GPU acceleration of brain image proccessing

Durante los últimos años se ha venido demostrando el alto poder computacional que ofrecen las GPUs a la hora de resolver determinados problemas. Al mismo tiempo, existen campos en los que no es posible beneficiarse completamente de las mejoras conseguidas por los investigadores, debido principalmente a que los tiempos de ejecución de las aplicaciones llegan a ser extremadamente largos. Este es por ejemplo el caso del registro de imágenes en medicina. A pesar de que se han conseguido aceleraciones sobre el registro de imágenes, su uso en la práctica clínica es aún limitado. Entre otras cosas, esto se debe al rendimiento conseguido. Por lo tanto se plantea como objetivo de este proyecto, conseguir mejorar los tiempos de ejecución de una aplicación dedicada al resgitro de imágenes en medicina, con el fin de ayudar a aliviar este problema

GPU acceleration for statistical gene classification

The use of Bioinformatic tools in routine clinical diagnostics is still facing a number of issues. The more complex and advanced bioinformatic tools become, the more performance is required by the computing platforms. Unfortunately, the cost of parallel computing platforms is usually prohibitive for both public and small private medical practices. This paper presents a successful experience in using the parallel processing capabilities of Graphical Processing Units (GPU) to speed up bioinformatic tasks such as statistical classification of gene expression profiles. The results show that using open source CUDA programming libraries allows to obtain a significant increase in performances and therefore to shorten the gap between advanced bioinformatic tools and real medical practic

GPU Acceleration of Image Convolution using Spatially-varying Kernel

Image subtraction in astronomy is a tool for transient object discovery such as asteroids, extra-solar planets and supernovae. To match point spread functions (PSFs) between images of the same field taken at different times a convolution technique is used. Particularly suitable for large-scale images is a computationally intensive spatially-varying kernel. The underlying algorithm is inherently massively parallel due to unique kernel generation at every pixel location. The spatially-varying kernel cannot be efficiently computed through the Convolution Theorem, and thus does not lend itself to acceleration by Fast Fourier Transform (FFT). This work presents results of accelerated implementation of the spatially-varying kernel image convolution in multi-cores with OpenMP and graphic processing units (GPUs). Typical speedups over ANSI-C were a factor of 50 and a factor of 1000 over the initial IDL implementation, demonstrating that the techniques are a practical and high impact path to terabyte-per-night image pipelines and petascale processing.Comment: 4 pages. Accepted to IEEE-ICIP 201

GIFT: A Real-time and Scalable 3D Shape Search Engine

Projective analysis is an important solution for 3D shape retrieval, since human visual perceptions of 3D shapes rely on various 2D observations from different view points. Although multiple informative and discriminative views are utilized, most projection-based retrieval systems suffer from heavy computational cost, thus cannot satisfy the basic requirement of scalability for search engines. In this paper, we present a real-time 3D shape search engine based on the projective images of 3D shapes. The real-time property of our search engine results from the following aspects: (1) efficient projection and view feature extraction using GPU acceleration; (2) the first inverted file, referred as F-IF, is utilized to speed up the procedure of multi-view matching; (3) the second inverted file (S-IF), which captures a local distribution of 3D shapes in the feature manifold, is adopted for efficient context-based re-ranking. As a result, for each query the retrieval task can be finished within one second despite the necessary cost of IO overhead. We name the proposed 3D shape search engine, which combines GPU acceleration and Inverted File Twice, as GIFT. Besides its high efficiency, GIFT also outperforms the state-of-the-art methods significantly in retrieval accuracy on various shape benchmarks and competitions.Comment: accepted by CVPR16, achieved the first place in Shrec2016 competition: Large-Scale 3D Shape Retrieval under the perturbed cas