Parallel bio-inspired methods for model optimization and pattern recognition

Nature based computational models are usually inherently parallel. The collaborative intelligence in those models emerges from the simultaneous instruction processing by simple independent units (neurons, ants, swarm members, etc...). This dissertation investigates the benefits of such parallel models in terms of efficiency and accuracy. First, the viability of a parallel implementation of bio-inspired metaheuristics for function optimization on consumer-level graphic cards is studied in detail. Then, in an effort to expose those parallel methods to the research community, the metaheuristic implementations were abstracted and grouped in an open source parameter/function optimization library libCudaOptimize. The library was verified against a well known benchmark for mathematical function minimization, and showed significant gains in both execution time and minimization accuracy. Crossing more into the application side, a parallel model of the human neocortex was developed. This model is able to detect, classify, and predict patterns in time-series data in an unsupervised way. Finally, libCudaOptimize was used to find the best parameters for this neocortex model, adapting it to gesture recognition within publicly available datasets

METADOCK: A parallel metaheuristic schema for virtual screening methods

Virtual screening through molecular docking can be translated into an optimization problem, which can be tackled with metaheuristic methods. The interaction between two chemical compounds (typically a protein, enzyme or receptor, and a small molecule, or ligand) is calculated by using highly computationally demanding scoring functions that are computed at several binding spots located throughout the protein surface. This paper introduces METADOCK, a novel molecular docking methodology based on parameterized and parallel metaheuristics and designed to leverage heterogeneous computers based on heterogeneous architectures. The application decides the optimization technique at running time by setting a configuration schema. Our proposed solution finds a good workload balance via dynamic assignment of jobs to heterogeneous resources which perform independent metaheuristic executions when computing different molecular interactions required by the scoring functions in use. A cooperative scheduling of jobs optimizes the quality of the solution and the overall performance of the simulation, so opening a new path for further developments of virtual screening methods on high-performance contemporary heterogeneous platforms.Ingeniería, Industria y Construcció

GeNN: a code generation framework for accelerated brain simulations

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/

Radial Basis Functions: Biomedical Applications and Parallelization

Radial basis function (RBF) is a real-valued function whose values depend only on the distances between an interpolation point and a set of user-specified points called centers. RBF interpolation is one of the primary methods to reconstruct functions from multi-dimensional scattered data. Its abilities to generalize arbitrary space dimensions and to provide spectral accuracy have made it particularly popular in different application areas, including but not limited to: finding numerical solutions of partial differential equations (PDEs), image processing, computer vision and graphics, deep learning and neural networks, etc. The present thesis discusses three applications of RBF interpolation in biomedical engineering areas: (1) Calcium dynamics modeling, in which we numerically solve a set of PDEs by using meshless numerical methods and RBF-based interpolation techniques; (2) Image restoration and transformation, where an image is restored from its triangular mesh representation or transformed under translation, rotation, and scaling, etc. from its original form; (3) Porous structure design, in which the RBF interpolation used to reconstruct a 3D volume containing porous structures from a set of regularly or randomly placed points inside a user-provided surface shape. All these three applications have been investigated and their effectiveness has been supported with numerous experimental results. In particular, we innovatively utilize anisotropic distance metrics to define the distance in RBF interpolation and apply them to the aforementioned second and third applications, which show significant improvement in preserving image features or capturing connected porous structures over the isotropic distance-based RBF method. Beside the algorithm designs and their applications in biomedical areas, we also explore several common parallelization techniques (including OpenMP and CUDA-based GPU programming) to accelerate the performance of the present algorithms. In particular, we analyze how parallel programming can help RBF interpolation to speed up the meshless PDE solver as well as image processing. While RBF has been widely used in various science and engineering fields, the current thesis is expected to trigger some more interest from computational scientists or students into this fast-growing area and specifically apply these techniques to biomedical problems such as the ones investigated in the present work

Neuromorphic Learning Systems for Supervised and Unsupervised Applications

The advancements in high performance computing (HPC) have enabled the large-scale implementation of neuromorphic learning models and pushed the research on computational intelligence into a new era. Those bio-inspired models are constructed on top of unified building blocks, i.e. neurons, and have revealed potentials for learning of complex information. Two major challenges remain in neuromorphic computing. Firstly, sophisticated structuring methods are needed to determine the connectivity of the neurons in order to model various problems accurately. Secondly, the models need to adapt to non-traditional architectures for improved computation speed and energy efficiency. In this thesis, we address these two problems and apply our techniques to different cognitive applications. This thesis first presents the self-structured confabulation network for anomaly detection. Among the machine learning applications, unsupervised detection of the anomalous streams is especially challenging because it requires both detection accuracy and real-time performance. Designing a computing framework that harnesses the growing computing power of the multicore systems while maintaining high sensitivity and specificity to the anomalies is an urgent research need. We present AnRAD (Anomaly Recognition And Detection), a bio-inspired detection framework that performs probabilistic inferences. We leverage the mutual information between the features and develop a self-structuring procedure that learns a succinct confabulation network from the unlabeled data. This network is capable of fast incremental learning, which continuously refines the knowledge base from the data streams. Compared to several existing anomaly detection methods, the proposed approach provides competitive detection accuracy as well as the insight to reason the decision making. Furthermore, we exploit the massive parallel structure of the AnRAD framework. Our implementation of the recall algorithms on the graphic processing unit (GPU) and the Xeon Phi co-processor both obtain substantial speedups over the sequential implementation on general-purpose microprocessor (GPP). The implementation enables real-time service to concurrent data streams with diversified contexts, and can be applied to large problems with multiple local patterns. Experimental results demonstrate high computing performance and memory efficiency. For vehicle abnormal behavior detection, the framework is able to monitor up to 16000 vehicles and their interactions in real-time with a single commodity co-processor, and uses less than 0.2ms for each testing subject. While adapting our streaming anomaly detection model to mobile devices or unmanned systems, the key challenge is to deliver required performance under the stringent power constraint. To address the paradox between performance and power consumption, brain-inspired hardware, such as the IBM Neurosynaptic System, has been developed to enable low power implementation of neural models. As a follow-up to the AnRAD framework, we proposed to port the detection network to the TrueNorth architecture. Implementing inference based anomaly detection on a neurosynaptic processor is not straightforward due to hardware limitations. A design flow and the supporting component library are developed to flexibly map the learned detection networks to the neurosynaptic cores. Instead of the popular rate code, burst code is adopted in the design, which represents numerical value using the phase of a burst of spike trains. This does not only reduce the hardware complexity, but also increases the result\u27s accuracy. A Corelet library, NeoInfer-TN, is implemented for basic operations in burst code and two-phase pipelines are constructed based on the library components. The design can be configured for different tradeoffs between detection accuracy, hardware resource consumptions, throughput and energy. We evaluate the system using network intrusion detection data streams. The results show higher detection rate than some conventional approaches and real-time performance, with only 50mW power consumption. Overall, it achieves 10^8 operations per Joule. In addition to the modeling and implementation of unsupervised anomaly detection, we also investigate a supervised learning model based on neural networks and deep fragment embedding and apply it to text-image retrieval. The study aims at bridging the gap between image and natural language. It continues to improve the bidirectional retrieval performance across the modalities. Unlike existing works that target at single sentence densely describing the image objects, we elevate the topic to associating deep image representations with noisy texts that are only loosely correlated. Based on text-image fragment embedding, our model employs a sequential configuration, connects two embedding stages together. The first stage learns the relevancy of the text fragments, and the second stage uses the filtered output from the first one to improve the matching results. The model also integrates multiple convolutional neural networks (CNN) to construct the image fragments, in which rich context information such as human faces can be extracted to increase the alignment accuracy. The proposed method is evaluated with both synthetic dataset and real-world dataset collected from picture news website. The results show up to 50% ranking performance improvement over the comparison models

Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.This work is jointly supported by the FundaciónSéneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants 15290/PI/2010 and 18946/JLI/13, by the Spanish MEC and European Commission FEDER under grant with reference TEC2012-37945-C02-02 and TIN2012-31345, by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). We also thank NVIDIA for hardware donation within UCAM GPU educational and research centers.Ingeniería, Industria y Construcció

A General Framework for Accelerating Swarm Intelligence Algorithms on FPGAs, GPUs and Multi-core CPUs

Swarm intelligence algorithms (SIAs) have demonstrated excellent performance when solving optimization problems including many real-world problems. However, because of their expensive computational cost for some complex problems, SIAs need to be accelerated effectively for better performance. This paper presents a high-performance general framework to accelerate SIAs (FASI). Different from the previous work which accelerate SIAs through enhancing the parallelization only, FASI considers both the memory architectures of hardware platforms and the dataflow of SIAs, and it reschedules the framework of SIAs as a converged dataflow to improve the memory access efficiency. FASI achieves higher acceleration ability by matching the algorithm framework to the hardware architectures. We also design deep optimized structures of the parallelization and convergence of FASI based on the characteristics of specific hardware platforms. We take the quantum behaved particle swarm optimization algorithm (QPSO) as a case to evaluate FASI. The results show that FASI improves the throughput of SIAs and provides better performance through optimizing the hardware implementations. In our experiments, FASI achieves a maximum of 290.7Mbit/s throughput which is higher than several existing systems, and FASI on FPGAs achieves a better speedup than that on GPUs and multi-core CPUs. FASI is up to 123 times and not less than 1.45 times faster in terms of optimization time on Xilinx Kintex Ultrascale xcku040 when compares to Intel Core i7-6700 CPU/ NVIDIA GTX1080 GPU. Finally, we compare the differences of deploying FASI on hardware platforms and provide some guidelines for promoting the acceleration performance according to the hardware architectures

Real time motion estimation using a neural architecture implemented on GPUs

This work describes a neural network based architecture that represents and estimates object motion in videos. This architecture addresses multiple computer vision tasks such as image segmentation, object representation or characterization, motion analysis and tracking. The use of a neural network architecture allows for the simultaneous estimation of global and local motion and the representation of deformable objects. This architecture also avoids the problem of finding corresponding features while tracking moving objects. Due to the parallel nature of neural networks, the architecture has been implemented on GPUs that allows the system to meet a set of requirements such as: time constraints management, robustness, high processing speed and re-configurability. Experiments are presented that demonstrate the validity of our architecture to solve problems of mobile agents tracking and motion analysis.This work was partially funded by the Spanish Government DPI2013-40534-R grant and Valencian Government GV/2013/005 grant

Fully automatized parallel segmentation of the optic disc in retinal fundus images

This paper presents a fully automatic parallel software for the localization of the optic disc (OD) in retinal fundus color images. A new method has been implemented with the Graphics Processing Units (GPU) technology. Image edges are extracted using a new operator, called AGP-color segmentator. The resulting image is binarized with Hamadani’s technique and, finally, a new algorithm called Hough circle cloud is applied for the detection of the OD. The reliability of the tool has been tested with 129 images from the public databases DRIVE and DIARETDB1 obtaining an average accuracy of 99.6% and a mean consumed time per image of 7.6 and 16.3 s respectively. A comparison with several state-of-the-art algorithms shows that our algorithm represents a significant improvement in terms of accuracy and efficiency.Ministerio de Economía y Competitividad TIN2012-3743