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1,782 results for “Algorithm”
Data Set "Systematic partitioning of proteins for quantum-chemical fragmentation methods using graph algorithms"
<p>Data set accompanying the publication "Systematic partitioning of proteins for quantum-chemical fragmentation methods using graph algorithms"</p> <p>The data set contains:</p> <p>- Input script for PyADF (v0.97) for calculating (a) all two body terms to use as graph weights and (b) fragmentation error for all k and nmax (aspf)</p> <p>- PDB files of proteins and the "regions of interest" (RoI) used in this work.</p> <p>- Raw data: protein graph representations, resulting partitions, data underlying all figures shown in our article.</p> <p>- Jupiter notebook to create all figures shown in the article and in the supporting information from data in the results folder.</p> <p>- Images of protein structures and graph representations of ubiquitin.</p>
Searching for evidence of algorithmic randomness and incomputability in the output of quantum random number generators
<p>This upload contains the data and code used in the following paper:</p> <p>J. T. Kavulich, B. P. Van Deren, and M. Schlosshauer, “Searching for evidence of algorithmic randomness and incomputability in the output of quantum random number generators,” <em>Phys. Lett. A</em> 388, 127032 (2021), <a href="https://doi.org/10.1016/j.physleta.2020.127032">doi.org/10.1016/j.physleta.2020.127032</a></p> <p>The contents of the data set are as follows:</p> <p>1) Random strings for two QRNGs and four PRNGs. For each RNG, a zip archive provides 100 strings containing 25 x 2<sup>26</sup> = 1,677,721,600 bits each.</p> <p>2) C++ code for the Chaitin–Schwartz–Solovay–Strassen (CSSS) and Borel-normality tests (code.zip, 13 KB).</p> <p>The bulk of this code is not ours, but was written and made publicly available at <a href="https://www.cs.auckland.ac.nz/research/groups/CDMTCS/export/80_random_seqs">this link</a> by the authors of the following paper:</p> <p>A. A. Abbott, C. S. Calude, M. J. Dinneen, and N. Huang, <em>Phys. Scri.</em> 94 (2019) 045103, <a href="https://doi.org/10.1088/1402-4896/aaf36a">doi:10.1088/1402-4896/aaf36a</a></p> <p>We have made just a few small modifications to their original code:</p> <ul> <li>For the CSSS tests, a text file containing the Carmichael numbers (for tests 1–3) and odd composites up to 100 (for test 4) is read in and used to perform the tests. (Note: The set of Carmichael numbers used in the tests was generously provided to us by R. G. E. Pinch. Reference: R. G. E. Pinch, The Carmichael numbers up to 10<sup>21</sup>, in: A.-M. Ernvall-Hytönen (Ed.), Proceedings of Conference on Algorithmic Number Theory, Vol. 46, Turku Centre for Computer Science, Turku, Finland, 2007, pp. 129–131.)</li> <li>We combined the first and second CSSS tests into a single program.</li> <li>We reformatted the display of the output, and included a VERBOSE flag for additional status output.</li> </ul> <p>3) Results from CSSS and Borel-normality tests in Python format (results.zip, 22 KB). This archive also contains a Python script (analyze.py) that reads the result files, carries out the statistical analysis, and displays the plots.</p>
The impact of cardiopulmonary resuscitation on a cannot intubate, cannot oxygenate condition – a randomised crossover simulation research study of the interaction between two algorithms
<p>This is the original data file of the publication entiteled:</p> <p>The impact of cardiopulmonary resuscitation on a cannot intubate, cannot oxygenate condition – A randomised crossover simulation research study of the interaction between two algorithms</p> <p> </p>
Data from: Using branch-and-bound algorithms to optimize selection of a fixed-size breeding population under a relatedness constraint
Tree breeders often face the challenge of conserving genetic diversity, while at the same time maximizing response to selection. When selecting advanced-generation breeding populations, the best-performing candidates will quite often be closely related and selecting them without consideration of their relatedness will very quickly erode genetic diversity. Optimal selection will not completely avoid kinship, but rather maximize gain while imposing a constraint on average relatedness. Genetic contributions are most easily optimized if breeders can manage a real, continuous distribution of contributions from parents. While generally possible when establishing seed orchards, unequal contributions to a breeding population may present difficult and time-consuming operational constraints. In these situations, a specified number of parents contributing equally may be a preferred configuration for the breeding population. Here we formulate the selection of a fixed-size breeding population while imposing a constraint on relatedness of the population members. The problem is expressed as a Mixed Integer Quadratically Constrained Optimization (MIQCO) and solved using branch-and-bound techniques (BB). An open-source solver, dsOpt, was developed and embedded into a user-friendly tool, OPSEL, designed to simplify the process of optimizing selection of breeding populations. Case studies optimizing selection of breeding populations for Scots pine and loblolly pine illustrate the superiority of the BB solution compared with selection from ranked lists with restrictions on numbers of genotypes contributed by each full-sib family, and with solutions from GENCONT, a publically available optimum selection program using an algorithm with Lagrangian multipliers. The case studies also illustrate the extreme differences that can occur with respect to time required to confirm the optimality of solutions found by BB.
Data from: A single microphone noise reduction algorithm based on the detection and reconstruction of spectro-temporal features
Animals throughout the animal kingdom excel at extracting individual sounds from competing background sounds, yet current state-of-the-art signal processing algorithms struggle to process speech in the presence of even modest background noise. Recent psychophysical experiments in humans and electrophysiological recordings in animal models suggest that the brain is adapted to process sounds within the restricted domain of spectro-temporal modulations found in natural sounds. Here, we describe a novel single microphone noise reduction algorithm called spectro-temporal detection–reconstruction (STDR) that relies on an artificial neural network trained to detect, extract and reconstruct the spectro-temporal features found in speech. STDR can significantly reduce the level of the background noise while preserving the foreground speech quality and improving estimates of speech intelligibility. In addition, by leveraging the strong temporal correlations present in speech, the STDR algorithm can also operate on predictions of upcoming speech features, retaining similar performance levels while minimizing inherent throughput delays. STDR performs better than a competing state-of-the-art algorithm for a wide range of signal-to-noise ratios and has the potential for real-time applications such as hearing aids and automatic speech recognition.
Data from: Accelerating adaptive inverse distance weighting interpolation algorithm on a graphics processing unit
This paper focuses on designing and implementing parallel adaptive inverse distance weighting (AIDW) interpolation algorithms by using the graphics processing unit (GPU). The AIDW is an improved version of the standard IDW, which can adaptively determine the power parameter according to the data points' spatial distribution pattern and achieve more accurate predictions than those predicted by IDW. In this paper, we first present two versions of the GPU-accelerated AIDW, i.e. the naive version without profiting from the shared memory and the tiled version taking advantage of the shared memory. We also implement the naive version and the tiled version using two data layouts, structure of arrays and array of aligned structures, on both single and double precision. We then evaluate the performance of parallel AIDW by comparing it with its corresponding serial algorithm on three different machines equipped with the GPUs GT730M, M5000 and K40c. The experimental results indicate that: (i) there is no significant difference in the computational efficiency when different data layouts are employed; (ii) the tiled version is always slightly faster than the naive version; and (iii) on single precision the achieved speed-up can be up to 763 (on the GPU M5000), while on double precision the obtained highest speed-up is 197 (on the GPU K40c). To benefit the community, all source code and testing data related to the presented parallel AIDW algorithm are publicly available.
Data from: Comparison of photo-matching algorithms commonly used for photographic capture-recapture studies
Photographic capture–recapture is a valuable tool for obtaining demographic information on wildlife populations due to its noninvasive nature and cost-effectiveness. Recently, several computer-aided photo-matching algorithms have been developed to more efficiently match images of unique individuals in databases with thousands of images. However, the identification accuracy of these algorithms can severely bias estimates of vital rates and population size. Therefore, it is important to understand the performance and limitations of state-of-the-art photo-matching algorithms prior to implementation in capture–recapture studies involving possibly thousands of images. Here, we compared the performance of four photo-matching algorithms; Wild-ID, I3S Pattern+, APHIS, and AmphIdent using multiple amphibian databases of varying image quality. We measured the performance of each algorithm and evaluated the performance in relation to database size and the number of matching images in the database. We found that algorithm performance differed greatly by algorithm and image database, with recognition rates ranging from 100% to 22.6% when limiting the review to the 10 highest ranking images. We found that recognition rate degraded marginally with increased database size and could be improved considerably with a higher number of matching images in the database. In our study, the pixel-based algorithm of AmphIdent exhibited superior recognition rates compared to the other approaches. We recommend carefully evaluating algorithm performance prior to using it to match a complete database. By choosing a suitable matching algorithm, databases of sizes that are unfeasible to match "by eye" can be easily translated to accurate individual capture histories necessary for robust demographic estimates.
Data from: The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis
The inference of population genetic structures is essential in many research areas in population genetics, conservation biology and evolutionary biology. Recently, unsupervised Bayesian clustering algorithms have been developed to detect a hidden population structure from genotypic data, assuming among others that individuals taken from the population are unrelated. Because of this hypothesis, markers in a sample taken from a subpopulation can be considered to be in Hardy-Weinberg and linkage equilibrium. However, close relatives might be sampled from the same subpopulation, and consequently, might cause Hardy-Weinberg and linkage disequilibrium and thus bias a population genetic structure analysis. In this study, we used simulated and real data to investigate the impact of close relatives in a sample on Bayesian population structure analysis. We also showed that, when close relatives were identified by a pedigree reconstruction approach and removed, the accuracy of a population genetic structure analysis can be greatly improved. The results indicate that unsupervised Bayesian clustering algorithms cannot be used blindly to detect genetic structure in a sample with closely related individuals. Rather, when closely related individuals are suspected to be frequent in a sample, these individuals should be first identified and removed before conducting a population structure analysis.
Data from: Improving HybrID: how to best combine indirect and direct encoding in evolutionary algorithms
Many challenging engineering problems are regular, meaning solutions to one part of a problem can be reused to solve other parts. Evolutionary algorithms with indirect encoding perform better on regular problems because they reuse genomic information to create regular phenotypes. However, on problems that are mostly regular, but contain some irregularities, which describes most real-world problems, indirect encodings struggle to handle the irregularities, hurting performance. Direct encodings are better at producing irregular phenotypes, but cannot exploit regularity. An algorithm called HybrID combines the best of both: it first evolves with indirect encoding to exploit problem regularity, then switches to direct encoding to handle problem irregularity. While HybrID has been shown to outperform both indirect and direct encoding, its initial implementation required the manual specification of when to switch from indirect to direct encoding. In this paper, we test two new methods to improve HybrID by eliminating the need to manually specify this parameter. Auto-Switch-HybrID automatically switches from indirect to direct encoding when fitness stagnates. Offset-HybrID simultaneously evolves an indirect encoding with directly encoded offsets, eliminating the need to switch. We compare the original HybrID to these alternatives on three different problems with adjustable regularity. The results show that both Auto-Switch-HybrID and Offset-HybrID outperform the original HybrID on different types of problems, and thus offer more tools for researchers to solve challenging problems. The Offset-HybrID algorithm is particularly interesting because it suggests a path forward for automatically and simultaneously combining the best traits of indirect and direct encoding.
Data from: Multiresponse algorithms for community-level modeling: review of theory, applications, and comparison to species distribution models
1.Community-level models (CLMs) consider multiple, co-occurring species in model fitting and are lesser known alternatives to species distribution models (SDMs) for analyzing and predicting biodiversity patterns. CLMs simultaneously model multiple species, including rare species, while reducing overfitting and implicitly considering drivers of co-occurrence. Many CLMs are direct extensions of well-known SDMs and therefore should be familiar to ecologists. However, CLMs remain underutilized, and there have been few tests of their potential benefits and no systematic reviews of their assumptions and implementations. Here we review this emerging field and provide examples in R to fit common CLMs. Our goal is to introduce CLMs to a broader audience, and discuss their attributes, benefits, and limitations relative to SDMs. 2.We review i) statistical implementations and applications of CLMs, ii) their advantages and limitations, and iii) comparative analyses of CLMs and SDMs. We also suggest directions for future research. 3.We identify seven CLM algorithms with similar data structures and predictive outputs as SDMs that should be most accessible to ecologists familiar with species-level modeling, including five methods that predict assemblage composition and individual species distributions and two methods that model compositional turnover along environmental gradients. CLMs have been applied to numerous taxa, regions, and spatial scales, and a variety of topics (e.g., studying drivers of community structure or assessing relationships between community composition and functional traits). Studies suggest that the relative benefits of CLMs and SDMs may be case specific, especially in terms of predicting species distributions and community composition. However, CLMs may offer advantages in terms of computational efficiency, modeling rare species, and projecting to no-analog climates. A major shortcoming of CLMs is their reliance on presence-absence community composition data. 4.Studies are needed to assess the relative merits of SDMs and CLMs, and different CLM algorithms, with a focus on three key areas: i) under which circumstances CLMs improve predictions for rare species, ii) how CLMs perform under different community compositions (e.g. relative abundance of rare vs. common species), including the extent to which co-occurrence patterns are structured by biotic interactions, and iii) ability to project across time/space.
Data from: An advanced shape-fitting algorithm applied to quadrupedal mammals: improving volumetric mass estimates
Body mass is a fundamental physical property of an individual and has enormous bearing upon ecology and physiology. Generating reliable estimates for body mass is therefore a necessary step in many palaeontological studies. Whilst early reconstructions of mass in extinct species relied upon isolated skeletal elements, volumetric techniques are increasingly applied to fossils when skeletal completeness allows. We apply a new 'alpha shapes' (α-shapes) algorithm to volumetric mass estimation in quadrupedal mammals. α-shapes are defined by: (i) the underlying skeletal structure to which they are fitted; and (ii) the value α, determining the refinement of fit. For a given skeleton, a range of α-shapes may be fitted around the individual, spanning from very coarse to very fine. We fit α-shapes to three-dimensional models of extant mammals and calculate volumes, which are regressed against mass to generate predictive equations. Our optimal model is characterized by a high correlation coefficient and mean square error (r 2=0.975, m.s.e.=0.025). When applied to the woolly mammoth (Mammuthus primigenius) and giant ground sloth (Megatherium americanum), we reconstruct masses of 3635 and 3706 kg, respectively. We consider α-shapes an improvement upon previous techniques as resulting volumes are less sensitive to uncertainties in skeletal reconstructions, and do not require manual separation of body segments from skeletons.
Data from: Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice
The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive web-service implementing this algorithm. Compared to our previous method, the new algorithm is up to four orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world datasets, we show that, our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116,334 taxa each. Using simulated datasets we show that, when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum likelihood trees that are topologically closer to the respective true trees.
Self-adaptive Search Equation-Based Artificial Bee Colony Algorithm with CMA-ES on the Noiseless BBOB Testbed
<p>This file contains the data for results of SSEABC algorithm on BBOB functions testbed.</p>
Arctic sea ice snow melt onset dates from the Advanced Horizontal Range Algorithm, version 5 (1979 - 2022)
<h2>Data</h2><p>This data set includes one NetCDF (.nc) file containing the full set of annual Arctic sea ice melt onset dates and statistical summaries for the 1979 - 2022 period derived with the Advanced Horizontal Range Algorithm (AHRA) V5. The remaining .png files include browse images of each data layer contained within the primary NetCDF file.</p><p>A full description of the data provided herein can be found in the following publication: </p><p>Bliss, A. C. (submitted 2023), Passive microwave observations of Arctic sea ice melt onset from the Advanced Horizontal Range Algorithm 1979 – 2022, <i>Scientific Data</i>.</p><h2>Future updates</h2><p>This data set is distributed on an ongoing basis by the NASA Distributed Active Archive Center at the National Snow and Ice Data Center. Future updates to the AHRA V5 data set including annual updates of the data product will be available at the NSIDC archive below:</p><p>Bliss, A. C., M. Anderson, and S. Drobot. (2022). Snow Melt Onset Over Arctic Sea Ice from SMMR and SSM/I-SSMIS Brightness Temperatures, Version 5. Boulder, Colorado USA. NASA National Snow and Ice Data Center Distributed Active Archive Center. <a href="https://doi.org/10.5067/TRGWQ0ONTQG5">https://doi.org/10.5067/TRGWQ0ONTQG5</a>.</p>
High-resolution snow depth prediction using Random Forest algorithm with topographic parameters
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Data Used for Article: Speeding up large wind farms layout optimization using gradients, parallelization, and a heuristic algorithm for the initial layout
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A Soft Range Limited K-Nearest Neighbors Algorithm for Indoor Localization Enhancement
<p>WIFI RSSI Indoor Positioning Dataset</p> <p>A reliable and comprehensive public WiFi fingerprinting database for researchers to implement and compare the indoor localization’s methods.The database contains RSSI information from 6 APs conducted in different days with the support of autonomous robot.</p> <p>We use an autonomous robot to collect the WiFi fingerprint data. Our 3-wheel robot has multiple sensors including wheel odometer, an inertial measurement unit (IMU), a LIDAR, sonar sensors and a color and depth (RGB-D) camera. The robot can navigate to a target location to collect WiFi fingerprints automatically. The localization accuracy of the robot is 0.07 m ± 0.02 m. The dimension of the area is 21 m × 16 m. It has three long corridors. There are six APs and five of them provide two distinct MAC address for 2.4- and 5-GHz communications channels, respectively, except for one that only operates on 2.4-GHz frequency. There is one router can provide CSI information.<br>Data Format</p> <p>X Position (m), Y Position (m), RSSI Feature 1 (dBm), RSSI Feature 2 (dBm), RSSI Feature 3 (dBm), RSSI Feature 4 (dBm), ...</p>
Static electric equivalent circuit of commercial lithium-ion battery cells using genetic algorithms
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Data for cloud retrieval algorithm
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Supplementary Materials for "Landscape-aware Automated Algorithm Configuration using Multi-Output Mixed Regression and Classification"
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ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.