Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

In my dissertation, I will present my research which contributes to solve the following three open problems from biomedical informatics: (1) Multi-task approaches for microarray classification; (2) Multi-label classification of gene and protein prediction from multi-source biological data; (3) Spatial scan for movement data. In microarray…

A large body of literature exists on evolutionary computing, genetic algorithms, decision trees, codified knowledge, and knowledge management systems; however, the intersection of these computing topics has not been widely researched. Moving through the set of all possible solutions--or traversing the search space--at random exhibits no control…

With increasing Internet connectivity and traffic volume, recent intrusion incidents have reemphasized the importance of network intrusion detection systems for combating increasingly sophisticated network attacks. Techniques such as pattern recognition and the data mining of network events are often used by intrusion detection systems to classify…

Ontology not only is considered to be the backbone of the semantic web but also plays a significant role in distributed and heterogeneous information systems. However, ontology still faces limited application and adoption to date. One of the major problems is that prevailing engineering-oriented methodologies for building ontologies do not…

This dissertation presents a novel effort to develop ITS technologies that adapt by observing student behavior. In particular, we define an evolving expert knowledge base (EEKB) that structures a domain's information as a set of nodes and the relationships that exist between those nodes. The structure of this model is not the particularly novel…

Graphs are widely used to model structures and relationships of objects in various scientific and commercial fields. Chemical molecules, proteins, malware system-call dependencies and three-dimensional mechanical parts are all modeled as graphs. In this dissertation, we propose to mine and index those graph data to enable fast and scalable search.…

Incorporating relevant numerical information into decision-making is a fundamental and important aspect of numeracy. However, the process through which weight is assigned to particular numerical values is not well understood. The central theory proposed in this dissertation is that the weight assigned to numerical information may be conceptualized…

Spatial or temporal data mining tasks are performed in the context of the relevant space, defined by a spatial neighborhood, and the relevant time period, defined by a specific time interval. Furthermore, when mining large spatio-temporal datasets, interesting patterns typically emerge where the dataset is most dynamic. This dissertation is…

Developing nations are poised to spend billions on information and communication technology (ICT) innovation in 2020. A study of the historical adoption of ICT in developing nations has indicated that their adoption patterns do not follow typical technology innovation adoption models. This study addressed the weaknesses found in existing…

Sender anonymity in Location-based services (LBS) refers to hiding the identity of a mobile device user who sends requests to the LBS provider for services in her proximity (e.g. "find the nearest gas station etc."). The goal is to keep the requester's interest private even from attackers who (via hacking or subpoenas) gain access to the LBS…

In recent years, new bioinformatics technologies, such as gene expression microarray, genome-wide association study, proteomics, and metabolomics, have been widely used to simultaneously identify a huge number of human genomic/genetic biomarkers, generate a tremendously large amount of data, and dramatically increase the knowledge on human…

Data visualizations designed for academic scientists are not immediately meaningful to everyday scientists. Communicating between a specialized, expert audience and a general, novice public is non-trivial; it requires careful translation. However, more widely available visualization technologies and platforms, including new three-dimensional…

This dissertation investigates the interaction between form and function in Mandarin Chinese by empirically examining the interactions of core semantic roles (Agent and Patient) and the syntactic representation of those interactions in semantically transitive events. First, I demonstrate that syntactic structures and functions are intertwined with…

This dissertation investigates clitic doubling of both dative and accusative objects in adult and child language. It reports on three experimental studies designed to discover the specific distributional properties of this phenomenon, with particular attention to the effect of "rheme" and "kontrast," two distinct concepts often collapsed as…