Counting Constraint Satisfaction Problems

This chapter surveys counting Constraint Satisfaction Problems (counting CSPs, or #CSPs) and their computational complexity. It aims to provide an introduction to the main concepts and techniques, and present a representative selection of results and open problems. It does not cover holants, which are the subject of a separate chapter

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Complex event types for agent-based simulation

This thesis presents a novel formal modelling language, complex event types (CETs), to describe behaviours in agent-based simulations. CETs are able to describe behaviours at any computationally represented level of abstraction. Behaviours can be specified both in terms of the state transition rules of the agent-based model that generate them and in terms of the state transition structures themselves. Based on CETs, novel computational statistical methods are introduced which allow statistical dependencies between behaviours at different levels to be established. Different dependencies formalise different probabilistic causal relations and Complex Systems constructs such as ‘emergence’ and ‘autopoiesis’. Explicit links are also made between the different types of CET inter-dependency and the theoretical assumptions they represent. With the novel computational statistical methods, three categories of model can be validated and discovered: (i) inter-level models, which define probabilistic dependencies between behaviours at different levels; (ii) multi-level models, which define the set of simulations for which an inter-level model holds; (iii) inferred predictive models, which define latent relationships between behaviours at different levels. The CET modelling language and computational statistical methods are then applied to a novel agent-based model of Colonic Cancer to demonstrate their applicability to Complex Systems sciences such as Systems Biology. This proof of principle model provides a framework for further development of a detailed integrative model of the system, which can progressively incorporate biological data from different levels and scales as these become available

NASA/ASEE Summer Faculty Fellowship Program, 1990, Volume 1

The 1990 Johnson Space Center (JSC) NASA/American Society for Engineering Education (ASEE) Summer Faculty Fellowship Program was conducted by the University of Houston-University Park and JSC. A compilation of the final reports on the research projects are presented. The topics covered include: the Space Station; the Space Shuttle; exobiology; cell biology; culture techniques; control systems design; laser induced fluorescence; spacecraft reliability analysis; reduced gravity; biotechnology; microgravity applications; regenerative life support systems; imaging techniques; cardiovascular system; physiological effects; extravehicular mobility units; mathematical models; bioreactors; computerized simulation; microgravity simulation; and dynamic structural analysis

Optimization of high-throughput real-time processes in physics reconstruction

La presente tesis se ha desarrollado en colaboración entre la Universidad de Sevilla y la Organización Europea para la Investigación Nuclear, CERN. El detector LHCb es uno de los cuatro grandes detectores situados en el Gran Colisionador de Hadrones, LHC. En LHCb, se colisionan partículas a altas energías para comprender la diferencia existente entre la materia y la antimateria. Debido a la cantidad ingente de datos generada por el detector, es necesario realizar un filtrado de datos en tiempo real, fundamentado en los conocimientos actuales recogidos en el Modelo Estándar de física de partículas. El filtrado, también conocido como High Level Trigger, deberá procesar un throughput de 40 Tb/s de datos, y realizar un filtrado de aproximadamente 1 000:1, reduciendo el throughput a unos 40 Gb/s de salida, que se almacenan para posterior análisis. El proceso del High Level Trigger se subdivide a su vez en dos etapas: High Level Trigger 1 (HLT1) y High Level Trigger 2 (HLT2). El HLT1 transcurre en tiempo real, y realiza una reducción de datos de aproximadamente 30:1. El HLT1 consiste en una serie de procesos software que reconstruyen lo que ha sucedido en la colisión de partículas. En la reconstrucción del HLT1 únicamente se analizan las trayectorias de las partículas producidas fruto de la colisión, en un problema conocido como reconstrucción de trazas, para dictaminar el interés de las colisiones. Por contra, el proceso HLT2 es más fino, requiriendo más tiempo en realizarse y reconstruyendo todos los subdetectores que componen LHCb. Hacia 2020, el detector LHCb, así como todos los componentes del sistema de adquisici´on de datos, serán actualizados acorde a los últimos desarrollos técnicos. Como parte del sistema de adquisición de datos, los servidores que procesan HLT1 y HLT2 también sufrirán una actualización. Al mismo tiempo, el acelerador LHC será también actualizado, de manera que la cantidad de datos generada en cada cruce de grupo de partículas aumentare en aproxidamente 5 veces la actual. Debido a las actualizaciones tanto del acelerador como del detector, se prevé que la cantidad de datos que deberá procesar el HLT en su totalidad sea unas 40 veces mayor a la actual. La previsión de la escalabilidad del software actual a 2020 subestim´ó los recursos necesarios para hacer frente al incremento en throughput. Esto produjo que se pusiera en marcha un estudio de todos los algoritmos tanto del HLT1 como del HLT2, así como una actualización del código a nuevos estándares, para mejorar su rendimiento y ser capaz de procesar la cantidad de datos esperada. En esta tesis, se exploran varios algoritmos de la reconstrucción de LHCb. El problema de reconstrucción de trazas se analiza en profundidad y se proponen nuevos algoritmos para su resolución. Ya que los problemas analizados exhiben un paralelismo masivo, estos algoritmos se implementan en lenguajes especializados para tarjetas gráficas modernas (GPUs), dada su arquitectura inherentemente paralela. En este trabajo se dise ˜nan dos algoritmos de reconstrucción de trazas. Además, se diseñan adicionalmente cuatro algoritmos de decodificación y un algoritmo de clustering, problemas también encontrados en el HLT1. Por otra parte, se diseña un algoritmo para el filtrado de Kalman, que puede ser utilizado en ambas etapas. Los algoritmos desarrollados cumplen con los requisitos esperados por la colaboración LHCb para el año 2020. Para poder ejecutar los algoritmos eficientemente en tarjetas gráficas, se desarrolla un framework especializado para GPUs, que permite la ejecución paralela de secuencias de reconstrucción en GPUs. Combinando los algoritmos desarrollados con el framework, se completa una secuencia de ejecución que asienta las bases para un HLT1 ejecutable en GPU. Durante la investigación llevada a cabo en esta tesis, y gracias a los desarrollos arriba mencionados y a la colaboración de un pequeño equipo de personas coordinado por el autor, se completa un HLT1 ejecutable en GPUs. El rendimiento obtenido en GPUs, producto de esta tesis, permite hacer frente al reto de ejecutar una secuencia de reconstrucción en tiempo real, bajo las condiciones actualizadas de LHCb previstas para 2020. As´ı mismo, se completa por primera vez para cualquier experimento del LHC un High Level Trigger que se ejecuta únicamente en GPUs. Finalmente, se detallan varias posibles configuraciones para incluir tarjetas gr´aficas en el sistema de adquisición de datos de LHCb.The current thesis has been developed in collaboration between Universidad de Sevilla and the European Organization for Nuclear Research, CERN. The LHCb detector is one of four big detectors placed alongside the Large Hadron Collider, LHC. In LHCb, particles are collided at high energies in order to understand the difference between matter and antimatter. Due to the massive quantity of data generated by the detector, it is necessary to filter data in real-time. The filtering, also known as High Level Trigger, processes a throughput of 40 Tb/s of data and performs a selection of approximately 1 000:1. The throughput is thus reduced to roughly 40 Gb/s of data output, which is then stored for posterior analysis. The High Level Trigger process is subdivided into two stages: High Level Trigger 1 (HLT1) and High Level Trigger 2 (HLT2). HLT1 occurs in real-time, and yields a reduction of data of approximately 30:1. HLT1 consists in a series of software processes that reconstruct particle collisions. The HLT1 reconstruction only analyzes the trajectories of particles produced at the collision, solving a problem known as track reconstruction, that determines whether the collision data is kept or discarded. In contrast, HLT2 is a finer process, which requires more time to execute and reconstructs all subdetectors composing LHCb. Towards 2020, the LHCb detector and all the components composing the data acquisition system will be upgraded. As part of the data acquisition system, the servers that process HLT1 and HLT2 will also be upgraded. In addition, the LHC accelerator will also be updated, increasing the data generated in every bunch crossing by roughly 5 times. Due to the accelerator and detector upgrades, the amount of data that the HLT will require to process is expected to increase by 40 times. The foreseen scalability of the software through 2020 underestimated the required resources to face the increase in data throughput. As a consequence, studies of all algorithms composing HLT1 and HLT2 and code modernizations were carried out, in order to obtain a better performance and increase the processing capability of the foreseen hardware resources in the upgrade. In this thesis, several algorithms of the LHCb recontruction are explored. The track reconstruction problem is analyzed in depth, and new algorithms are proposed. Since the analyzed problems are massively parallel, these algorithms are implemented in specialized languages for modern graphics cards (GPUs), due to their inherently parallel architecture. From this work stem two algorithm designs. Furthermore, four additional decoding algorithms and a clustering algorithms have been designed and implemented, which are also part of HLT1. Apart from that, an parallel Kalman filter algorithm has been designed and implemented, which can be used in both HLT stages. The developed algorithms satisfy the requirements of the LHCb collaboration for the LHCb upgrade. In order to execute the algorithms efficiently on GPUs, a software framework specialized for GPUs is developed, which allows executing GPU reconstruction sequences in parallel. Combining the developed algorithms with the framework, an execution sequence is completed as the foundations of a GPU HLT1. During the research carried out in this thesis, the aforementioned developments and a small group of collaborators coordinated by the author lead to the completion of a full GPU HLT1 sequence. The performance obtained on GPUs allows executing a reconstruction sequence in real-time, under LHCb upgrade conditions. The developed GPU HLT1 constitutes the first GPU high level trigger ever developed for an LHC experiment. Finally, various possible realizations of the GPU HLT1 to integrate in a production GPU-equipped data acquisition system are detailed