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Dataset results
102 results for “Network simulation”
Simulated results from an agent-based model examining inequality and innovation in social networks
<p>Theories of innovation often balance contrasting views that either smart people create smart things or smartly constructed institutions create smart things. While population models have shown factors including population size, connectivity, and agent behavior as crucial for innovation, few have taken the individual-central approach seriously by examining the role individuals play within their groups. To explore how network structures influence not only population-level innovation but also performance among individuals, we studied an agent-based model of the Potions Task, a paradigm developed to test how structure affects a group's ability to solve a difficult exploration task. We explore how size, connectivity, and rates of information sharing in a network influence innovation and how these have an impact on the emergence of inequality in terms of agent contributions. We find, in line with prior work, population size has a positive effect on innovation, but that large and small populations perform similarly per capita; that many small groups outperform fewer large groups; that random changes to structure have few effects on innovation; and that the highest performing agents tend to occupy more central network positions. Moreover, we show that every network factor which facilitates innovation leads to a proportional increase in inequality of performance, creating "genius effects" among otherwise "dumb" agents in both idealized and real-world networks.</p>
Exploring Kv1.2 channel inactivation through MD simulations and network analysis
<p>MD equilibration trajectories of Kv1.2 WT and mutants in dcd format can be visualized using visualization tools such as VMD or PyMol after uploading the topology file (.prmtop).</p>
A Tungsten Deep Neural-Network Potential for Simulating Mechanical Property Degradation Under Fusion Service Environment
<p>The DP-HYB and DP-SE2potential and the W training database.</p>
Replication Data for: ``Impact of Parameterized Isopycnal Diffusivity on Shelf-Ocean Exchanges under Upwelling-Favorable Winds: Offline Tracer Simulations Augmented by Artificial Neural Network''
<p>This dataset contains the modified MAMEBUS source code, configuration files for the MITgcm and MAMEBUS simulations, model diagnostics used in the paper, and scripts to train the Artificial Neural Networks.</p>
Assessing Pairwise Ecological Association Inference using a novel Ecological Network Inference Simulation-Validation Framework - Data Repository
<p>Accompanying data for manuscript entitled "<span>A novel Network Inference Simulation-Validation Framework for Assessment of Ecological Network Inference Performance</span>" whose submission is imminent.</p>
Ground-state dataset "Zero-temperature Monte Carlo simulations of two-dimensional quantum spin glasses guided by neural network states"
<h1>2D QUANTUM EDWARDS-ANDERSON GROUND-STATE DATASET:</h1> <p>The dataset contains coupling and energy data for 50 instances of a 2D quantum Edwards-Anderson model at Gamma (transverse field) = 1.8, featuring N=LxL=100 spins on a square lattice of side-length L=10 with periodic boundary conditions. The couplings are sampled from a Gaussian distribution with zero mean and unit variance.<br>The dataset consists of two text files containing coupling values and the corresponding ground-state energies.</p> <h2>Coupling Data (`coup_dataset.txt`)</h2> <p>The file `coup_dataset.txt` contains fifty sets of coupling data. Each set consists of three columns representing the indices `i`, `j`, and the coupling value `J_ij`, respectively.<br>The spin indices range from 1 to 100, ordered progressively by rows. Each set of coupling data is separated by two empty lines.</p> <h2>Energy Data (eng_dataset.txt)</h2> <p>The file `eng_dataset.txt` contains fifty rows of energy data corresponding to the coupling sets in `coup_dataset.txt`. Each row contains two columns representing the energy value and its associated statistical error-bar, rounded to the fifth decimal digit.</p>
Thermodynamics of alkali feldspar solid solutions with varying Al–Si order: atomistic simulations using a neural network potential - Accompanying Data
<p>This dataset accompanies the manuscript: "Thermodynamics of alkali feldspar solid solutions with varying Al–Si order: atomistic simulations using a neural network potential". It contains:</p> <ul> <li>LAMMPS-data files of the relaxed 8x6x8 systems for the three ordering types across Na-K composition, </li> <li>template input files for the minimization and for the semi grand canonical Monte Carlo + molecular dynamics simulation,</li> <li>the training and testing data with and without the point charge correction,</li> <li>the neural network potential committee and a modified n2p2 source that is necessary for running the special weighted atom centered symmetry functions. </li> </ul> <p>The algorithm to create the Al-Si and Na-K disorder is hosted on <a href="https://github.com/alexgorfer/Alkali-feldspar-disorder-generator">https://github.com/alexgorfer/Alkali-feldspar-disorder-generator</a> instead.</p>
Vehicle trajectory data in simulation network
<p>The project will use vehicle trajectory data generated from simulation platform. The simulation network was built in VISSIM containing a four-leg intersection with left-turn, through, and right-turn movements. The trajectory data were generated based on various traffic demand levels. The data set contains second-by-second vehicle speed and location. Details of the data set are explained as:</p> <p>Column 1 (NO): Number (Number/Index of the vehicle)<br> Column 2 (SimSec): Simulation second (Simulation time [s]) [s]<br> Column 3 (Lane\Link\No): Lane\Link\Number (Unique number of the link or connector)<br> Column 4 (Lane\Index): Lane\Index (Unique number of the lane)<br> Column 5 (Speed): Speed (Speed at the end of the time step) [km/h]<br> Column 6 (Pos): Position (Distance on the link from the beginning of the link or connector) [m]</p>
Data and code for training neural network parameterizations from an near-global aqua-planet simulation
<p>This commit contains the code, coarse-grained data, processed training data, neural network models, and coupled NN-GCM simulations. It can be extracted by running</p> <pre><code>tar xzf <archive></code></pre> <p>While this archive contains code (it is slightly out of date). This is the up-to-date code: <a href="https://zenodo.org/record/3248586">https://zenodo.org/record/3248586</a></p> <p>Move the "nn", "debiased", and "data" folders from this archive into that code directory.</p> <p> </p> <p> </p>
Updated Smoke Exposure Estimate for Indonesian Peatland Fires using a Network of Low-cost PM2.5 sensors and a regional air quality model - Model Simulation Data
<p>WRF-Chem simulated daily mean PM2.5 concentrations for:</p> <p>1) with fires </p> <p>2) without fires</p> <p>simulations. </p>
Surfaces/regoliths used in the training and testing of the deep neural network for surface reconstruction from simulated exospheric measurements
<p>This dataset contains the surfaces/regoliths in terms of elemental surface composition used in v2.0 - v2.5 of the paper collection: "Conceptual framework for the application of deep neural networks to surface composition reconstruction from Mercury’s exosphere".</p>
Inputs and outputs for exospheric simulations used in the deep neural network for surface reconstruction from simulated exospheric measurements
<p>This dataset contains the inputs and outputs of the exospheric simulations performed for v2.0 - v2.5 of the paper collection: "Conceptual framework for the application of deep neural networks to surface composition reconstruction from Mercury’s exosphere".</p>
Inputs and outputs for the training and testing of a deep neural network for surface reconstruction from simulated exospheric measurements
<p>This dataset contains inputs (datasets) and outputs (trainings and tests) used in v2.0 - v2.5 of the paper collection: "Conceptual framework for the application of deep neural networks to surface composition reconstruction from Mercury’s exosphere".</p>
Dataset for the numerical simulation in the article "Catalytically biased self-assembly by hybridization of reversibility and irreversibility in a reaction network"
<p>This dataset includes the essential source code and the corresponding numerical data for the self-assembly of a M6L4 square-based pyramid (SP) complex. </p> <p>The associated study is described in </p> <p><strong>"Catalytically biased self-assembly by hybridization of reversibility and irreversibility in a reaction network"</strong>, by T. Abe, S. Takahashi, H. Sato, and S. Hiraoka.</p>
Data and code for: Generation and applications of simulated datasets to integrate social network and demographic analyses
<p class="MsoNormal"><span>Social networks are tied to population dynamics; interactions are driven by population density and demographic structure, while social relationships can be key determinants of survival and reproductive success. However, difficulties integrating models used in demography and network analysis have limited research at this interface. We introduce the R package genNetDem for simulating integrated network-demographic datasets. It can be used to create longitudinal social networks and/or capture-recapture datasets with known properties. It incorporates the ability to generate populations and their social networks, generate grouping events using these networks, simulate social network effects on individual survival, and flexibly sample these longitudinal datasets of social associations. By generating co-capture data with known statistical relationships it provides functionality for methodological research. We demonstrate its use with case studies testing how imputation and sampling design influence the success of adding network traits to conventional Cormack-Jolly-Seber (CJS) models. We show that incorporating social network effects in CJS models generates qualitatively accurate results, but with downward-biased parameter estimates when network position influences survival. Biases are greater when fewer interactions are sampled or fewer individuals are observed in each interaction. While our results indicate the potential of incorporating social effects within demographic models, they show that imputing missing network measures alone is insufficient to accurately estimate social effects on survival, pointing to the importance of incorporating network imputation approaches. genNetDem provides a flexible tool to aid these methodological advancements and help researchers test other sampling considerations in social network studies.</span></p>
Data Set "Protein network centralities as descriptor for QM region construction in QM/MM simulations of enzymes"
<p>This data set accompanies the publication "Efficient automatic construction of atom-economical QM regions with point-charge variation analysis" by Felix Brandt and Christoph R. Jacob (TU Braunschweig, Germany) </p> <p>It contains:</p> <p>- PDB files of the starting structures</p> <p>- modified AMBER95 force field file</p> <p>- AMS fragment files for the substrates and ions</p> <p>- AMS input files for all geometry optimizations and single point calculations</p> <p>- Python script for WISP and centrality analysis</p>
Discovery of indole alkaloids crienamides A and B from penicillium citrinum by a simulated MS/MS-guided molecular network strategy
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Data from: Resistance of plant–plant networks to biodiversity loss and secondary extinctions following simulated environmental changes
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Data from: Performance-based Egress safety assessment of underground tunnels: Simulation and artificial neural network approaches
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Data from: Simulated poaching affects global connectivity and efficiency in social networks of African savanna elephants—An exemplar of how human disturbance impacts group-living species
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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.