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Moving to smaller libraries via clustering and genetic algorithms

G. Antoniol, M. Di Penta, M. Neteler
Seventh European Conference onSoftware Maintenance and Reengineering, 2003. Proceedings.  
The first step defines an initial solution based on clustering methods, while the subsequent phase refines the initial solution via genetic algorithms.  ...  The approach has been applied to several medium and large-size open source software systems such as GRASS, KDE-QT, Samba and MySQL, allowing to effectively produce smaller, loosely coupled libraries, and  ...  Acknowledgments We are grateful to the GRASS development team for the support, the information provided, and the feedback on the re-factored artifacts.  ... 
doi:10.1109/csmr.2003.1192439 dblp:conf/csmr/AntoniolPN03 fatcat:zefm555cvrhrlpoioazjbmt7m4

Sphericalk-Means Clustering

Kurt Hornik, Ingo Feinerer, Martin Kober, Christian Buchta
2012 Journal of Statistical Software  
k-means clustering featuring several solvers: a fixed-point and genetic algorithm, and interfaces to two external solvers (CLUTO and Gmeans).  ...  Spherical k-means clustering is one approach to address both issues, employing cosine dissimilarities to perform prototype-based partitioning of term weight representations of the documents.  ...  optimization problems, such as genetic algorithms) may be able to find "better" partitions (with a smaller criterion value).  ... 
doi:10.18637/jss.v050.i10 fatcat:5rdopo7n6rfaxnd4swzroyljuq

Computational Method For Annotation Of Protein Sequence According To Gene Ontology Terms

Razib M. Othman, Safaai Deris, Rosli M. Illias
2007 Zenodo  
The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process.  ...  This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method.  ...  Three real data sets of iris, breast cancer, and subcellcycle are [65] can automatically determine the correct number of clusters using various moves: birth move, death move, split move, merge move,  ... 
doi:10.5281/zenodo.1072129 fatcat:vz5sofxjgvbi7dqdyyp5pzgl3e

TensorFlow Enabled Genetic Programming [article]

Kai Staats, Edward Pantridge, Marco Cavaglia, Iurii Milovanov, Arun Aniyan
2017 arXiv   pre-print
Genetic Programming, a kind of evolutionary computation and machine learning algorithm, is shown to benefit significantly from the application of vectorized data and the TensorFlow numerical computation  ...  library on both CPU and GPU architectures.  ...  the LIGO Scienti c Collaboration for use of the glitch classi cation data; and the anonymous reviewers who provided valuable feedback to the improvement of this paper.  ... 
arXiv:1708.03157v1 fatcat:2z2knig3cjcevi77xvt6zsd2eu

Strategies for the Parallel Implementation of Metaheuristics [chapter]

Van-Dat Cung, Simone L. Martins, Celso C. Ribeiro, Catherine Roucairol
2002 Operations Research/Computer Science Interfaces Series  
Basically, a cluster is a collection of PCs or workstations connected via a network and using off-the-shelf components. The sig-  ...  Parallel implementations of tabu search, GRASP, genetic algorithms, simulated annealing, and ant colonies are reviewed and discussed to illustrate the main strategies used in the parallelization of different  ...  Some libraries to support the development of parallel genetic algorithms based on the island model were already cited in Section 4.2.2.  ... 
doi:10.1007/978-1-4615-1507-4_13 fatcat:syvr7spvynhntdp6ya44ntlimq

Exploring the Visual Styles of Arcade Game Assets [chapter]

Antonios Liapis
2016 Lecture Notes in Computer Science  
Due to constraints on the final spaceships' plausibility, the paper investigates two-population constrained optimization and constrained novelty search methods.  ...  A sample of visual styles is tested, each a combination of visual metrics which primarily evaluate balance and shape complexity.  ...  Acknowledgements The sprite components used to construct the spaceships are freely licensed art assets found in OpenGameArt ( and are not the intellectual property  ... 
doi:10.1007/978-3-319-31008-4_7 fatcat:u467gn6iwnbf5dz53xeliqp3eu

A language-independent software renovation framework

M. Di Penta, M. Neteler, G. Antoniol, E. Merlo
2005 Journal of Systems and Software  
Refactoring has been 17 implemented in the SRF using a hybrid approach based on hierarchical clustering, on genetic algorithms and hill climbing, also tak-18 ing into account the developersÕ feedback.  ...  As a consequence, the size of binaries and libraries tends to grow and system maintainability tends to decrease.  ...  All rights reserved. 25 Keywords: Refactoring; Software renovation; Clustering; Genetic algorithms; Hill climbing 26 27 1.  ... 
doi:10.1016/j.jss.2004.03.033 fatcat:5fhysb5zxndojntyuth47dj6oe

greed: An R Package for Model-Based Clustering by Greedy Maximization of the Integrated Classification Likelihood [article]

Etienne Côme, Nicolas Jouvin
2022 arXiv   pre-print
This combinatorial problem is handled through an efficient hybrid genetic algorithm, while a final hierarchical step allows accessing coarser partitions and extract an ordering of the clusters.  ...  Based on the direct maximization of the exact Integrated Classification Likelihood with respect to the partition, it allows jointly performing clustering and selection of the number of groups.  ...  Merge moves are used twice in the algorithm: first in the GA in order to merge redundant clusters after the cross-partition operator in Equation ( 6 ), and second in the hierarchical clustering algorithm  ... 
arXiv:2204.14063v1 fatcat:za3vw3qvkbcplfkgcupu2b6yry

Inferring local movement of pathogen vectors among hosts [article]

Zhen Fu, Brendan Epstein, Joanna L Kelley, Qi Zheng, Alan O Bergland, Carmen I Castillo Carrillo, Andrew S Jensen, William E Snyder
2016 bioRxiv   pre-print
Herbivores often move among spatially interspersed host plants, tracking high-quality resources through space and time. This dispersal is of particular interest for vectors of plant pathogens.  ...  Existing molecular tools to track such movement have yielded important insights, but often provide insufficient genetic resolution to infer spread at finer spatiotemporal scales.  ...  NextRAD sequencing overcomes these limitations by fragmenting and ligating adaptor sequences to genomic DNA via engineered transposomes (Nextera DNA Library Prep Reference Guide), detailing genetic differentiation  ... 
doi:10.1101/046540 fatcat:ro3codb26rhyzfmcolwgpagfhm

Deep-Sequencing of the Peach Latent Mosaic Viroid Reveals New Aspects of Population Heterogeneity

Jean-Pierre Sehi Glouzon, François Bolduc, Shengrui Wang, Rafael J. Najmanovich, Jean-Pierre Perreault, Yury E. Khudyakov
2014 PLoS ONE  
Using a novel hierarchical clustering algorithm, the different variants obtained were grouped into either 7 or 8 clusters depending on the library being analyzed.  ...  Two distinct libraries were analyzed, and yielded 1125 and 1061 different PLMVd variants respectively, making this study the most productive to date (by more than an order of magnitude) in terms of the  ...  of plasmid pPD2-4, and Tengke Xiong for his assistance with the DHCS algorithm and programs.  ... 
doi:10.1371/journal.pone.0087297 pmid:24498066 pmcid:PMC3907566 fatcat:q54al2mso5dqjaicc3qciheiz4

Shape: automatic conformation prediction of carbohydrates using a genetic algorithm

Jimmy Rosen, Laurence Miguet, Serge Pérez
2009 Journal of Cheminformatics  
A trivial user interface coupled to an efficient genetic algorithm conformation search makes it a powerful tool for automated modelling.  ...  It can also be deployed on computer clusters for increased capacity.  ...  Acknowledgements Acknowledgements go to Abraham Nahmany, Francesco Strino, Graham Kemp, and Per-Georg Nyholm for informative discussions around the concept of using genetic algorithms for conformational  ... 
doi:10.1186/1758-2946-1-16 pmid:20298520 pmcid:PMC2820494 fatcat:mp3wdst4lfbn5lkfxpr4uv7gkq

Chemoinformatics and Drug Discovery

Jun Xu, Arnold Hagler
2002 Molecules  
The main data mining approaches used in cheminformatics, such as descriptor computations, structural similarity matrices, and classification algorithms, are outlined.  ...  The applications of cheminformatics in drug discovery, such as compound selection, virtual library generation, virtual high throughput screening, HTS data mining, and in silico ADMET are discussed.  ...  Acknowledgements We would like to thank Mr. Richard Shaps for his comments and advice.  ... 
doi:10.3390/70800566 fatcat:vsf3iljr45cy3j7qadvq35pbcq

SNP Discovery with EST and NextGen Sequencing in Switchgrass (Panicum virgatum L.)

Elhan S. Ersoz, Mark H. Wright, Jasmyn L. Pangilinan, Moira J. Sheehan, Christian Tobias, Michael D. Casler, Edward S. Buckler, Denise E. Costich, Baohong Zhang
2012 PLoS ONE  
EST libraries were used to generate unigene clusters and establish a gene-space reference sequence, thus providing a framework for assembly of the short sequence reads.  ...  Identification of high-density molecular markers, such as single nucleotide polymorphisms (SNPs), that are amenable to high-throughput genotyping approaches, is the first step in a quantitative genetics  ...  Acknowledgments We would like to thank Dr. Ainong Shi and Dr. Rajandeep Sekhon for their help with the initial RNA extractions. Also, we are grateful to Dr.  ... 
doi:10.1371/journal.pone.0044112 pmid:23049744 pmcid:PMC3458043 fatcat:f3rofzifnbdj3pdmdwvebxnqie

A survey on search-based software design

Outi Räihä
2010 Computer Science Review  
Search-based approaches have been used in research from high architecture level design to software clustering and finally software refactoring.  ...  The choices regarding fundamental decisions, such as representation and fitness function, when using in meta-heuristic search algorithms, are emphasized and discussed in detail.  ...  Given a system composed by applications and libraries, the idea is to re-factor the biggest libraries, splitting them into two or more smaller clusters, so that each cluster contains symbols used by a  ... 
doi:10.1016/j.cosrev.2010.06.001 fatcat:waovgesm7nf4talmxyduok7r4e

Bayesian statistics workshop [article]

Olivier Gimenez
2020 Figshare  
Bayesian statistics - Olivier Gimenez, July 2020Slides codes and dataAll material prepared in R.R Markdown used to write reproducible material.Material available via  ...  analyses (in Jags), safely hopefully.ScheduleBayesian inference: Motivation and simple example.The likelihood.A detour to explore priors.Markov chains Monte Carlo methods (MCMC).Bayesian analyses in R  ...  We spin a continuous spinner that lands anywhere from 0 to 1 -call the random spin X . If X is smaller than R, we move to the candidate location, and otherwise we remain at the current location. 5.  ... 
doi:10.6084/m9.figshare.12656894.v1 fatcat:4rkgpam5crdfbmwz4pxcryc7nu
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