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Articles 181 - 190 of 190
Full-Text Articles in Engineering
Biological Sequence Simulation For Testing Complex Evolutionary Hypotheses: Indel-Seq-Gen Version 2.0, Cory L. Strope
Biological Sequence Simulation For Testing Complex Evolutionary Hypotheses: Indel-Seq-Gen Version 2.0, Cory L. Strope
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Reconstructing the evolutionary history of biological sequences will provide a better understanding of mechanisms of sequence divergence and functional evolution. Long-term sequence evolution includes not only substitutions of residues but also more dynamic changes such as insertion, deletion, and long-range rearrangements. Such dynamic changes make reconstructing sequence evolution history difficult and affect the accuracy of molecular evolutionary methods, such as multiple sequence alignments (MSAs) and phylogenetic methods. In order to test the accuracy of these methods, benchmark datasets are required. However, currently available benchmark datasets have limitations in their sizes and evolutionary histories of the included sequences are unknown. These …
Classification, Clustering And Data-Mining Of Biological Data, Thomas Triplet
Classification, Clustering And Data-Mining Of Biological Data, Thomas Triplet
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are currently over 1100 molecular biology databases dispersed throughout the Internet. However, very few of them integrate data from multiple sources. To assist in the functional and evolutionary analysis of the abundant number of novel proteins, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database that integrates data from various biological sources. PROFESS is freely available athttp://cse.unl.edu/~profess/. Our database is designed to be versatile and expandable and will not …
Deployed Software Analysis, Madeline M. Diep
Deployed Software Analysis, Madeline M. Diep
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Profiling can offer a valuable characterization of software behavior. The richer the characterization is, the more effective the client analyses are in supporting quality assurance activities. For today's complex software, however, obtaining a rich characterization with the input provided by in-house test suites is becoming more difficult and expensive. Extending the profiling activity to deployed environments can mitigate this shortcoming by exposing more program behavior reflecting real software usage. To make profiling of deployed software plausible, however, we need to take into consideration that there are fundamental differences between the development and the deployed environments. Deployed environments allow for less …
Adaptive Interpolation Algorithms For Temporal-Oriented Datasets, Jun Gao
Adaptive Interpolation Algorithms For Temporal-Oriented Datasets, Jun Gao
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Spatiotemporal datasets can be classified into two categories: temporal-oriented and spatial-oriented datasets depending on whether missing spatiotemporal values are closer to the values of its temporal or spatial neighbors. We present an adaptive spatiotemporal interpolation model that can estimate the missing values in both categories of spatiotemporal datasets. The key parameters of the adaptive spatiotemporal interpolation model can be adjusted based on experience.
Experimental Evaluation Of Constraint Automata Solutions To The Genome Map Assembly Problem, Viswanathan Ramanathan
Experimental Evaluation Of Constraint Automata Solutions To The Genome Map Assembly Problem, Viswanathan Ramanathan
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
DNA sequences are really huge having a length of around 3-4 million base pairs. Hence, each DNA sequence has to be cut down into small fragments using restriction enzymes. Once analyzed, these fragments have to be arranged or assembled into a single set of sequences called a genome map, to obtain the original DNA sequence. This problem is called the Genome Map Assembly Problem. A Constraint-Automata Solution was proposed for this purpose [11]. This thesis improves and implements the Constraint-Automata Solution to find all the possible solutions. The Modified Constraint-Automata Solution was implemented in Perl and executed on parts of …
Constraint Datalog In Trust Management, Scot Anderson
Constraint Datalog In Trust Management, Scot Anderson
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Constraint Datalog holds an increasing role in Trust Management. We discuss several Trust Management systems and give a description of the environment and requirements for Trust Management. Constraint Datalog using addition constraints and approximation theory provides an expressive semantic with which to describe security policies for credentials, delegations and authorizations. Approximation theory allows halting in Constraint Datalog over addition constraints. We use the decision problem of Diophantine equations to show that Constraint Datalog over addition constraints is complete. Combining these two concepts provides an approximately complete, safe language. The problem of constant additions to closed languages provides reasons for using …
User Interface Improvement For Mlpq System, Shasha Wu
User Interface Improvement For Mlpq System, Shasha Wu
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
This thesis describes the experience of migrating the MLPQ constraint database system, a complex standalone Multiple Document Interface (MDI) application, to a server-based remote accessible application. Centralized, standalone MDI application is a common style for personal software products in Windows. For a database management system, server-based, thin-client computing is a more popular infrastructure. Migrating an existing standalone constraint database application to be a web accessible constraint database server is the main goal of this thesis. This migration process provides a method for the constraint database system to collaborate with other specific applications. We rebuild the desktop MLPQ constraint database system …
Implementation Of A Database System With Boolean Algebra Constraints, András Salamon
Implementation Of A Database System With Boolean Algebra Constraints, András Salamon
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
This thesis describes an implementation of a constraint database system with constraints over a Boolean Algebra of sets. The system allows within the input database as well as the queries equality, subset-equality and monotone inequality constraints between Boolean Algebra terms built up using the operators of union, intersection and complement. Hence the new system extends the earlier DISCO system, which only allowed equality and subset-equality constraints between Boolean algebra variables and constants. The new system allows Datalog with Boolean Algebra constraints as the query lan- guage. The implementation includes an extension of Naive and Semi-Naive evaluation methods for Datalog programs …
Mlpq: A Linear Constraint Database System With Aggregate Operators, Yiming Li
Mlpq: A Linear Constraint Database System With Aggregate Operators, Yiming Li
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
In this project report, I will discuss a Multiple Linear Programming Query (MLPQ) system and the theoretical background of this system.The MPLQ system is developed to solve some realistic problems involving both linear programming (UP) techniques and linear constraint databases (LCDBs) theory. The MLPQ system is aimed at providing a mechanism of bridging these two important areas. system basically consists of three parts which are a linear constraint database, an LP solver, and an interface between the LCDB and the LP solver. The LCDB of the MLPQ system contains multiple linear programming problems. The LP solver used in the MPLQ …
A Sign-To-Speech Translation System, Koka Veera Raghava Rao
A Sign-To-Speech Translation System, Koka Veera Raghava Rao
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
This thesis describes sign-to-speech translation using neural networks. Sign language translation is an interesting but difficult problem for which neural network techniques seem promising because of their ability to adjust to the user's hand movements, which is not possible to do by most other techniques. However, even using neural networks and artificial sign languages, the translation is hard, and the best-known system, that of Fels & Hinton (1993), is capable of translating only 66 root words and 203 words including their conjugations. This research improves their results to 790 root signs and 2718 words including their conjugations while preserving a …