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Fast Genetic Programming and Artificial Developmental Systems on GPUs

Simon Harding, Wolfgang Banzhaf
2007 21st International Symposium on High Performance Computing Systems and Applications (HPCS'07)  
Feasibility of this approach to efficiently evaluate artificial developmental systems based on cellular automata is demonstrated.  ...  This increase in performance also extends to artificial developmental systems, where evolved programs are used to construct cellular systems.  ...  Cellular Developmental Systems There are many forms of artificial developmental system, but here we limit our investigation to ones based on Table 5 .  ... 
doi:10.1109/hpcs.2007.17 dblp:conf/hpcs/HardingB07 fatcat:yfrxmhug6fhzlcgflangrfkqaq

Implementation Method of Genetic Algorithms to the CUDA Environment using Data Parallelization
CUDA 環境におけるデータ並列化を用いた遺伝的アルゴリズムの実装手法

Masashi OISO, Yoshiyuki MATSUMURA, Toshiyuki YASUDA, Kazuhiro OHKURA
2011 Journal of Japan Society for Fuzzy Theory and Intelligent Informatics  
Genetic Programming Through Graphics Processing Units Fast Genetic Programming and Artificial Developmental Systems on GPUs GP on SPMD parallel graphics hardware for mega Bioinformatics data mining  ...  A SIMD interpreter for Genetic Programming on GPU Graphics Cards Population Parallel GP on the G80 GPU Solving Quadratic Assign ment Problems by Genetic Algorithms with GPU Computation: A Case  ... 
doi:10.3156/jsoft.23.18 fatcat:4u76nupd5rhajch5463xcuhdhu

Systemic Computation Using Graphics Processors [chapter]

Marjan Rouhipour, Peter J Bentley, Hooman Shayani
2010 Lecture Notes in Computer Science  
The GPU Systemic Computation Architecture is the first implementation that enables parallel systemic computation by exploiting multiple cores available in graphics processors.  ...  The approach has been proven through two existing implementations and many biological models and visualizations.  ...  There are also many fields of computer science that focuses on bio-inspired algorithms such as genetic algorithms, artificial immune systems, developmental algorithms, neural networks, and swarm intelligence  ... 
doi:10.1007/978-3-642-15323-5_11 fatcat:tbn5orotbzdtzi3b2cvgn43upm

Accelerating steady-state genetic algorithms based on CUDA architecture

Masashi Oiso, Toshiyuki Yasuda, Kazuhiro Ohkura, Yoshiyuki Matumura
2011 2011 IEEE Congress of Evolutionary Computation (CEC)  
CUDA is a general-purpose computation environment for GPUs. The major characteristic of this study is that a steady-state GA is implemented on a GPU based on concurrent kernel execution.  ...  Parallel computation can be applied to genetic algorithms (GAs) in terms of the processes of individuals in a population.  ...  W., 'Fast Genetic Programming and Artificial Developmental Systems on GPUs', Proceedings of the 21st International Symposium on High Performance Computing and Applications (HPCS'07), pp.2, 2007. [11] Imade  ... 
doi:10.1109/cec.2011.5949685 dblp:conf/cec/OisoYOM11 fatcat:c7m4is3pr5cuxctuwvtlrpag3a

Building Image Feature Kinetics for Cement Hydration Using Gene Expression Programming With Similarity Weight Tournament Selection

Lin Wang, Bo Yang, Shoude Wang, Zhifeng Liang
2015 IEEE Transactions on Evolutionary Computation  
Genetic Programming and Evolvable Machines. Vol. 10, No. 3, 2009, p. 231-262 2009 J 1 27.4.2009 Harding S., Wolfgang B.: Genetic Programming on GPUs for Image Processing.  ...  .: Phenotypic, Developmental and Computational Resources: Scaling in Artificial Development.  ... 
doi:10.1109/tevc.2014.2367111 fatcat:dsfdt3ngn5htfdg4ydmofrqznm

Fast bio-inspired computation using a GPU-based systemic computer

Marjan Rouhipour, Peter J. Bentley, Hooman Shayani
2010 Parallel Computing  
Models of biological systems and bio-inspired algorithms also share this parallelism, although most are simulated on serial computers.  ...  The GPU Systemic Computation Architecture is the first implementation that enables parallel systemic computation by exploiting the multiple cores available in graphics processors.  ...  There are also many fields of computer science that focuses on bio-inspired algorithms such as genetic algorithms [6] , artificial immune systems [7] , developmental algorithms [8] , neural networks  ... 
doi:10.1016/j.parco.2010.07.004 fatcat:oyxyfaxntbebjmubeipdbuphma

Graphics Processing Unit–Enhanced Genetic Algorithms for Solving the Temporal Dynamics of Gene Regulatory Networks

Raúl García-Calvo, JL Guisado, Fernando Diaz-del-Rio, Antonio Córdoba, Francisco Jiménez-Morales
2018 Evolutionary Bioinformatics  
In addition, a comparative study of the performance obtained by the different parallel implementations on GPU versus a sequential application on CPU is carried out.  ...  This work can provide useful guidance to researchers in biology, medicine, or bioinformatics in how to take advantage of the parallelization on massively parallel devices and GPUs to apply novel metaheuristic  ...  Author Contributions RGC, JLG, FDR, and AC conceived and designed the experiments. RGC implemented the programs and carried out the experiments. RGC, JLG, FDR, AC, and FJM analyzed the data.  ... 
doi:10.1177/1176934318767889 pmid:29662297 pmcid:PMC5898668 fatcat:774widqxjzgv3b2en7ljy6afqi

Born to learn: The inspiration, progress, and future of evolved plastic artificial neural networks

Andrea Soltoggio, Kenneth O. Stanley, Sebastian Risi
2018 Neural Networks  
, and plasticity rules: these artificial systems are composed of inputs, outputs, and plastic components that change in response to experiences in an environment.  ...  These systems may autonomously discover novel adaptive algorithms, and lead to hypotheses on the emergence of biological adaptation. EPANNs have seen considerable progress over the last two decades.  ...  The proposed evolutionary developmental system focused in particular on abstraction levels and principles such as Neural Darwinism (Edelman and Tononi, 2000).  ... 
doi:10.1016/j.neunet.2018.07.013 pmid:30142505 fatcat:gfgtbfalrbh6hnjwwj5lxj2dla

Evolving Reaction-Diffusion Systems on GPU [chapter]

Lidia Yamamoto, Wolfgang Banzhaf, Pierre Collet
2011 Lecture Notes in Computer Science  
Reaction-diffusion systems contribute to various morphogenetic processes, and can also be used as computation models in real and artificial chemistries.  ...  We compare parameter optimization and reaction network optimization on the evolution of reaction-diffusion solutions leading to simple spot patterns.  ...  This is analogous to finding a program (here, a chemical program) that solves a given problem, therefore it can be considered as a form of genetic programming (GP).  ... 
doi:10.1007/978-3-642-24769-9_16 fatcat:k253x5z77vapthpagqkt3gb4qq

Qualities, challenges and future of genetic algorithms: a literature review [article]

Aymeric Vie, Alissa M. Kleinnijenhuis, Doyne J. Farmer
2021 arXiv   pre-print
Genetic algorithms, computer programs that simulate natural evolution, are increasingly applied across many disciplines.  ...  Genetic algorithms are capable of exploring large and complex spaces of possible solutions, to quickly locate promising elements, and provide an adequate modelling tool to describe evolutionary systems  ...  This publication is based on work supported [or partially supported] by the EP-SRC Centre for Doctoral Training in Mathematics of Random Systems: Analysis, Modelling and Simulation (EP/S023925/1)  ... 
arXiv:2011.05277v3 fatcat:7wltstikf5crxkf73vekiee2hi

What machine learning can do for developmental biology

Paul Villoutreix
2021 Development  
Specifically, I focus on how machine learning is improving microscopy and single-cell 'omics' techniques and data analysis.  ...  In this Spotlight, I introduce the key concepts, advantages and limitations of machine learning, and discuss how these methods are being applied to problems in developmental biology.  ...  Acknowledgements I would like to thank the anonymous reviewers for insightful comments on the various versions of the manuscript.  ... 
doi:10.1242/dev.188474 pmid:33431591 fatcat:g6umzaselzeznak4uu7lhx2nsy

Neurodevelopmental Age Estimation of Infants Using a 3D-Convolutional Neural Network Model based on Fusion MRI Sequences [article]

M. Shabanian, A. Siddiqui, H. Chen, J.P. DeVincenzo
2020 arXiv   pre-print
An objective measure of brain developmental age estimation (BDAE) could be a useful tool in helping physicians identify developmental delay as well as other neurological diseases.  ...  We investigated a three-dimensional convolutional neural network (3D CNN) to rapidly classify brain developmental age using common MRI sequences.  ...  Courtney-Bricker and Ms. Hines for copy editing and proofreading the manuscript.  ... 
arXiv:2010.03963v1 fatcat:tprn6h35ajfd5ilckq6xnctt44

An Online Bioinformatics Curriculum

David B. Searls, Fran Lewitter
2012 PLoS Computational Biology  
This course focuses first on GPU programming with CUDA and then on MapReduce/Hadoop programming on the Amazon Cloud.  ...  and genetic bases for the exceptional cellular and developmental strategies adopted by plants  ... 
doi:10.1371/journal.pcbi.1002632 pmid:23028269 pmcid:PMC3441465 fatcat:n2ckzvbcf5fqfnw6vm4t7p3goi

Accuracy of New Deep Learning Model-Based Segmentation and Key-Point Multi-Detection Method for Ultrasonographic Developmental Dysplasia of the Hip (DDH) Screening

Si-Wook Lee, Hee-Uk Ye, Kyung-Jae Lee, Woo-Young Jang, Jong-Ha Lee, Seok-Min Hwang, Yu-Ran Heo
2021 Diagnostics  
Thus, a multi-detection deep learning artificial intelligence (AI)-based computer-aided diagnosis (CAD) system was developed and evaluated.  ...  Of the original 921 images, 320 (34.7%) were deemed appropriate for screening by both the system and human observer.  ...  Acknowledgments: We thank Young-Hee Son, Yoon-Jung Kang, and Chul-Woo Jegal for their support with data collection. Diagnostics 2021, 11, 1174  ... 
doi:10.3390/diagnostics11071174 fatcat:2r3rp6jhwbgltlh6nvyrffk5yu

High-resolution line-scan Brillouin microscopy for live-imaging of mechanical properties during embryo development [article]

Carlo Bevilacqua, Juan Manuel Gomez, Ulla-Maj Fiuza, Chii Jou Chan, Ling Wang, Sebastian Hambura, Manuel Eguren, Jan Ellenberg, Alba Diz-Muñoz, Maria Leptin, Robert Prevedel
2022 bioRxiv   pre-print
Here, we present a line-scanning Brillouin microscope optimized for fast and high-resolution live-imaging of dynamic biological processes with low photo-toxicity.  ...  such as fruit flies, ascidians, and mouse embryos.  ...  and Koki Watanabe for help with mouse imaging experiments; Sergio Lembo for help with confocal imaging of the stained embryos; EMBL LAR for mouse husbandry and ascidian support.  ... 
doi:10.1101/2022.04.25.489364 fatcat:v4ip26bnl5glfdqljxgjbjz674
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