 Thesis
Authors: He, Jingwu (2006)  The most intriguing problems in genetics epidemiology are to predict genetic disease susceptibility and to associate single nucleotide polymorphisms (SNPs) with diseases. In such these studies, it is necessary to resolve the ambiguities in genetic data. The primary obstacle for ambiguity resolution is that the physical methods for separating two haplotypes from an individual genotype (phasing) are too expensive. Although computational haplotype inference is a wellexplored problem, high error rates continue to deteriorate association accuracy. Secondly, it is essential to use a small subset of informative SNPs (tag SNPs) accurately representing the rest of the SNPs (tagging). Tagging can achieve budget savings by genotyping only a limited number of SNPs and computationally inferring...

 Thesis
Authors: Cicco, Tracey Martine Westbrook (2006)  Algorithms for Computing Restricted Root Systems and Weyl Groups. (Under the direction of Dr. Aloysius Helminck.)
While the computational packages LiE, Gap4, Chevie, and Magma are sufficient for work with Lie Groups and their corresponding Lie Algebras, no such packages exist for computing the kstructure of a group or the structure of symmetric spaces. My goal is to examine the kstructure of groups and the structure of symmetric spaces and arrive at various algorithms for computing in these spaces.

 
Authors: Zaslavsky, Elena (2006)  A major objective in molecular biology is to understand how a genome encodes the information that speci es when and where a gene will be transcribed into its protein product. Mediating proteins, known as transcription factors, facilitate this process by interacting with the cell 's sDNA and the transcription machinery. It is of central importance to identify all sequencespeci c DNA binding sites of transcription factors. In this thesis, we consider two relevant computational problems.
The first problem is to develop a representation for a group of known binding sites of a particular transcription factor, in order to facilitate recognition of other binding sites of the same protein. We evaluate the e ectiveness of several approaches commonly used for this problem, and show that the...

 Thesis
Authors: Sai Ranga, Prashanth C. (2006)  Current heterogeneous metacomputing systems, such as computational clusters and grids offer a low cost alternative to supercomputers. In addition they are highly scalable and flexible. They consist of a host of diverse computational devices which collaborate via a high speed network and may execute highperformance applications. Many highperformance applications are an aggregate of modules. Efficient scheduling of such applications on metacomputing systems is critical to meeting deadlines. In this dissertation, we introduce three new algorithms, the Heterogeneous Critical Node First (HCNF) algorithm, the Heterogeneous Largest Task First (HLTF) algorithm and the Earliest Finish Time with Dispatch Time (EFTDT) algorithm. HCNF is used to schedule
parallel applications of forms r...

 Thesis
Authors: El Badawy, Ossama (2006)  This thesis presents data structures and algorithms for the analysis of the 2D shape of patterns. In this work, a pattern is typically an object in a bilevel image and analyzing it involves two main ingredients: representing it in computer memory; and determining its degree of similarity to other patterns.
The core idea around which this work is based is that of the convex hull of a set of points in the plane; after all, an object is a set of pixels in the plane of the image. From the simple concept of the convex hull stems the more involved concept of a concavity tree, a data structure that has remained largely unstudied, especially in connection to shape analysis.
We present an efficient contourbased algorithm for concavity tree extraction, detailing its use in the decomposit...

 Thesis
Authors: Haataja, Steven P. (2006)  We focus on three constructions: amalgamated free products of inverse semigroups, C*algebras of inverse semigroups, and amalgamated free products of C*algebras. The starting point is an amalgam [S1, S2, U] of inverse semigroups that is full, i.e., the embeddings of U into S1 and S2 are bijective on the semilattice of idempotents. Although the order structure of the amalgamated free product is wellunderstood, the structure of the maximal subgroups was somewhat mysterious prior to this work. We use BassSerre theory to characterize these maximal subgroups and determine which graphs of groups arise in this setting. We obtain necessary and sufficient conditions for the amalgamated free product to have trivial subgroups. One surprising consequence is that an amalgamated free product ...

 Thesis
Authors: Harroud, Hamid (2006)  Recent advances in portable computing devices and wireless technology make it possible to provide seamless and ubiquitous services for mobile users. As users move from one location to another, there is a greater need to automatically provide officelike environments that normally have to be configured and setup on an individual basis by each user at each visited location. Due to occasional disconnections, device capabilities and network heterogeneity, users' mobility places a considerable burden on applications to be used by mobile users. On the other hand, it receives little assistance from existing infrastructure and Internet protocols for tracing users' movement and adapting services to satisfy unique characteristics of mobility.
This thesis recognizes the importance of managing...

 Thesis
Authors: Jett, William S. (2006)  In this work, we extend the current field of objectoriented software engineering by deriving a more complete set of objectoriented metapatterns. We use our metapatterns to decompose objectoriented design patterns and separate the concerns that cause shortcomings in the area of software evolution. We then extend our objectoriented metapatterns by using the agent concepts to reduce the cost and risk associated with each cycle of software evolution. We finally compose a set of agentbased patterns from the agentbased metapatterns and demonstrate that they are a worthwhile improvement to the field of software evolution.

 Thesis
Authors: Boicu, Cristina E. (2007)  Our research addresses the problem of developing knowledgebased agents that incorporate the knowledge of subject matter experts. Our approach is to develop a learning and problem solving agent, which can be directly taught by a subject matter expert by explaining it how to solve specific problems, and by critiquing its attempts to solve new problems. Because the accuracy of the agent's reasoning depends on the rules from its knowledge base, the process of rule improvement is very important. This dissertation presents an integrated set of methods to assist a subject matter expert in refining the rules from an agent's knowledge base, to incorporate his problem solving expertise. This dissertation presents methods to discover incompletely refined rules and to propose suggestions for t...

 Thesis
Authors: Rodriguez, Arnoldo (2006)  This research focuses on the application of principles and techniques of artificial intelligence for the generation, testing and recommendation of teaching materials, and for providing Webbased contextsensitive help to teachers engaged in authoring Educational Adaptive Hypermedia (EAH). We study how to apply Machine Learning (ML) techniques to support teachers in authoring learning sessions. This investigation also studies the use of data related to teachers to support the recommendation of teaching materials and the adaptation of Webbased help.
Our research also pays attention to the teacher's problems in authoring learning sessions for teaching decisionmaking in network design. Specifically, this research addresses two problems that university teachers face when they are auth...
