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Disparate data fusion for protein phosphorylation prediction

Annals of Operations Research

Gray, Genetha A.; Williams, Pamela J.; Brown, W.M.; Faulon, Jean-Loup M.; Sale, Kenneth L.

New challenges in knowledge extraction include interpreting and classifying data sets while simultaneously considering related information to confirm results or identify false positives. We discuss a data fusion algorithmic framework targeted at this problem. It includes separate base classifiers for each data type and a fusion method for combining the individual classifiers. The fusion method is an extension of current ensemble classification techniques and has the advantage of allowing data to remain in heterogeneous databases. In this paper, we focus on the applicability of such a framework to the protein phosphorylation prediction problem. © Springer Science+Business Media, LLC 2008.

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Dakota, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis:version 4.0 developers manual

Brown, Shannon L.; Griffin, Joshua G.; Hough, Patricia D.; Kolda, Tamara G.; Martinez-Canales, Monica L.; Williams, Pamela J.; Adams, Brian M.; Dunlavy, Daniel D.; Swiler, Laura P.; Giunta, Anthony A.; Hart, William E.; Watson, Jean-Paul W.; Eddy, John P.

The DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. DAKOTA contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic finite element methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the DAKOTA toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a developers manual for the DAKOTA software and describes the DAKOTA class hierarchies and their interrelationships. It derives directly from annotation of the actual source code and provides detailed class documentation, including all member functions and attributes.

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DAKOTA, a multilevel parellel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis:version 4.0 uers's manual

Swiler, Laura P.; Giunta, Anthony A.; Hart, William E.; Watson, Jean-Paul W.; Eddy, John P.; Griffin, Joshua G.; Hough, Patricia D.; Kolda, Tamara G.; Martinez-Canales, Monica L.; Williams, Pamela J.; Eldred, Michael S.; Brown, Shannon L.; Adams, Brian M.; Dunlavy, Daniel D.

The DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. DAKOTA contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic finite element methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the DAKOTA toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a user's manual for the DAKOTA software and provides capability overviews and procedures for software execution, as well as a variety of example studies.

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DAKOTA, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis:version 4.0 reference manual

Brown, Shannon L.; Griffin, Joshua G.; Hough, Patricia D.; Kolda, Tamara G.; Martinez-Canales, Monica L.; Williams, Pamela J.; Adams, Brian M.; Dunlavy, Daniel D.; Swiler, Laura P.; Giunta, Anthony A.; Hart, William E.; Watson, Jean-Paul W.; Eddy, John P.

The DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. DAKOTA contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic finite element methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the DAKOTA toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a reference manual for the commands specification for the DAKOTA software, providing input overviews, option descriptions, and example specifications.

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Data fusion on a distributed heterogeneous sensor network

Williams, Pamela J.

Alarm-based sensor systems are being explored as a tool to expand perimeter security for facilities and force protection. However, the collection of increased sensor data has resulted in an insufficient solution that includes faulty data points. Data analysis is needed to reduce nuisance and false alarms, which will improve officials decision making and confidence levels in the system's alarms. Moreover, operational costs can be allayed and losses mitigated if authorities are alerted only when a real threat is detected. In the current system, heuristics such as persistence of alarm and type of sensor that detected an event are used to guide officials responses. We hypothesize that fusing data from heterogeneous sensors in the sensor field can provide more complete situational awareness than looking at individual sensor data. We propose a two stage approach to reduce false alarms. First, we use self organizing maps to cluster sensors based on global positioning coordinates and then train classifiers on the within cluster data to obtain a local view of the event. Next, we train a classifier on the local results to compute a global solution. We investigate the use of machine learning techniques, such as k-nearest neighbor, neural networks, and support vector machines to improve alarm accuracy. On simulated sensor data, the proposed approach identifies false alarms with greater accuracy than a weighted voting algorithm.

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14 Results
14 Results