Fine-grained parallelization of fitness functions in bioinformatics optimization problems: gene selection for cancer classification and biclustering of gene expression data

ANTECEDENTES: las metaheurísticas se utilizan ampliamente para resolver grandes problemas de optimización combinatoria en bioinformática debido al enorme conjunto de posibles soluciones. Dos problemas representativos son la selección de genes para la clasificación del cáncer y el agrupamiento de los datos de expresión génica. En la mayoría de los casos, estas metaheurísticas, así como otras técnicas no lineales, aplican una función de adecuación a cada solución posible con una población de tamaño limitado, y ese paso involucra latencias más altas que otras partes de los algoritmos, lo cual es la razón por la cual el tiempo de ejecución de las aplicaciones dependerá principalmente del tiempo de ejecución de la función de aptitud. Además, es habitual encontrar formulaciones aritméticas de punto flotante para las funciones de fitness. De esta manera, una paralelización cuidadosa de estas funciones utilizando la tecnología de hardware reconfigurable acelerará el cálculo, especialmente si se aplican en paralelo a varias soluciones de la población. RESULTADOS: una paralelización de grano fino de dos funciones de aptitud de punto flotante de diferentes complejidades y características involucradas en el biclustering de los datos de expresión génica y la selección de genes para la clasificación del cáncer permitió obtener mayores aceleraciones y cómputos de potencia reducida con respecto a los microprocesadores habituales. CONCLUSIONES: Los resultados muestran mejores rendimientos utilizando tecnología de hardware reconfigurable en lugar de los microprocesadores habituales, en términos de tiempo de consumo y consumo de energía, no solo debido a la paralelización de las operaciones aritméticas, sino también gracias a la evaluación de aptitud concurrente para varios individuos de la población en La metaheurística. Esta es una buena base para crear soluciones aceleradas y de bajo consumo de energía para escenarios informáticos intensivos.BACKGROUND: Metaheuristics are widely used to solve large combinatorial optimization problems in bioinformatics because of the huge set of possible solutions. Two representative problems are gene selection for cancer classification and biclustering of gene expression data. In most cases, these metaheuristics, as well as other non-linear techniques, apply a fitness function to each possible solution with a size-limited population, and that step involves higher latencies than other parts of the algorithms, which is the reason why the execution time of the applications will mainly depend on the execution time of the fitness function. In addition, it is usual to find floating-point arithmetic formulations for the fitness functions. This way, a careful parallelization of these functions using the reconfigurable hardware technology will accelerate the computation, specially if they are applied in parallel to several solutions of the population. RESULTS: A fine-grained parallelization of two floating-point fitness functions of different complexities and features involved in biclustering of gene expression data and gene selection for cancer classification allowed for obtaining higher speedups and power-reduced computation with regard to usual microprocessors. CONCLUSIONS: The results show better performances using reconfigurable hardware technology instead of usual microprocessors, in computing time and power consumption terms, not only because of the parallelization of the arithmetic operations, but also thanks to the concurrent fitness evaluation for several individuals of the population in the metaheuristic. This is a good basis for building accelerated and low-energy solutions for intensive computing scenarios.• Ministerio de Economía y Competitividad y Fondos FEDER. Contrato TIN2012-30685 (I+D+i) • Gobierno de Extremadura. Ayuda GR15011 para grupos TIC015 • CONICYT/FONDECYT/REGULAR/1160455. Beca para Ricardo Soto Guzmán • CONICYT/FONDECYT/REGULAR/1140897. Beca para Broderick CrawfordpeerReviewe

SuperCam, a 64-pixel heterodyne imaging array for the 870 micron atmospheric window

We report on the development of SuperCam, a 64 pixel, superheterodyne camera designed for operation in the astrophysically important 870 micron atmospheric window. SuperCam will be used to answer fundamental questions about the physics and chemistry of molecular clouds in the Galaxy and their direct relation to star and planet formation. The advent of such a system will provide an order of magnitude increase in mapping speed over what is now available and revolutionize how observational astronomy is performed in this important wavelength regime. Unlike the situation with bolometric detectors, heterodyne receiver systems are coherent, retaining information about both the amplitude and phase of the incident photon stream. From this information a high resolution spectrum of the incident light can be obtained without multiplexing. SuperCam will be constructed by stacking eight, 1x8 rows of fixed tuned, SIS mixers. The IF output of each mixer will be connected to a low-noise, broadband MMIC amplifier integrated into the mixer block. The instantaneous IF bandwidth of each pixel will be ~2 GHz, with a center frequency of 5 GHz. A spectrum of the central 500 MHz of each IF band will be provided by the array spectrometer. Local oscillator power is provided by a frequency multiplier whose output is divided between the pixels by using a matrix of waveguide power dividers. The mixer array will be cooled to 4K by a closed-cycle refrigeration system. SuperCam will reside at the Cassegrain focus of the 10m Heinrich Hertz telescope (HHT). A prototype single row of the array will be tested on the HHT in 2006, with the first engineering run of the full array in late 2007. The array is designed and constructed so that it may be readily scaled to higher frequencies.Comment: 12 pages, 14 figures, to be published in the Proceedings of SPIE Vol. 6275, "Astronomical Telescopes and Instrumentation, Millimeter and Submillimeter Detectors and Instrumentation for Astronomy III

Design of Timer for Application in ATM using FPGA and VHDL

A watchdog timer is a computer hardware timing device that triggers a system reset if the main program, due to some fault condition, such as a hang, neglects to regularly service the watchdog (writing a “service pulse” to it, also referred to as “petting the dog”). The intention is to bring the system back from the hung state into normal operation. Such a timer has got various important applications, one of them being in ATMs (Automated Teller Machine) which we have studied and designed in our project

Hardware acceleration of photon mapping

PhD ThesisThe quest for realism in computer-generated graphics has yielded a range of algorithmic techniques, the most advanced of which are capable of rendering images at close to photorealistic quality. Due to the realism available, it is now commonplace that computer graphics are used in the creation of movie sequences, architectural renderings, medical imagery and product visualisations. This work concentrates on the photon mapping algorithm [1, 2], a physically based global illumination rendering algorithm. Photon mapping excels in producing highly realistic, physically accurate images. A drawback to photon mapping however is its rendering times, which can be significantly longer than other, albeit less realistic, algorithms. Not surprisingly, this increase in execution time is associated with a high computational cost. This computation is usually performed using the general purpose central processing unit (CPU) of a personal computer (PC), with the algorithm implemented as a software routine. Other options available for processing these algorithms include desktop PC graphics processing units (GPUs) and custom designed acceleration hardware devices. GPUs tend to be efficient when dealing with less realistic rendering solutions such as rasterisation, however with their recent drive towards increased programmability they can also be used to process more realistic algorithms. A drawback to the use of GPUs is that these algorithms often have to be reworked to make optimal use of the limited resources available. There are very few custom hardware devices available for acceleration of the photon mapping algorithm. Ray-tracing is the predecessor to photon mapping, and although not capable of producing the same physical accuracy and therefore realism, there are similarities between the algorithms. There have been several hardware prototypes, and at least one commercial offering, created with the goal of accelerating ray-trace rendering [3]. However, properties making many of these proposals suitable for the acceleration of ray-tracing are not shared by photon mapping. There are even fewer proposals for acceleration of the additional functions found only in photon mapping. All of these approaches to algorithm acceleration offer limited scalability. GPUs are inherently difficult to scale, while many of the custom hardware devices available thus far make use of large processing elements and complex acceleration data structures. In this work we make use of three novel approaches in the design of highly scalable specialised hardware structures for the acceleration of the photon mapping algorithm. Increased scalability is gained through: • The use of a brute-force approach in place of the commonly used smart approach, thus eliminating much data pre-processing, complex data structures and large processing units often required. • The use of Logarithmic Number System (LNS) arithmetic computation, which facilitates a reduction in processing area requirement. • A novel redesign of the photon inclusion test, used within the photon search method of the photon mapping algorithm. This allows an intelligent memory structure to be used for the search. The design uses two hardware structures, both of which accelerate one core rendering function. Renderings produced using field programmable gate array (FPGA) based prototypes are presented, along with details of 90nm synthesised versions of the designs which show that close to an orderof- magnitude speedup over a software implementation is possible. Due to the scalable nature of the design, it is likely that any advantage can be maintained in the face of improving processor speeds. Significantly, due to the brute-force approach adopted, it is possible to eliminate an often-used software acceleration method. This means that the device can interface almost directly to a frontend modelling package, minimising much of the pre-processing required by most other proposals

Accelerating Gauss-Newton filters on FPGA's

Includes bibliographical references (leaves 123-128).Radar tracking filters are generally computationally expensive, involving the manipulation of large matrices and deeply nested loops. In addition, they must generally work in real-time to be of any use. The now-common Kalman Filter was developed in the 1960's specifically for the purposes of lowering its computational burden, so that it could be implemented using the limited computational resources of the time. However, with the exponential increases in computing power since then, it is now possible to reconsider more heavy-weight, robust algorithms such as the original nonrecursive Gauss-Newton filter on which the Kalman filter is based. This dissertation investigates the acceleration of such a filter using FPGA technology, making use of custom, reduced-precision number formats