980 research outputs found
JPEG steganography with particle swarm optimization accelerated by AVX
Digital steganography aims at hiding secret messages in digital data transmitted over insecure channels. The JPEG format is prevalent in digital communication, and images are often used as cover objects in digital steganography. Optimization methods can improve the properties of images with embedded secret but introduce additional computational complexity to their processing. AVX instructions available in modern CPUs are, in this work, used to accelerate data parallel operations that are part of image steganography with advanced optimizations.Web of Science328art. no. e544
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 TecnologÃa, 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.IngenierÃa, Industria y Construcció
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A Survey on Nature-Inspired Medical Image Analysis: A Step Further in Biomedical Data Integration
EvoX: A Distributed GPU-accelerated Library towards Scalable Evolutionary Computation
During the past decades, evolutionary computation (EC) has demonstrated
promising potential in solving various complex optimization problems of
relatively small scales. Nowadays, however, ongoing developments in modern
science and engineering are bringing increasingly grave challenges to the
conventional EC paradigm in terms of scalability. As problem scales increase,
on the one hand, the encoding spaces (i.e., dimensions of the decision vectors)
are intrinsically larger; on the other hand, EC algorithms often require
growing numbers of function evaluations (and probably larger population sizes
as well) to work properly. To meet such emerging challenges, not only does it
require delicate algorithm designs, but more importantly, a high-performance
computing framework is indispensable. Hence, we develop a distributed
GPU-accelerated algorithm library -- EvoX. First, we propose a generalized
workflow for implementing general EC algorithms. Second, we design a scalable
computing framework for running EC algorithms on distributed GPU devices.
Third, we provide user-friendly interfaces to both researchers and
practitioners for benchmark studies as well as extended real-world
applications. To comprehensively assess the performance of EvoX, we conduct a
series of experiments, including: (i) scalability test via numerical
optimization benchmarks with problem dimensions/population sizes up to
millions; (ii) acceleration test via a neuroevolution task with multiple GPU
nodes; (iii) extensibility demonstration via the application to reinforcement
learning tasks on the OpenAI Gym. The code of EvoX is available at
https://github.com/EMI-Group/EvoX
LEA: Beyond Evolutionary Algorithms via Learned Optimization Strategy
Evolutionary algorithms (EAs) have emerged as a powerful framework for
expensive black-box optimization. Obtaining better solutions with less
computational cost is essential and challenging for black-box optimization. The
most critical obstacle is figuring out how to effectively use the target task
information to form an efficient optimization strategy. However, current
methods are weak due to the poor representation of the optimization strategy
and the inefficient interaction between the optimization strategy and the
target task. To overcome the above limitations, we design a learned EA (LEA) to
realize the move from hand-designed optimization strategies to learned
optimization strategies, including not only hyperparameters but also update
rules. Unlike traditional EAs, LEA has high adaptability to the target task and
can obtain better solutions with less computational cost. LEA is also able to
effectively utilize the low-fidelity information of the target task to form an
efficient optimization strategy. The experimental results on one synthetic
case, CEC 2013, and two real-world cases show the advantages of learned
optimization strategies over human-designed baselines. In addition, LEA is
friendly to the acceleration provided by Graphics Processing Units and runs 102
times faster than unaccelerated EA when evolving 32 populations, each
containing 6400 individuals
Proceedings of the First PhD Symposium on Sustainable Ultrascale Computing Systems (NESUS PhD 2016)
Proceedings of the First PhD Symposium on Sustainable Ultrascale Computing Systems (NESUS PhD 2016) Timisoara, Romania. February 8-11, 2016.The PhD Symposium was a very good opportunity for the young researchers to share information and knowledge, to
present their current research, and to discuss topics with other students in order to look for synergies and common research
topics. The idea was very successful and the assessment made by the PhD Student was very good. It also helped to
achieve one of the major goals of the NESUS Action: to establish an open European research network targeting sustainable
solutions for ultrascale computing aiming at cross fertilization among HPC, large scale distributed systems, and big
data management, training, contributing to glue disparate researchers working across different areas and provide a meeting
ground for researchers in these separate areas to exchange ideas, to identify synergies, and to pursue common activities in
research topics such as sustainable software solutions (applications and system software stack), data management, energy
efficiency, and resilience.European Cooperation in Science and Technology. COS
FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks.
Mathematical models of biochemical networks can largely facilitate the comprehension of the mechanisms at the basis of cellular processes, as well as the formulation of hypotheses that can be tested by means of targeted laboratory experiments. However, two issues might hamper the achievement of fruitful outcomes. On the one hand, detailed mechanistic models can involve hundreds or thousands of molecular species and their intermediate complexes, as well as hundreds or thousands of chemical reactions, a situation generally occurring in rule-based modeling. On the other hand, the computational analysis of a model typically requires the execution of a large number of simulations for its calibration, or to test the effect of perturbations. As a consequence, the computational capabilities of modern Central Processing Units can be easily overtaken, possibly making the modeling of biochemical networks a worthless or ineffective effort. To the aim of overcoming the limitations of the current state-of-the-art simulation approaches, we present in this paper FiCoS, a novel "black-box" deterministic simulator that effectively realizes both a fine-grained and a coarse-grained parallelization on Graphics Processing Units. In particular, FiCoS exploits two different integration methods, namely, the Dormand-Prince and the Radau IIA, to efficiently solve both non-stiff and stiff systems of coupled Ordinary Differential Equations. We tested the performance of FiCoS against different deterministic simulators, by considering models of increasing size and by running analyses with increasing computational demands. FiCoS was able to dramatically speedup the computations up to 855×, showing to be a promising solution for the simulation and analysis of large-scale models of complex biological processes
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