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73 results for “Parameter optimization”
Dataset: Simulation-based parameter optimization for fetal brain MRI super-resolution reconstruction
<p>This dataset contains the data used in the paper</p> <blockquote> <p>de Dumast, P., Sanchez, T., Lajous, H., Bach Cuadra, M. (2023). Simulation-Based Parameter Optimization for Fetal Brain MRI Super-Resolution Reconstruction. MICCAI 2023. LNCS, vol 14226. Springer, Cham. https://doi.org/10.1007/978-3-031-43990-2_32</p> </blockquote> <p>A preprint can also be found on <a href="https://arxiv.org/abs/2211.14274">arXiv</a>. If you found this dataset useful or used it in your research, please cite this reference.</p> <p>This paper studied the impact of the regularization parameter <span class="math-tex">\(\alpha \)</span> on the super-resolution reconstruction of fetal brain magnetic resonance (MR) images. It used simulated T2-weighted data MR images generated using FaBiAN v2.0, a Fetal Brain magnetic resonance Acquisition Numerical phantom that simulates fast spin echo (FSE) sequences of the developing fetal brain throughout gestation. The dataset contains the raw simulated data, the corresponding ground truths as well as corresponding super-resolution (SR) reconstructions using MIALSRTK and NiftyMIC with varying regularization parameters <span class="math-tex">\(\alpha \)</span>.</p> <p>Copyright (c) - All rights reserved. Medical Image Analysis Laboratory - Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland & CIBM Center for Biomedical Imaging. 2023.</p>
The top performer: towards optimized parameters for Reduced graphene oxide uniformity by Spin coating
<p>This dataset contains the raw data used for the publication:</p> <p>-------------------------------------------------------------------------------------------------------------------------------------------------------<br> "The top performer: towards optimized parameters for Reduced graphene oxide uniformity by Spin coating"<br> by C. Reiner-Rozman, R. Hasler, J. Andersson, T. Rodrigues, A. Bozdogan and P. Aspermair<br> --------------------------------------------------------------------------------------------------------------------------------------------------------</p> <p><br> It consists of the SEM images (in .tif format) and the determined surface coverages (in .dat format) as well as the measured electrical data (in .dat format) of the prepared graphene field-effect transistor chips. Headers/information in the data files are in English. When using this data in any form please refer to the above-mentioned publication.</p> <p>The data is structured according to the figures of the paper. Each folder contains the data relevant to validate the results presented in the respective figure of the publication. The files are labeled according to the following description:</p> <p>"measurement-type"_"chip-number"_"GO-concentration"_"spin-coating speed"</p> <p>"measurement-type": SEM, IDVG, baseline<br> "chip-number": an increasing number of fabricated device (only used when needed)<br> "GO-concentration": 143/214/285 µg/mL of graphene oxide (GO) in solution<br> "spin-coating speed": in rpm</p>
Surrogate-based optimization using an artificial neural network for a parameter identification in a 3D marine ecosystem model
<p><strong>Abstract:</strong></p> <p>Parameter identification for marine ecosystem models is important for the assessment and validation of marine ecosystem models against observational data. The surrogate-based optimization (SBO) is a computationally efficient method to optimize complex models. SBO replaces the computationally expensive (high-fidelity) model by a surrogate constructed from a less accurate but computationally cheaper (low-fidelity) model in combination with an appropriate correction approach, which improves the accuracy of the low-fidelity model. To construct a computationally cheap low-fidelity model, we tested three different approaches to compute an approximation of the annually periodic solution (i.e., a steady annual cycle) of a marine ecosystem model: firstly, a reduced number of spin-up iterations (several decades instead of millennia), secondly, an artificial neural network (ANN) approximating the steady annual cycle and, finally, a combination of the both approaches. Except for the low-fidelity model using only the ANN, the SBO yielded a solution close to the target and reduced the computational effort significantly. If an ANN approximating appropriately a marine ecosystem model is available, the SBO using this ANN as low-fidelity model presents a promising and computational efficient method for the validation.</p> <p> </p> <p><strong>Content:</strong></p> <ul> <li>SQLite database including the data of the different optimization runs</li> <li>Structure and weights of the used artificial neural network</li> <li>Tracer concentrations obtain from the high-fidelity model for the different optimization runs</li> </ul>
Data and Code for: Performance Evaluation of the Particle Swarm Optimization Algorithm to Unambiguously Estimate Plasma Parameters from Incoherent Scatter Radar Signals
<p>This repository contains the datasets and scripts used to obtain the figures of the paper "Performance Evaluation of the Particle Swarm Optimization Algorithm to Unambiguously Estimate Plasma Parameters from Incoherent Scatter Radar Signals".</p> <p>The repository is organized as follows:<br> - Part I) Monte Carlo simulation codes</p> <p>- Part II) Monte Carlo simulations using the parameter configuration "Param. 1" of Shi et al. (1999)</p> <p>- Part III) Monte Carlo simulation using the parameter configuration "Param. 1" of Shi et al. (1999) and a limited ion composition search space</p> <p>- Part IV) Monte Carlo simulations using the parameter configuration "Param. 2" of Wang et al. (2012)</p> <p>- Part V) Monte Carlo simulation using the parameter configuration "Param. 2" of Wang et al. (2012) and a limited ion composition search space</p> <p>- Part VI) Codes to generate all figures of the manuscript</p> <p>All datasets and scripts were generated and tested using Matlab 2017. Simulations have been executed in parallel on a SLURM cluster, compilation and running scripts are provided.</p>
Data for analysis in "Towards optimal cosmological parameter recovery from compressed bispectrum statistics"
<p>Measures of the three point function extracted from a suite of simulations using 4 different estimators: namely, the bispectrum, modal estimator, integrated bispectrum, line correlation function. Also supplied are power spectrum measures across the same simulations. <br> <br> The measures are done across 200 fiducial and 60 non-fiducial cosmology simulations, at 3 redshifts. Further details on what was done can be attained by reading the document, Overview.md/Overview.pdf, attached to the bundle. Even more details can be acquired by reading the paper this data was prepared for at https://arxiv.org/abs/1705.04392! </p>
Auxiliary data release for "Fast marginalization algorithm for optimizing gravitational wave detection, parameter estimation and sky localization"
<p>This release contains parameter estimation runs on synthetic injections, described in https://arxiv.org/abs/2404.02435 .</p> <p>Important note: The posterior samples provided are weighted, the weights are stored in a column named 'weights' . </p>
Supporting data sets for "Estimating Carbon Fixation of Plant Organs for Afforestation Monitoring using a Process-based Ecosystem Model and Ecophysiological Parameter Optimization". (the survey of tree breast diameter and tree height in 11-year old Eucommia ulmoides plantation, values of simulation results used in figures and tables.)
<p>Supporting data sets for Miyauchi et al., Ecology and Evolution, 2019 (accepted).</p> <p>The files store: </p> <p>(1) The survey of tree breast diameter and tree height in <em>Eucommia ulmoides</em> plantation<em>.</em> The ring and stem analysis and dry weight of seven harvested sample trees in the plantation.</p> <p>(2) Values of optimization result used fig.7.</p> <p>(3) Values of prediction result used fig.8. and table 4.</p> <p>(4) Values of optimized parameters by optimization methods, parameter range and constrain.</p>
AiNU data for Physics-based material parameters extraction from perovskite experiments via Bayesian optimization
<p>This file contains the AiNU data used for the article entitled by <em>Physics-based material parameters extraction from perovskite experiments via Bayesian optimization</em> (https://arxiv.org/abs/2402.11101).</p>
Using the Genetic Algorithm for the Optimization of Dynamic School Bus Routing Problem-Figure 7. Application main form which includes route, bus stops and GA parameters
<p>For this study, the school bus routes within the Ankara Province were used as case studies. The school bus routes were recorded by using the Android application and instantaneous GPS monitoring method. The home address of each student was taken as a stopping point. At the end of each route, the distances between the beginning and end points were recorded. After transferring the obtained route data into the database, the ill-adapted points were eliminated. By means of the developed application, the existing school bus routes are dynamically optimized using GA. It was developed both as a mobile and desktop application. Using Android- based mobile software, the information regarding GPS locations of bus stops and school buses is transferred to the server on a real-time basis. Using the desktop software, where GAs are run, these coordinates are shown on a Google map, and the most suitable route is produced and sent to the school bus via server. This method provides the opportunity to dynamically reflect certain factors such as a different initial point for the school bus, some students being absent from the school on a particular day, and eventual changes on the existing roads on the route production process.</p>
SPUSPO: Spatially Partitioned Unsupervised Segmentation Parameter Optimization for Efficiently Segmenting Large Heterogeneous Areas
<p>This dataset contains several data, results and processing material from the application of GEOBIA-based, Spatially Partitioned Segmentation Parameter Optimization (SPUSPO) in the city of Ouagadougou. In detail in contains:</p> <ul> <li><strong>A Land Use - Land Cover map of Ouagadougou derived through SPUSPO. The classifier used was Extreme Gradient Boosting (XGBoost). </strong> <p>Labels :</p> <p>2 : Artificial Ground Surface</p> <p>0 : Building</p> <p>5 : Low Vegetation</p> <p>4 : Tree</p> <p>1 : Swimming Pool</p> <p>3 : Bare Ground</p> <p>7 : Shadow</p> <p>6 : Inland Water</p> </li> </ul> <p> </p> <ul> <li><strong>The training and test data used in the study (SPUSPO and benchmark approach). </strong></li> </ul> <p>The data are given in a csv format.</p> <ul> <li><strong>The Jupyter notebook code which involves Python and GRASS GIS to automatize and efficiently perform SPUSPO in a large dataset.</strong></li> </ul> <p>Python code calling GRASS GIS functions for automatizing the procedure.</p> <p> </p> <ul> <li><strong>The segmentation layers coming from SPUSPO and the benchmark approaches (in raster formats due to data limitations).</strong></li> </ul> <p>Segmentation rasters for each approach.</p> <ul> <li><strong>The R code for optimization of XGBoost as well as feature selection with VSURF and classification of the whole dataset.</strong></li> </ul> <p> </p> <ul> <li><strong>Segmentation evaluation metrics.</strong></li> </ul> <p>A csv file with the data sued to compute the Area Fit Index for each approach.</p> <ul> <li><strong>Morphological zones of Ouagadougou as created by Grippa et al. 2017 a shp format.</strong></li> </ul>
Test data set for macros accompanying the publication Multi-parameter screening method for developing optimized red fluorescent proteins
<p>This a bundle of test data can be used to run the macros accompanying the publication Multi-parameter screening method for developing optimized red fluorescent proteins.</p> <p>These data sets can be used to run the following macros that can be found on GitHub:</p> <ol> <li><a href="https://github.com/molcyto/MC-Ratio-96-wells">https://github.com/molcyto/MC-Ratio-96-wells</a></li> <li><a href="https://github.com/molcyto/MC-Ratio-Petri-dish">https://github.com/molcyto/MC-Ratio-Petri-dish</a></li> <li><a href="https://github.com/molcyto/MC-FLIM-Petri-dish">https://github.com/molcyto/MC-FLIM-Petri-dish</a></li> <li><a href="https://github.com/molcyto/MC-Bleach-96-wells">https://github.com/molcyto/MC-Bleach-96-wells</a></li> <li><a href="https://github.com/molcyto/MC-Scatter5D">https://github.com/molcyto/MC-Scatter5D</a></li> <li><a href="https://github.com/molcyto/MC-FLIM-96-wells">https://github.com/molcyto/MC-FLIM-96-wells</a></li> </ol> <p>Funding:<br> This work was supported by the NWO CW-Echo grant 711.011.018 (M.A.H. and T.W.J.G.), grant 12149 (T.W.J.G.) from the Foundation for Technological Sciences (STW) from the Netherlands</p> <p> </p>
Fig. 4. Geometric parameters for the numerical optimization process. a in Scientific Note Proposal of a Sluice-type Fish Pass
Fig. 4. Geometric parameters for the numerical optimization process. a) water level in the pool, b) intermediate wall height c) level difference between the pools, d) opening under the sluice, e) the dimension of the pool and f) position of the wall (see Fig. 3 for legend).
Data for: Parameter selection and optimization of a computational network model of blood flow in single-ventricle patients
Open the record for dataset details and reuse information.
Optimal parameters of GR4J and HBV hydrological models used in the OpenForecast v2 system
<p>The database contains optimal parameters of GR4J and HBV hydrological models, which are operationally used in the second version of the OpenForecast system (openforecast.github.io).</p>
MATLAB scripts and raw experimental data for the paper "Optimizing measurements of linear changes of NMR signal parameters" by Javier Agustin Romero, Krzysztof Kazimierczuk and Paweł Kasprzak
<p>Classical_fit.m - Comparison of simulation results and theoretical predictions for the linear fit of the resonance frequencies. </p> <p>Radon_transform - the same, but using Radon transform to determine linear coefficients.</p> <p>Amplitude.m - Comparison of errors of the linear coefficients for varying amplitude fit in simulations and theory.</p> <p>process_measurements.m - script to process experimental data (caffeine peak at 7.90 ppm). The data are stored in real.mat and imag.mat</p> <p>For the details of theoretical formulas, see the paper "Optimizing measurements of linear changes of NMR signal parameters" by Javier Agustin Romero, Krzysztof Kazimierczuk, and Paweł Kasprzak. The scripts were used to generate Figures in the paper.</p>
(D2.1_dataset01) Parameter values used in the optimal loads split algorithm to find the baseload
<p>In Task 2.1 of hybridGEOTABS project, an <em>optimal load splitting algorithm (OLSA) </em>was developed and validated. The OLSA splits the building thermal loads (calculated in T2.2 of the project) to the baseload and residual loads. The baseload is defined as the maximum share of GEOTABS that allows to minimise the energy use of the entire (primary + secondary) heating and cooling system, while maintaining thermal comfort in the building and by using and taking into account the thermal storage in the TABS. The algorithm is documented in detail in D2.1 of the hybridGEOTABS project. This document reports all the parameter values used in the OLSA.</p>
Determination of the Optimal Parameters for Self-Healing Efficiency of Encapsulated bacteria in Concrete Simulated Subtropical Climate
<p>Concrete is a remarkable construction material. However, its low tensile strength makes it prone to cracking, which negatively affects its durability. To address this issue, bacterial concrete has been implemented as a self-healing alternative due to its capability to seal microcracks through microbial-induced calcium carbonate precipitation (MICCP). In this study, a bacterial strain (i.e, Bacillus Pseudiformus) was encapsulated through three different methods: encapsulation through hydrogel beads, vacuum impregnation on lightweight aggregates, and attachment to cellulose nanocrystals. Furthermore, three precursor types were used, magnesium acetate, calcium lactate, and sodium lactate were implemented. Compressive strength tests and flexural strength tests were performed on mortar specimens to characterize their mechanical properties. Once the crack was induced, samples were subjected to 28 days of wet/dry cycles in which the corresponding crack width was monitored. At the end of this period, the beams were retested to determine the strength recovery of the specimens. The results showed that the specimen groups in which calcium lactate was added to the cementitious matrix displayed the highest values in compressive strength. In terms of flexural strength, no major difference was found among the specimens. Moreover, the flexural strength recovery of the specimens did not show any significant difference as well. In terms of the healing efficiency, the sample that displayed the best results was the one containing calcium lactate as a precursor along with bacteria and yeast extract encapsulated in hydrogel beads. In addition, scanning electron microscopy (SEM) along with x-ray energy dispersive spectroscopy (EDS) was performed on the cracked specimens to characterize the healing products. Furthermore, a scale study was performed on concrete samples to determine the long-term implications of adding encapsulated bacteria along with calcium lactate and yeast extract in concrete.</p>
Multi-objective optimization of equation of state molecular parameters: SAFT-VR Mie models for water
<p>Supporting document containing information on the Pareto points and thermodynamic calculations.</p>
Dataset for the publication of "WRF model parameter calibration to improve the prediction of tropicalcyclones over the Bay of Bengal using Machine Learning-basedMultiobjective Optimization"
<p>The dataset consists of the modified WRF model software, that can be extracted and used in any Linux system with preinstalled required software.</p> <p>The namelists_file.zip consists of the namelist.input files that are used for the default and calibration simulations with different driving data namely, FNL files at 1deg with two nested domains, ERA files at 1deg with two nested domains, ERA files at 0.25deg with a single domain, and the ERA files at 0.25deg with two nested domains.</p>
Optimizing parameters for using the parallel auditory brainstem response (pABR) to quickly estimate hearing thresholds
<p><b>Objectives: </b>Timely assessments are critical to providing early intervention and better hearing and spoken language outcomes for children with hearing loss. To facilitate faster diagnostic hearing assessments in infants, the authors developed the parallel auditory brainstem response (pABR), which presents randomly timed trains of tone pips at five frequencies to each ear simultaneously. The pABR yields high-quality waveforms that are similar to the standard, single-frequency serial ABR but in a fraction of the recording time. While well-documented for standard ABRs, it is yet unknown how presentation rate and level interact to affect responses collected in parallel. Furthermore, the stimuli are yet to be calibrated to perceptual thresholds. Therefore, this study aimed to determine the optimal range of parameters for the pABR and to establish the normative stimulus level correction values for the ABR stimuli.</p> <p><b>Design: </b>Two experiments were completed, each with a group of 20 adults (18 – 35 years old) with normal hearing thresholds (≤ 20 dB HL) from 250 to 8000 Hz. First, pABR electroencephalographic (EEG) responses were recorded for six stimulation rates and two intensities. The changes in component wave V amplitude and latency were analyzed, as well as the time required for all responses to reach a criterion signal-to-noise ratio of 0 dB. Second, behavioral thresholds were measured for pure tones and for the pABR stimuli at each rate to determine the correction factors that relate the stimulus level in dB peSPL to perceptual thresholds in dB nHL.</p> <p><b>Results:</b> The pABR showed some adaptation with increased stimulation rate. A wide range of rates yielded robust responses in under 15 minutes, but 40 Hz was the optimal singular presentation rate. Extending the analysis window to include later components of the response offered further time-saving advantages for the temporally broader responses to low frequency tone pips. The perceptual thresholds to pABR stimuli changed subtly with rate, giving a relatively similar set of correction factors to convert the level of the pABR stimuli from dB peSPL to dB nHL.</p> <p><b>Conclusions: </b>The optimal stimulation rate for the pABR is 40 Hz, but using multiple rates may prove useful. Perceptual thresholds that subtly change across rate allow for a testing paradigm that easily transitions between rates, which may be useful for quickly estimating thresholds for different configurations of hearing loss. These optimized parameters facilitate expediency and effectiveness of the pABR to estimate hearing thresholds in a clinical setting.</p>
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.