Algorithmic Techniques in Gene Expression Processing. From Imputation to Visualization

The amount of biological data has grown exponentially in recent decades. Modern biotechnologies, such as microarrays and next-generation sequencing, are capable to produce massive amounts of biomedical data in a single experiment. As the amount of the data is rapidly growing there is an urgent need for reliable computational methods for analyzing and visualizing it. This thesis addresses this need by studying how to efficiently and reliably analyze and visualize high-dimensional data, especially that obtained from gene expression microarray experiments. First, we will study the ways to improve the quality of microarray data by replacing (imputing) the missing data entries with the estimated values for these entries. Missing value imputation is a method which is commonly used to make the original incomplete data complete, thus making it easier to be analyzed with statistical and computational methods. Our novel approach was to use curated external biological information as a guide for the missing value imputation. Secondly, we studied the effect of missing value imputation on the downstream data analysis methods like clustering. We compared multiple recent imputation algorithms against 8 publicly available microarray data sets. It was observed that the missing value imputation indeed is a rational way to improve the quality of biological data. The research revealed differences between the clustering results obtained with different imputation methods. On most data sets, the simple and fast k-NN imputation was good enough, but there were also needs for more advanced imputation methods, such as Bayesian Principal Component Algorithm (BPCA). Finally, we studied the visualization of biological network data. Biological interaction networks are examples of the outcome of multiple biological experiments such as using the gene microarray techniques. Such networks are typically very large and highly connected, thus there is a need for fast algorithms for producing visually pleasant layouts. A computationally efficient way to produce layouts of large biological interaction networks was developed. The algorithm uses multilevel optimization within the regular force directed graph layout algorithm.Siirretty Doriast

Design Space Exploration for MPSoC Architectures

Multiprocessor system-on-chip (MPSoC) designs utilize the available technology and communication architectures to meet the requirements of the upcoming applications. In MPSoC, the communication platform is both the key enabler, as well as the key differentiator for realizing efficient MPSoCs. It provides product differentiation to meet a diverse, multi-dimensional set of design constraints, including performance, power, energy, reconfigurability, scalability, cost, reliability and time-to-market. The communication resources of a single interconnection platform cannot be fully utilized by all kind of applications, such as the availability of higher communication bandwidth for computation but not data intensive applications is often unfeasible in the practical implementation. This thesis aims to perform the architecture-level design space exploration towards efficient and scalable resource utilization for MPSoC communication architecture. In order to meet the performance requirements within the design constraints, careful selection of MPSoC communication platform, resource aware partitioning and mapping of the application play important role. To enhance the utilization of communication resources, variety of techniques such as resource sharing, multicast to avoid re-transmission of identical data, and adaptive routing can be used. For implementation, these techniques should be customized according to the platform architecture. To address the resource utilization of MPSoC communication platforms, variety of architectures with different design parameters and performance levels, namely Segmented bus (SegBus), Network-on-Chip (NoC) and Three-Dimensional NoC (3D-NoC), are selected. Average packet latency and power consumption are the evaluation parameters for the proposed techniques. In conventional computing architectures, fault on a component makes the connected fault-free components inoperative. Resource sharing approach can utilize the fault-free components to retain the system performance by reducing the impact of faults. Design space exploration also guides to narrow down the selection of MPSoC architecture, which can meet the performance requirements with design constraints.Siirretty Doriast

Proceedings of the Second International Mobile Satellite Conference (IMSC 1990)

Presented here are the proceedings of the Second International Mobile Satellite Conference (IMSC), held June 17-20, 1990 in Ottawa, Canada. Topics covered include future mobile satellite communications concepts, aeronautical applications, modulation and coding, propagation and experimental systems, mobile terminal equipment, network architecture and control, regulatory and policy considerations, vehicle antennas, and speech compression

Thermal-Aware Networked Many-Core Systems

Advancements in IC processing technology has led to the innovation and growth happening in the consumer electronics sector and the evolution of the IT infrastructure supporting this exponential growth. One of the most difficult obstacles to this growth is the removal of large amount of heatgenerated by the processing and communicating nodes on the system. The scaling down of technology and the increase in power density is posing a direct and consequential effect on the rise in temperature. This has resulted in the increase in cooling budgets, and affects both the life-time reliability and performance of the system. Hence, reducing on-chip temperatures has become a major design concern for modern microprocessors. This dissertation addresses the thermal challenges at different levels for both 2D planer and 3D stacked systems. It proposes a self-timed thermal monitoring strategy based on the liberal use of on-chip thermal sensors. This makes use of noise variation tolerant and leakage current based thermal sensing for monitoring purposes. In order to study thermal management issues from early design stages, accurate thermal modeling and analysis at design time is essential. In this regard, spatial temperature profile of the global Cu nanowire for on-chip interconnects has been analyzed. It presents a 3D thermal model of a multicore system in order to investigate the effects of hotspots and the placement of silicon die layers, on the thermal performance of a modern ip-chip package. For a 3D stacked system, the primary design goal is to maximise the performance within the given power and thermal envelopes. Hence, a thermally efficient routing strategy for 3D NoC-Bus hybrid architectures has been proposed to mitigate on-chip temperatures by herding most of the switching activity to the die which is closer to heat sink. Finally, an exploration of various thermal-aware placement approaches for both the 2D and 3D stacked systems has been presented. Various thermal models have been developed and thermal control metrics have been extracted. An efficient thermal-aware application mapping algorithm for a 2D NoC has been presented. It has been shown that the proposed mapping algorithm reduces the effective area reeling under high temperatures when compared to the state of the art.Siirretty Doriast

An integrated study of earth resources in the state of California using remote sensing techniques

The author has identified the following significant results. A weighted stratified double sample design using hardcopy LANDSAT-1 and ground data was utilized in developmental studies for snow water content estimation. Study results gave a correlation coefficient of 0.80 between LANDSAT sample units estimates of snow water content and ground subsamples. A basin snow water content estimate allowable error was given as 1.00 percent at the 99 percent confidence level with the same budget level utilized in conventional snow surveys. Several evapotranspiration estimation models were selected for efficient application at each level of data to be sampled. An area estimation procedure for impervious surface types of differing impermeability adjacent to stream channels was developed. This technique employs a double sample of 1:125,000 color infrared hightflight transparency data with ground or large scale photography

Data systems elements technology assessment and system specifications, issue no. 2

The ability to satisfy the objectives of future NASA Office of Applications programs is dependent on technology advances in a number of areas of data systems. The hardware and software technology of end-to-end systems (data processing elements through ground processing, dissemination, and presentation) are examined in terms of state of the art, trends, and projected developments in the 1980 to 1985 timeframe. Capability is considered in terms of elements that are either commercially available or that can be implemented from commercially available components with minimal development

Actas do 10º Encontro Português de Computação Gráfica

Actas do 10º Encontro Portugês de Computação Gráfica, Lisboa, 1-3 de Outubro de 2001A investigação, o desenvolvimento e o ensino na área da Computação Gráfica constituem, em Portugal, uma realidade positiva e de largas tradições. O Encontro Português de Computação Gráfica (EPCG), realizado no âmbito das actividades do Grupo Português de Computação Gráfica (GPCG), tem permitido reunir regularmente, desde o 1º EPCG realizado também em Lisboa, mas no já longínquo mês de Julho de 1988, todos os que trabalham nesta área abrangente e com inúmeras aplicações. Pela primeira vez no historial destes Encontros, o 10º EPCG foi organizado em ligação estreita com as comunidades do Processamento de Imagem e da Visão por Computador, através da Associação Portuguesa de Reconhecimento de Padrões (APRP), salientando-se, assim, a acrescida colaboração, e a convergência, entre essas duas áreas e a Computação Gráfica. Este é o livro de actas deste 10º EPCG.INSATUniWebIcep PortugalMicrografAutodes

Pattern Recognition

Pattern recognition is a very wide research field. It involves factors as diverse as sensors, feature extraction, pattern classification, decision fusion, applications and others. The signals processed are commonly one, two or three dimensional, the processing is done in real- time or takes hours and days, some systems look for one narrow object class, others search huge databases for entries with at least a small amount of similarity. No single person can claim expertise across the whole field, which develops rapidly, updates its paradigms and comprehends several philosophical approaches. This book reflects this diversity by presenting a selection of recent developments within the area of pattern recognition and related fields. It covers theoretical advances in classification and feature extraction as well as application-oriented works. Authors of these 25 works present and advocate recent achievements of their research related to the field of pattern recognition

The Telecommunications and Data Acquisition Report

This publication reports on developments in programs managed by JPL's office of Telecommunications and Data Acquisition (TDA). In space communications, radio navigation, radio science, and ground based radio astronomy, it reports on activities of the Deep Space Network (DSN) and its associated Ground Communications Facility (GCF) in planning, in supporting research and technology, in implementation and in operations. In geodynamics, the publication reports on the application of radio interferometry at microwave frequencies for geodynamic measurements. This publication also reports on implementation and operations for searching the microwave spectrum