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  • 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 sequence-speci 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 meta-computing 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 high-performance applications. Many high-performance applications are an aggregate of modules. Efficient scheduling of such applications on meta-computing 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 (EFT-DT) 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 2-D shape of patterns. In this work, a pattern is typically an object in a bi-level 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 contour-based 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 semi-groups, 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 well-understood, the structure of the maximal subgroups was somewhat mysterious prior to this work. We use Bass-Serre 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 office-like 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 object-oriented software engineering by deriving a more complete set of object-oriented meta-patterns. We use our meta-patterns to decompose object-oriented design patterns and separate the concerns that cause shortcomings in the area of software evolution. We then extend our object-oriented meta-patterns by using the agent concepts to reduce the cost and risk associated with each cycle of software evolution. We finally compose a set of agent-based patterns from the agent-based meta-patterns 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 knowledge-based 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 Web-based context-sensitive 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 Web-based help. Our research also pays attention to the teacher's problems in authoring learning sessions for teaching decision-making in network design. Specifically, this research addresses two problems that university teachers face when they are auth...

  • Thesis


  • Authors: Cho, Hong-Ray (2006)

  • In this thesis we consider the generalization of automatic groups to a larger class called counter groups. A counter group is an automatic group with deterministic counter languages substituted for regular languages. Automatic groups were introduced by David Epstein et al in 1985. They attracted the interest of many mathematicians because of their connection with the problem of classifying compact three dimensional manifolds. This problem includes as a special case the famous Poincar'e Conjecture. A solution was announced by Grigori Perelman a few years ago. Automatic groups are defined in terms of formal languages. A formal language is a subset of a finitely generated free monoid. We present the definition of automatic groups, main theorems and some examples of automatic grou...