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Articles 1 - 7 of 7
Full-Text Articles in Physical Sciences and Mathematics
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 …
Temporal Data Classification Using Linear Classifiers, Peter Revesz, Thomas Triplet
Temporal Data Classification Using Linear Classifiers, Peter Revesz, Thomas Triplet
CSE Conference and Workshop Papers
Data classification is usually based on measurements recorded at the same time. This paper considers temporal data classification where the input is a temporal database that describes measurements over a period of time in history while the predicted class is expected to occur in the future. We describe a new temporal classification method that improves the accuracy of standard classification methods. The benefits of the method are tested on weather forecasting using the meteorological database from the Texas Commission on Environmental Quality.
Exploiting Set-Level Non-Uniformity Of Capacity Demand To Enhance Cmp Cooperative Caching, Dongyuan Zhan, Hong Jiang, Sharad C. Seth
Exploiting Set-Level Non-Uniformity Of Capacity Demand To Enhance Cmp Cooperative Caching, Dongyuan Zhan, Hong Jiang, Sharad C. Seth
CSE Technical Reports
As the Memory Wall remains a bottleneck for Chip Multiprocessors (CMP), the effective management of CMP last level caches becomes of paramount importance in minimizing expensive off-chip memory accesses. For the CMPs with private last level caches, Cooperative Caching (CC) has been proposed to enable capacity sharing among private caches by spilling an evicted block from one cache to another. But this eviction-driven CC does not necessarily promote cache performance since it implicitly favors the applications full of block evictions regardless of their real capacity demand. The recent Dynamic Spill-Receive (DSR) paradigm improves cooperative caching by prioritizing applications with higher …
Design Of An All-Optical Wdm Lightpath Concentrator, Shivashis Saha, Jitender S. Deogun
Design Of An All-Optical Wdm Lightpath Concentrator, Shivashis Saha, Jitender S. Deogun
CSE Technical Reports
A design of a nonblocking, all-optical lightpath concentrator using WOC and WDM crossbar switches is presented. The proposed concentrator is highly scalable, cost-efficient, and can switch signals in both space and wavelength domains without requiring a separate wavelength conversion stage.
Selection Of Switching Sites In All-Optical Nework Topology Design, Shivashis Saha, Eric D. Manley, Jitender S. Deogun
Selection Of Switching Sites In All-Optical Nework Topology Design, Shivashis Saha, Eric D. Manley, Jitender S. Deogun
CSE Technical Reports
In this paper, we consider the problem of topology design for optical networks. We investigate the problem of selecting switching sites to minimize total cost of the optical network. The cost of an optical network can be expressed as a sum of three main factors: the site cost, the link cost, and the switch cost. To the best of our knowledge, this problem has not been studied in its general form as investigated in this paper. We present a mixed integer quadratic programming (MIQP) formulation of the problem to find the optimal value of the total network cost. We also …
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 …