A framework for benchmarking of homogenisation algorithm performance on the global scale

The International Surface Temperature Initiative (ISTI) is striving towards substantively improving our ability to robustly understand historical land surface air temperature change at all scales. A key recently completed first step has been collating all available records into a comprehensive open access, traceable and version-controlled databank. The crucial next step is to maximise the value of the collated data through a robust international framework of benchmarking and assessment for product intercomparison and uncertainty estimation. We focus on uncertainties arising from the presence of inhomogeneities in monthly mean land surface temperature data and the varied methodological choices made by various groups in building homogeneous temperature products. The central facet of the benchmarking process is the creation of global-scale synthetic analogues to the real-world database where both the "true" series and inhomogeneities are known (a luxury the real-world data do not afford us). Hence, algorithmic strengths and weaknesses can be meaningfully quantified and conditional inferences made about the real-world climate system. Here we discuss the necessary framework for developing an international homogenisation benchmarking system on the global scale for monthly mean temperatures. The value of this framework is critically dependent upon the number of groups taking part and so we strongly advocate involvement in the benchmarking exercise from as many data analyst groups as possible to make the best use of this substantial effort.

Improved Techniques for Acquisition and Analysis of Dynamic Contrast-Enhanced Magnetic Resonance Imaging for Detecting Vascular Permeability in the Central Nervous System

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a noninvasive technique for quantitative assessment of the integrity of blood-brain barrier and blood-spinal cord barrier (BSCB) in the presence of central nervous system pathologies. However, the results of DCE-MRI show substantial variability. The high variability can be caused by a number of factors including inaccurate T1 estimation, insufficient temporal resolution and poor contrast-to-noise ratio. My thesis work is to develop improved methods to reduce the variability of DCE-MRI results. To obtain fast and accurate T1 map, the Look-Locker acquisition technique was implemented with a novel and truly centric k-space segmentation scheme. In addition, an original multi-step curve fitting procedure was developed to increase the accuracy of T1 estimation. A view sharing acquisition method was implemented to increase temporal resolution, and a novel normalization method was introduced to reduce image artifacts. Finally, a new clustering algorithm was developed to reduce apparent noise in the DCE-MRI data. The performance of these proposed methods was verified by simulations and phantom studies. As part of this work, the proposed techniques were applied to an in vivo DCE-MRI study of experimental spinal cord injury (SCI). These methods have shown robust results and allow quantitative assessment of regions with very low vascular permeability. In conclusion, applications of the improved DCE-MRI acquisition and analysis methods developed in this thesis work can improve the accuracy of the DCE-MRI results.

Gestión óptima de embalses en avenidas incorporando al concepto de incertidumbre : aplicación a embalses con central hidroeléctrica

Esta tesis realiza una contribución metodológica al problema de la gestión óptima de embalses hidroeléctricos durante eventos de avenidas, considerando un enfoque estocástico y multiobjetivo. Para ello se propone una metodología de evaluación de estrategias de laminación en un contexto probabilístico y multiobjetivo. Además se desarrolla un entorno dinámico de laminación en tiempo real con pronósticos que combina un modelo de optimización y algoritmos de simulación. Estas herramientas asisten a los gestores de las presas en la toma de decisión respecto de cuál es la operación más adecuada del embalse. Luego de una detallada revisión de la bibliografía, se observó que los trabajos en el ámbito de la gestión óptima de embalses en avenidas utilizan, en general, un número reducido de series de caudales o hidrogramas para caracterizar los posibles escenarios. Limitando el funcionamiento satisfactorio de un modelo determinado a situaciones hidrológicas similares. Por otra parte, la mayoría de estudios disponibles en este ámbito abordan el problema de la laminación en embalses multipropósito durante la temporada de avenidas, con varios meses de duración. Estas características difieren de la realidad de la gestión de embalses en España. Con los avances computacionales en materia de gestión de información en tiempo real, se observó una tendencia a la implementación de herramientas de operación en tiempo real con pronósticos para determinar la operación a corto plazo (involucrando el control de avenidas). La metodología de evaluación de estrategias propuesta en esta tesis se basa en determinar el comportamiento de éstas frente a un espectro de avenidas características de la solicitación hidrológica. Con ese fin, se combina un sistema de evaluación mediante indicadores y un entorno de generación estocástica de avenidas, obteniéndose un sistema implícitamente estocástico. El sistema de evaluación consta de tres etapas: caracterización, síntesis y comparación, a fin de poder manejar la compleja estructura de datos resultante y realizar la evaluación. En la primera etapa se definen variables de caracterización, vinculadas a los aspectos que se quieren evaluar (seguridad de la presa, control de inundaciones, generación de energía, etc.). Estas variables caracterizan el comportamiento del modelo para un aspecto y evento determinado. En la segunda etapa, la información de estas variables se sintetiza en un conjunto de indicadores, lo más reducido posible. Finalmente, la comparación se lleva a cabo a partir de la comparación de esos indicadores, bien sea mediante la agregación de dichos objetivos en un indicador único, o bien mediante la aplicación del criterio de dominancia de Pareto obteniéndose un conjunto de soluciones aptas. Esta metodología se aplicó para calibrar los parámetros de un modelo de optimización de embalse en laminación y su comparación con otra regla de operación, mediante el enfoque por agregación. Luego se amplió la metodología para evaluar y comparar reglas de operación existentes para el control de avenidas en embalses hidroeléctricos, utilizando el criterio de dominancia. La versatilidad de la metodología permite otras aplicaciones, tales como la determinación de niveles o volúmenes de seguridad, o la selección de las dimensiones del aliviadero entre varias alternativas. Por su parte, el entorno dinámico de laminación al presentar un enfoque combinado de optimización-simulación, permite aprovechar las ventajas de ambos tipos de modelos, facilitando la interacción con los operadores de las presas. Se mejoran los resultados respecto de los obtenidos con una regla de operación reactiva, aun cuando los pronósticos se desvían considerablemente del hidrograma real. Esto contribuye a reducir la tan mencionada brecha entre el desarrollo teórico y la aplicación práctica asociada a los modelos de gestión óptima de embalses. This thesis presents a methodological contribution to address the problem about how to operate a hydropower reservoir during floods in order to achieve an optimal management considering a multiobjective and stochastic approach. A methodology is proposed to assess the flood control strategies in a multiobjective and probabilistic framework. Additionally, a dynamic flood control environ was developed for real-time operation, including forecasts. This dynamic platform combines simulation and optimization models. These tools may assist to dam managers in the decision making process, regarding the most appropriate reservoir operation to be implemented. After a detailed review of the bibliography, it was observed that most of the existing studies in the sphere of flood control reservoir operation consider a reduce number of hydrographs to characterize the reservoir inflows. Consequently, the adequate functioning of a certain strategy may be limited to similar hydrologic scenarios. In the other hand, most of the works in this context tackle the problem of multipurpose flood control operation considering the entire flood season, lasting some months. These considerations differ from the real necessity in the Spanish context. The implementation of real-time reservoir operation is gaining popularity due to computational advances and improvements in real-time data management. The methodology proposed in this thesis for assessing the strategies is based on determining their behavior for a wide range of floods, which are representative of the hydrological forcing of the dam. An evaluation algorithm is combined with a stochastic flood generation system to obtain an implicit stochastic analysis framework. The evaluation system consists in three stages: characterizing, synthesizing and comparing, in order to handle the complex structure of results and, finally, conduct the evaluation process. In the first stage some characterization variables are defined. These variables should be related to the different aspects to be evaluated (such as dam safety, flood protection, hydropower, etc.). Each of these variables characterizes the behavior of a certain operating strategy for a given aspect and event. In the second stage this information is synthesized obtaining a reduced group of indicators or objective functions. Finally, the indicators are compared by means of an aggregated approach or by a dominance criterion approach. In the first case, a single optimum solution may be achieved. However in the second case, a set of good solutions is obtained. This methodology was applied for calibrating the parameters of a flood control model and to compare it with other operating policy, using an aggregated method. After that, the methodology was extent to assess and compared some existing hydropower reservoir flood control operation, considering the Pareto approach. The versatility of the method allows many other applications, such as determining the safety levels, defining the spillways characteristics, among others. The dynamic framework for flood control combines optimization and simulation models, exploiting the advantages of both techniques. This facilitates the interaction between dam operators and the model. Improvements are obtained applying this system when compared with a reactive operating policy, even if the forecasts deviate significantly from the observed hydrograph. This approach contributes to reduce the gap between the theoretical development in the field of reservoir management and its practical applications.

GANN: Genetic algorithm neural networks for the detection of conserved combinations of features in DNA

Background: The multitude of motif detection algorithms developed to date have largely focused on the detection of patterns in primary sequence. Since sequence-dependent DNA structure and flexibility may also play a role in protein-DNA interactions, the simultaneous exploration of sequence-and structure-based hypotheses about the composition of binding sites and the ordering of features in a regulatory region should be considered as well. The consideration of structural features requires the development of new detection tools that can deal with data types other than primary sequence. Results: GANN ( available at http://bioinformatics.org.au/gann) is a machine learning tool for the detection of conserved features in DNA. The software suite contains programs to extract different regions of genomic DNA from flat files and convert these sequences to indices that reflect sequence and structural composition or the presence of specific protein binding sites. The machine learning component allows the classification of different types of sequences based on subsamples of these indices, and can identify the best combinations of indices and machine learning architecture for sequence discrimination. Another key feature of GANN is the replicated splitting of data into training and test sets, and the implementation of negative controls. In validation experiments, GANN successfully merged important sequence and structural features to yield good predictive models for synthetic and real regulatory regions. Conclusion: GANN is a flexible tool that can search through large sets of sequence and structural feature combinations to identify those that best characterize a set of sequences.

Seizure detection algorithm for neonates based on wave-sequence analysis

Objective: The description and evaluation of the performance of a new real-time seizure detection algorithm in the newborn infant. Methods: The algorithm includes parallel fragmentation of EEG signal into waves; wave-feature extraction and averaging; elementary, preliminary and final detection. The algorithm detects EEG waves with heightened regularity, using wave intervals, amplitudes and shapes. The performance of the algorithm was assessed with the use of event-based and liberal and conservative time-based approaches and compared with the performance of Gotman's and Liu's algorithms. Results: The algorithm was assessed on multi-channel EEG records of 55 neonates including 17 with seizures. The algorithm showed sensitivities ranging 83-95% with positive predictive values (PPV) 48-77%. There were 2.0 false positive detections per hour. In comparison, Gotman's algorithm (with 30 s gap-closing procedure) displayed sensitivities of 45-88% and PPV 29-56%; with 7.4 false positives per hour and Liu's algorithm displayed sensitivities of 96-99%, and PPV 10-25%; with 15.7 false positives per hour. Conclusions: The wave-sequence analysis based algorithm displayed higher sensitivity, higher PPV and a substantially lower level of false positives than two previously published algorithms. Significance: The proposed algorithm provides a basis for major improvements in neonatal seizure detection and monitoring. Published by Elsevier Ireland Ltd. on behalf of International Federation of Clinical Neurophysiology.

A Fast Algorithm for Weber Problem on a Grid

AMS subject classification: 90B80.

CVaR minimization by the SRA algorithm

Using the risk measure CV aR in �nancial analysis has become more and more popular recently. In this paper we apply CV aR for portfolio optimization. The problem is formulated as a two-stage stochastic programming model, and the SRA algorithm, a recently developed heuristic algorithm, is applied for minimizing CV aR.

Enhanced skip -list search algorithm in 3-layer mediator framework

The Three-Layer distributed mediation architecture, designed by Secure System Architecture laboratory, employed a layered framework of presence, integration, and homogenization mediators. The architecture does not have any central component that may affect the system reliability. A distributed search technique was adapted in the system to increase its reliability. An Enhanced Chord-like algorithm (E-Chord) was designed and deployed in the integration layer. The E-Chord is a skip-list algorithm based on Distributed Hash Table (DHT) which is a distributed but structured architecture. DHT is distributed in the sense that no central unit is required to maintain indexes, and it is structured in the sense that indexes are distributed over the nodes in a systematic manner. Each node maintains three kind of routing information: a frequency list, a successor/predecessor list, and a finger table. None of the nodes in the system maintains all indexes, and each node knows about some other nodes in the system. These nodes, also called composer mediators, were connected in a P2P fashion. ^ A special composer mediator called a global mediator initiates the keyword-based matching decomposition of the request using the E-Chord. It generates an Integrated Data Structure Graph (IDSG) on the fly, creates association and dependency relations between nodes in the IDSG, and then generates a Global IDSG (GIDSG). The GIDSG graph is a plan which guides the global mediator how to integrate data. It is also used to stream data from the mediators in the homogenization layer which connected to the data sources. The connectors start sending the data to the global mediator just after the global mediator creates the GIDSG and just before the global mediator sends the answer to the presence mediator. Using the E-Chord and GIDSG made the mediation system more scalable than using a central global schema repository since all the composers in the integration layer are capable of handling and routing requests. Also, when a composer fails, it would only minimally affect the entire mediation system. ^

'Cooperative Automated worm Response and Detection ImmuNe ALgorithm (CARDINAL) inspired by T-cell Immunity and Tolerance'

The role of T-cells within the immune system is to confirm and assess anomalous situations and then either respond to or tolerate the source of the effect. To illustrate how these mechanisms can be harnessed to solve real-world problems, we present the blueprint of a T-cell inspired algorithm for computer security worm detection. We show how the three central T-cell processes, namely T-cell maturation, differentiation and proliferation, naturally map into this domain and further illustrate how such an algorithm fits into a complete immune inspired computer security system and framework.

'Cooperative Automated worm Response and Detection ImmuNe ALgorithm (CARDINAL) inspired by T-cell Immunity and Tolerance'

The role of T-cells within the immune system is to confirm and assess anomalous situations and then either respond to or tolerate the source of the effect. To illustrate how these mechanisms can be harnessed to solve real-world problems, we present the blueprint of a T-cell inspired algorithm for computer security worm detection. We show how the three central T-cell processes, namely T-cell maturation, differentiation and proliferation, naturally map into this domain and further illustrate how such an algorithm fits into a complete immune inspired computer security system and framework.