and recommendations are generated accordingly. In this thesis we use the recommendation results as a means for measuring the effectiveness of the clusters we have generated. We have compared the results obtained using the ontological data and the results obtained without using it and shown that semantic integrating semantic knowledge increases both precision and recall.

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The amount of information on the World Wide Web (WWW) is rapidly growing in pace and topic diversity. This has made it increasingly difficult, and often frustrating, for information seekers to retrieve the content they are looking for as information retrieval systems (e.g., search engines) are unable to decipher the relevance of the retrieved information as it pertains to the information they are searching for. This issue can be decomposed into two aspects: 1) variability of information relevance as it pertains to an information seeker. In other words, different information seekers may enter the same search text, or keywords, but expect completely different results. It is therefore, imperative that information retrieval systems possess an ability to incorporate a model of the information seeker in order to estimate the relevance and context of use of information before presenting results. Of course, in this context, by a model we mean the capture of trends in the information seeker's search behaviour. This is what many researchers refer to as the personalized search. 2) Information diversity. Information available on the World Wide Web today spans multitudes of inherently overlapping topics, and it is difficult for any information retrieval system to decide effectively on the relevance of the information retrieved in response to an information seeker's query. For example, the information seeker who wishes to use WWW to learn about a cure for a certain illness would receive a more relevant answer if the search engine was optimized into such domains of topics. This is what is being referred to in the WWW nomenclature as a 'specialized search'. This thesis maintains that the information seeker's search is not intended to be completely random and therefore tends to portray itself as consistent patterns of behaviour. Nonetheless, this behaviour, despite being consistent, can be quite complex to capture. To accomplish this goal the thesis proposes a Multi-Agent Personalized Information Retrieval with Specialization Ontology (MAPIRSO). MAPIRSO offers a complete learning framework that is able to model the end user's search behaviour and interests and to organize information into categorized domains so as to ensure maximum relevance of its responses as they pertain to the end user queries. Specialization and personalization are accomplished using a group of collaborative agents. Each agent employs a Reinforcement Learning (RL) strategy to capture end user's behaviour and interests. Reinforcement learning allows the agents to evolve their knowledge of the end user behaviour and interests as they function to serve him or her. Furthermore, REL allows each agent to adapt to changes in an end user's behaviour and interests. Specialization is the process by which new information domains are created based on existing information topics, allowing new kinds of content to be built exclusively for information seekers. One of the key characteristics of specialization domains is the seeker centric - which allows intelligent agents to create new information based on the information seekers' feedback and their behaviours. Specialized domains are created by intelligent agents that collect information from a specific domain topic. The task of these specialized agents is to map the user's query to a repository of specific domains in order to present users with relevant information. As a result, mapping users' queries to only relevant information is one of the fundamental challenges in Artificial Intelligent (AI) and machine learning research. Our approach employs intelligent cooperative agents that specialize in building personalized ontology information domains that pertain to each information seeker's specific needs. Specializing and categorizing information into unique domains is one of the challenge areas that have been addressed and various proposed solutions were evaluated and adopted to address growing information. However, categorizing information into unique domains does not satisfy each individualized information seeker. Information seekers might search for similar topics, but each would have different interests. For example, medical information of a specific medical domain has different importance to both the doctor and patients. The thesis presents a novel solution that will resolve the growing and diverse information by building seeker centric specialized information domains that are personalized through the information seekers' feedback and behaviours. To address this challenge, the research examines the fundamental components that constitute the specialized agent: an intelligent machine learning system, user input queries, an intelligent agent, and information resources constructed through specialized domains. Experimental work is reported to demonstrate the efficiency of the proposed solution in addressing the overlapping information growth. The experimental work utilizes extensive user-centric specialized domain topics. This work employs personalized and collaborative multi learning agents and ontology techniques thereby enriching the queries and domains of the user. Therefore, experiments and results have shown that building specialized ontology domains, pertinent to the information seekers' needs, are more precise and efficient compared to other information retrieval applications and existing search engines.

The amount of information on the World Wide Web (WWW) is rapidly growing in pace and topic diversity. This has made it increasingly difficult, and often frustrating, for information seekers to retrieve the content they are looking for as information retrieval systems (e.g., search engines) are unable to decipher the relevance of the retrieved information as it pertains to the information they are searching for. This issue can be decomposed into two aspects: 1) variability of information relevance as it pertains to an information seeker. In other words, different information seekers may enter the same search text, or keywords, but expect completely different results. It is therefore, imperative that information retrieval systems possess an ability to incorporate a model of the information seeker in order to estimate the relevance and context of use of information before presenting results. Of course, in this context, by a model we mean the capture of trends in the information seeker's search behaviour. This is what many researchers refer to as the personalized search. 2) Information diversity. Information available on the World Wide Web today spans multitudes of inherently overlapping topics, and it is difficult for any information retrieval system to decide effectively on the relevance of the information retrieved in response to an information seeker's query. For example, the information seeker who wishes to use WWW to learn about a cure for a certain illness would receive a more relevant answer if the search engine was optimized into such domains of topics. This is what is being referred to in the WWW nomenclature as a 'specialized search'. This thesis maintains that the information seeker's search is not intended to be completely random and therefore tends to portray itself as consistent patterns of behaviour. Nonetheless, this behaviour, despite being consistent, can be quite complex to capture. To accomplish this goal the thesis proposes a Multi-Agent Personalized Information Retrieval with Specialization Ontology (MAPIRSO). MAPIRSO offers a complete learning framework that is able to model the end user's search behaviour and interests and to organize information into categorized domains so as to ensure maximum relevance of its responses as they pertain to the end user queries. Specialization and personalization are accomplished using a group of collaborative agents. Each agent employs a Reinforcement Learning (RL) strategy to capture end user's behaviour and interests. Reinforcement learning allows the agents to evolve their knowledge of the end user behaviour and interests as they function to serve him or her. Furthermore, REL allows each agent to adapt to changes in an end user's behaviour and interests. Specialization is the process by which new information domains are created based on existing information topics, allowing new kinds of content to be built exclusively for information seekers. One of the key characteristics of specialization domains is the seeker centric - which allows intelligent agents to create new information based on the information seekers' feedback and their behaviours. Specialized domains are created by intelligent agents that collect information from a specific domain topic. The task of these specialized agents is to map the user's query to a repository of specific domains in order to present users with relevant information. As a result, mapping users' queries to only relevant information is one of the fundamental challenges in Artificial Intelligent (AI) and machine learning research. Our approach employs intelligent cooperative agents that specialize in building personalized ontology information domains that pertain to each information seeker's specific needs. Specializing and categorizing information into unique domains is one of the challenge areas that have been addressed and various proposed solutions were evaluated and adopted to address growing information. However, categorizing information into unique domains does not satisfy each individualized information seeker. Information seekers might search for similar topics, but each would have different interests. For example, medical information of a specific medical domain has different importance to both the doctor and patients. The thesis presents a novel solution that will resolve the growing and diverse information by building seeker centric specialized information domains that are personalized through the information seekers' feedback and behaviours. To address this challenge, the research examines the fundamental components that constitute the specialized agent: an intelligent machine learning system, user input queries, an intelligent agent, and information resources constructed through specialized domains. Experimental work is reported to demonstrate the efficiency of the proposed solution in addressing the overlapping information growth. The experimental work utilizes extensive user-centric specialized domain topics. This work employs personalized and collaborative multi learning agents and ontology techniques thereby enriching the queries and domains of the user. Therefore, experiments and results have shown that building specialized ontology domains, pertinent to the information seekers' needs, are more precise and efficient compared to other information retrieval applications and existing search engines.