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88 results for “differential evolution”
A Linked Application of Discrete Differential Evolution Algorithm Coupled with Simulation- Optimization Model and Comparative Analysis by Genetic Algorithm for Discrete Groundwater Management Problems
<p>Complete dataset of publication name as "The complete publication dataset is "A Discrete Differential Evolution- Linear Programming Algorithm for Groundwater Management Problems." You can find all the written codes in the zip file.</p>
Experimental Results for the study "A Modular Hybridization of Particle Swarm Optimization and Differential Evolution"
<p>This repository contains the experiment results and R scripts to analyze the data for the study "A Modular Hybridization of Particle Swarm Optimization andDifferential Evolution", which is accepted in <em>The Genetic and Evolutionary Computation Conference</em> (GECCO) '20 conference: </p> <p>Rick Boks, Hao Wang, and Thomas Bäck. 2020. A Modular Hybridization of Particle Swarm Optimization and Differential Evolution. In <em>Genetic and Evolutionary Computation Conference Companion (GECCO ’20 Companion), July 8–12, 2020, Cancún, Mexico. </em>ACM, New York, NY, USA, 8 pages. <a href="http://https: //doi.org/10.1145/3377929.3398123">https: //doi.org/10.1145/3377929.3398123</a></p> <p>Bibtex:</p> <pre><code class="language-markdown">@inproceedings{BoksWB20, author = {Rick Boks and Hao Wang and Thomas B\"ack}, title = {{A Modular Hybridization of Particle Swarm Optimization and Differential Evolution}}, booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference, {GECCO} 2020, Canc\'un, Mexico, July 8-12, 2020}, publisher = {{ACM}}, year = {2020}, url = {https://doi.org/10.1145/3321707.3321816}, doi = {doi.org/10.1145/3377929.3398123, }</code></pre> <p><strong>Data description:</strong> we benchmarked <strong>800 </strong>different<strong> </strong>hybridizations of the Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms on a well-known continuous black-box problem set called <a href="https://coco.gforge.inria.fr/">COCO/BBOB</a>, which consists of 24 test functions. 30 independent runs are conducted for each algorithm on each problem.</p> <ul> <li>'ERT.csv': a data frame with columns DIM (5D or 20D), funcId (F1-24), algId (algorithm names), target (<span class="math-tex">\(10^{\{-8,-7, \ldots, 1\}}\)</span>), ERT (expected running time), and sd (standard deviation).</li> <li>'raw-data.csv': the running time recorded in each independent run. </li> <li>'analysis.R': the R script that generates ERT tables in the paper.</li> <li>'ecdf.R': the R script that renders the ECDF (empirical cumulative distribution function) plots in the paper.</li> </ul>
Data accompanying the manuscript "Protocol Discovery for the Quantum Control of Majoranas by Differentiable Programming and Natural Evolution Strategies"
<p>Dataset for figures 2, A6 and A8 for the manuscript: "Protocol Discovery for the Quantum Control of Majoranas by Differentiable Programming and Natural Evolution Strategies." The dataset contains the optimal protocols for Majorana transport in both the Kitaev Chain model as well as the Proximity Coupled Semiconduncting Nanowire model obtained with Differentiable Programming and Natural Evolution Strategies. Also the Simulated Annealing (SA) optimal protocols for the Kitaev chain are included.</p>
Human-specific tandem repeat expansion and differential gene expression during primate evolution
<p>THIS DATASET IS PART OF THE FOLLOWING STUDY:<br> <a href="https://www.pnas.org/content/early/2019/10/22/1912175116">https://www.pnas.org/content/early/2019/10/22/1912175116</a></p> <p> </p> <p>THE RAW SEQUENCING 10x GENOMICS READS CAN BE DOWNLOADED FROM SRA:<br> <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056</a></p> <p><br> ORIGINAL UPLOAD: 09/06/2019</p> <p>UPDATES: 10/28/2019; 01/27/2020</p> <p>DESCRIPTION: Contigs were assembled using Phased-SV (<a href="https://www.nature.com/articles/s41467-018-08148-z">Chaisson et al, Nature Communications 2019</a>) on six human haplotypes (i.e., H0 and H1 in NA19240, HG00514, and HG00733), and six nonhuman haplotypes (this study, H0 and H1 in Clint the chimpanzee, Kamilah the gorilla, and Susie the orangutan). The long read data (PacBio CLR) from NHPs were phased into haplotypes H0 and H1 using linked reads from 10X Genomics prior to assembly, whenever possible. If not possible (e.g., in the case of long runs of homozygosity regions), long reads from both haplotypes were used to generate a "squished assembly". Using human haplotype data, we identified 21,442 polymorphic STRs/VNTRs, followed by a targetted phasing of these regions in the three NHPs. All of the human and nonhuman primate contigs were padded by 2 kbp both upstream and downstream, followed by mapping against the human reference (GRCh38). We did the same for "squished assemblies" from a Yoruban individual, CHM13, and three NHPs as described in <a href="https://science.sciencemag.org/content/360/6393/eaar6343">Kronenberg et al, Science 2018</a>. The BAM and BAI files in this dataset contain the alignment of all these contigs against GRCh38.</p>
Data from: A caste differentiation mutant elucidates the evolution of socially parasitic ants
<div> <div> <div> <div> <p>Most ant species have two distinct female castes – queens and workers – yet the developmental and genetic mechanisms that produce these alternative phenotypes remain poorly understood. Working with the clonal raider ant, <em>Ooceraea</em> <em>biroi</em>, we discovered a variant strain that expresses queen-like traits in individuals that would normally become workers. The variants show changes in morphology, behavior, and fitness that cause them to rely on workers in wild-type (WT) colonies for survival. Overall, they resemble the queens of many obligately parasitic ants that have evolutionarily lost the worker caste and live inside colonies of closely related hosts. <br><br>To understand the genetic basis of this variant strain, which we term the queen-like mutants (QLM), we re-analyzed published PacBio and Hi-C data (McKenzie and Kronauer 2018) using the Falcon pipeline. </p> </div> </div> </div> </div>
Evolution along allometric lines of least resistance: Morphological differentiation in Pristurus geckos
<p class="FirstParagraph"><span>Species living in distinct habitats often experience unique ecological selective pressures, which can drive phenotypic divergence. However, how ecophenotypic patterns are affected by allometric trends and trait integration levels is less well understood. Here we evaluate the role of allometry in shaping body size and body form diversity in <em>Pristurus</em> geckos utilizing differing habitats. We found that patterns of allometry and integration in body form were distinct in species with different habitat preferences, with ground-dwelling <em>Pristurus</em> displaying the most divergent allometric trend and high levels of integration. There was also strong concordance between intraspecific allometry across individuals and evolutionary allometry among species, revealing that differences in body form among individuals were predictive of evolutionary changes across the phylogeny at macroevolutionary scales. This suggested that phenotypic evolution occurred along allometric lines of least resistance, with allometric trajectories imposing a strong influence on the magnitude and direction of size and shape changes across the phylogeny. When viewed in phylomorphospace, the largest rock-dwelling species were most similar to the smallest ground-dwelling species, and vice versa. Thus, in <em>Pristurus</em>, phenotypic evolution along the differing habitat-based allometric trajectories resulted in similar body forms at differing body sizes in distinct ecological habitats.</span></p>
Differential selection for survival and for growth in adaptive laboratory evolution experiments with benzalkonium chloride
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Data from: Context-dependent body size evolution in lacertid lizards: Differential role of structural habitat and climate across radiations
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Data from: A caste differentiation mutant elucidates the evolution of socially parasitic ants
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Data from: Plasticity and the evolution of group-level regulation of cellular differentiation in the volvocine algae
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Evolution along allometric lines of least resistance: Morphological differentiation in Pristurus geckos
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Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans
<p>Ecological niche breadth and the mechanisms facilitating its evolution are fundamental to understanding adaptation to changing environments, persistence of generalist and specialist lineages and the formation of new species. Woody substrates are structurally complex resources utilized by organisms with specialized decay machinery. Wood-decaying fungi represent ideal model systems to study evolution of niche breadth, as they vary greatly in their host range and preferred decay stage of the substrate. In order to dissect the genetic basis for niche specialization in the invasive brown rot fungus <i>Serpula lacrymans</i>, we used phenotyping and integrative analysis of phylogenomic and transcriptomic data to compare this species to wild relatives in the Serpulaceae with a range of specialist to generalist decay strategies. Our results indicate specialist species have rewired regulatory networks active during wood decay towards decreased reliance on enzymatic machinery, and therefore nitrogen-intensive decay components. This shift was likely accompanied with adaptation to a narrow tree line habitat and switch to a pioneer decomposer strategy, both requiring rapid colonization of a nitrogen-limited substrate. Among substrate specialists with narrow niches, we also found evidence for pathways facilitating reversal to generalism, highlighting how evolution may move along different axes of niche space.</p>
Data from: Malagasy cichlids differentially limit impacts of body shape evolution on oral jaw functional morphology
Patterns of trait covariation, like integration and modularity, are vital factors that influence the evolution of vertebrate body plans. In functional systems, decoupling of morphological modules buffers functional change in one trait by reducing correlated variation with another. However, for complex morphologies with many-to-one mapping of form to function (MTOM), resistance to functional change may also be achieved by constraining morphological variation within a functionally stable region of morphospace. For this research, we used geometric morphometrics to evaluate the evolution of body shape and its relationship to jaw functional morphology in two independent radiations of endemic Malagasy cichlid (Teleostei: Cichlidae). Our results suggested that the two subfamilies used different strategies to mitigate impacts of body shape variation on a metric of jaw function, maxillary kinematic transmission (MKT): (1) modularity between cranial and postcranial morphologies, and (2) integration of body and jaw evolution, with jaw morphologies varying in a manner that limits change in MKT. This research shows that, unlike modularity, MTOM allows traits to retain strong evolutionary covariation while still reducing impacts on functionality. These results suggest that MTOM, and its influence on the evolution of correlated traits, is likely much more widespread than is currently understood.
Data set for ``Why is Differential Evolution Better than Grid Search for Tuning Defect Predictors?''
<p>One of the black arts of data mining is learning the magic parameters that control the learners. In software analytics, at least for defect prediction, several methods, like grid search and differential evolution(DE), have been proposed to learn those parameters. They’ve been proved to be able to improve learner performance.</p> <p>We want to evaluate which method can find better parameters in terms of performance score and runtime. This paper compares grid search to differential evolution, which is an evolutionary algorithm that makes extensive use of stochastic jumps around the search space. We find that the seemingly complete approach of grid search does no better, and sometimes worse, than the stochastic search. Yet, when repeated 20 times to check for conclusion validity, DE was over 210 times faster (6.2 hours for DE vs 54 days for grid search when both tuning Random Forest over 17 test data sets with F-measure as optimization objective).</p> <p>These results are puzzling: why does a quick partial search be just as effective as a much slower, and much more, extensive search? To answer that question, we turned to the theoretical optimization literature. Bergstra and Bengio conjecture that grid search is not more effective than more randomized searchers if the underlying search space is inherently low dimensional. This is significant since recent results show that defect prediction exhibits very low intrinsic dimensionality– an observation that explains why a fast method like DE may work as well as a seemingly more thorough grid search. This suggests, as a future research direction, that it might be possible to peek at data sets before doing any optimization in order to match the optimization algorithm to the problem at hand.</p>
Designing Optimal Convolutional Neural Network Architecture Using Differential Evolution Algorithm
<p>Convolutional Neural Networks (CNNs) are widely used deep learning models for solving various tasks such as computer vision, speech recognition, among others. However, CNNs are developed manually based on problem-specific domain knowledge and tricky settings, which are laborious, time-consuming and challenging. To address these issues, this study proposes an Improved Differential Evolution of Convolutional Neural Network algorithm, namely IDECNN, to design CNN layer architectures for image classification task. </p>
Data for: Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development
<p>Variation in the size and number of axial segments underlies much of the diversity in animal body plans. Here, we investigate the evolutionary, genetic, and developmental mechanisms driving tail-length differences between forest and prairie ecotypes of deer mice (<em>Peromyscus maniculatus</em>). We first show that long-tailed forest mice perform better in an arboreal locomotion assay, consistent with tails being important for balance during climbing. We then identify six genomic regions that contribute to differences in tail length, three of which associate with caudal vertebra length and the other three with vertebra number. For all six loci, the forest allele increases tail length, indicative of the cumulative effect of natural selection. Two of the genomic regions associated with variation in vertebra number contain Hox gene clusters. Of those, we find an allele-specific decrease in Hoxd13 expression in the embryonic tail bud of long-tailed forest mice, consistent with its role in axial elongation. Additionally, we find that forest embryos have more presomitic mesoderm than prairie embryos, and that this correlates with an increase in the number of neuromesodermal progenitors (NMPs), which are modulated by Hox13 paralogs. Together, these results suggest a role for Hoxd13 in the development of natural variation in adaptive morphology on a microevolutionary timescale.</p>
Data supporting "Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence"
<p>Data supporting </p> <p><strong>Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence </strong></p> <p>E. M. Windels, L. Cool, E. Persy, J. Swinnen, P. Matthay, B. Van den Bergh, T. Wenseleers, J. Michiels</p> <p>Version April 16th, 2024</p>
Dynamical ising dataset for the paper Machine learning stochastic differential equations for the evolution of order parameters of classical many-body systems in and out of equilibrium
<p>This dataset provide the evolution in time for the magnetizaion in the 2D Ising model evolved with Gluber dynamics for a lattice of size 64 x 64.</p>
Differential Evolution data from eCS (EVONANO)
<p>Data-set produced by and depicted in https://doi.org/10.1007/978-3-030-76928-4_17</p>
Data from: Optimal mating of Pinus taeda L. under different scenarios using differential evolution algorithm
<p>A newly developed software, AgMate, was used to perform optimized mating for monoecious <em>Pinus taeda L.</em> breeding. Using a computational optimization procedure called differential evolution (DE), AgMate was applied under different breeding population sizes scenarios (50, 100, 150, 200, 250) and candidate contribution scenarios (max use of each candidate was set to 1 or 8), to assess its efficiency in maximizing the genetic gain while controlling inbreeding. Real pedigree data set from North Carolina State University Tree Improvement Co-op with 962 Pinus taeda were used to optimize objective functions accounting for coancestry of parents and expected genetic gain and inbreeding of the future progeny. AgMate results were compared with those from another widely used mating software called MateSel (Kinghorn, 1999). For the proposed mating list for 200 progenies, AgMate resulted in an 83.7% increase in genetic gain compared with the candidate population. There was evidence that AgMate performed similarly to MateSel in managing coancestry and expected genetic gain, but MateSel was superior in avoiding inbreeding in proposed mate pairs. The developed algorithm was computationally efficient in maximizing the objective functions and flexible for practical application in monoecious diploid conifer breeding.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.