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1,880 results for “Dimensionality”
Large-scale Three-dimensional Hydraulic Tomography Analyses of Long-term Municipal Wellfield Operations
<p>This file includes all the datasets utilized to accomplish the above study. Basically, it includes the information of grid for groundwater modeling, the distribution of wells, as well as water-level variations for model calibration and validation.</p>
Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
<p>A detailed list of the selected scRNA-seq datasets used in the paper, also provided in Additional file <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1898-6#MOESM1">1</a>: Table S1-S2.</p>
Data set for "Intertwined spin, charge, and pair correlations in the two-dimensional Hubbard model in the thermodynamic limit"
<p>This data set is for the paper "Intertwined spin, charge, and pair correlations in the two-dimensional Hubbard model in the thermodynamic limit". It contains the raw DCA HD5 and DQMC plain text output files, as well as the scripts and final processed data used to generate figures 1-5 of the main text and supplementary figures 1-12. Copies of the figures and latex files are also included for completeness. </p>
Reproducible, high-dimensional imaging in archival human tissue by Multiplexed Ion Beam Imaging by Time-of-Flight (MIBI-TOF)
<p>1. SingleChannelMIBI.zip: Single-channel MIBI-TOF images</p> <p>All folders are labeled as Slide[Number]Stain[Number]_Point[Number]_[TMACoreIndex], where the slide number and stain number correspond to the slide and day of staining, the point number corresponds to the order in which the images were collected for each slide, and the TMA core index corresponds to the ID of the tissue microarray core. Each folder contains single-channel TIFFs for each marker. See paper for details.</p> <p>2. SegmentationOutput.zip: Segmentation output of MIBI-TOF images</p> <p>Cell segmentation was performed using Mesmer (Greenwald NF, Nature Biotechnology 2021, https://www.deepcell.org/predict). Output of Mesmer that delineates the single cells in each of the images is included here. Naming convention is the same as above.</p> <p>3. DataTables.zip: Data tables that are needed to run mpi_ppp_ihc_regression.ipynb</p> <p>Contains MIBI-TOF data (ionpath_processed_data.csv), MIBI-TOF calibration data (calibration_data.csv), IHC data (ihc_data.csv), and a map of each sample to its tissue type (tissue_data.csv). Also includes cell table output from Mesmer with the cell clusters appended to the table (cell_table_size_normalized_clusters.csv).</p>
Data for "Characteristics of earthquake cycles: a cross-dimensional comparison 0D to 3D"
<p>This is the data used in "Characteristics of earthquake cycles: a cross-dimensional comparison 0D to 3D". The paper is currently under review. See README.txt for more information.</p>
Stress-induced flow channelization in three-dimensional fractured layered rocks
<p>The manuscript data for the stress-induced flow channelization in three-dimensional fractured layered rocks.</p>
Diffusive regimes in a two-dimensional chiral fluid - Supplementary Material
<p>Supplementary datasets and additional videos. Data files are included for the experiments corresponding to Figures 1(a), 2 and 4(a), they are stored in a compressed pickle format, they can be easily read in Python with:</p> <pre><code class="language-python">df = pd.read_pickle('path_to_file', compression='xz')</code></pre> <p>The experiment ids of the experimental data files correspond to the following cases:</p> <ul> <li>155e9e3bf635544e8ff7240c760bee7b: packing fraction 0.45, mean vorticity -0.12</li> <li>f509f3b902a7ada8064a9247404d7019: packing fraction 0.45, mean vorticity 0.03</li> <li>edc6f35457554fd45382f6becdf41d97: packing fraction 0.45, mean vorticity 0.26</li> </ul>
Evaluating Feature Attribution Methods in the Image Domain: High-Dimensional Datasets
<p>Here you can find the versions of the Places-365 and Caltech-256 datasets used in the paper Evaluating Feature Attribution Methods in the Image Domain.</p>
Source data for "High-κ perovskite membranes as insulators for two-dimensional transistors"
<p>IMPORTANT: The data must not be reused in other studies or publications without the approval of the corresponding authors. Additional data related to this paper may be requested from the corresponding authors upon reasonable request.</p>
Predicting the failure of two-dimensional silica glasses
<p>Datasets for the paper: Font-Clos F, Zanchi M, Hiemer S, Bonfanti S, Guerra R, Zaiser M, Zapperi S. Predicting the failure of two-dimensional silica glasses. arXiv preprint arXiv:2201.09723. 2022 Jan 24. <a href="https://arxiv.org/abs/2201.09723">https://arxiv.org/abs/2201.09723</a></p> <p>The datasets can be used together with the codes available at <a href="https://github.com/ComplexityBiosystems/2D-silica-ML">https://github.com/ComplexityBiosystems/2D-silica-ML</a> to reproduce the resuts of the paper above.</p> <p>In particular, the datasets contain the the following data</p> <ul> <li>The dataset '20201222-var02-onethousand.zip' contains configurations at fixed disorder (s<sup>2</sup>= 0.2).</li> <li>The dataset '20210209-variable-disorder.zip' contains configurations at variable disorder.</li> <li>The dataset 'ml_dataset_fracture_atoms_var02.tar.gz' contains the images for the prediction of the crack path.</li> <li>The dataset 'ml_dataset_var02.tar.gz' contains images of silica at fixed disorder (s<sup>2</sup>= 0.2). for the prediction of disorder, rupture strain and location.</li> <li>The dataset 'ml_dataset_variable_var.tar.gz' contains images of silica at variable disorder for the prediction of disorder, rupture strain and location.</li> <li>The dataset 'trained_models' contains an example of a ResNet trained for predicting rupture strain at variable disorder (it can be used for testing the Grad-CAM method).</li> </ul> <p> </p> <p> </p>
Changing function landscape of two dimensional recombinations
<p>The videos show the changing function landscape of two dimensional recombinations, described in the paper 'Increasing Diversity of Benchmark Functions Sets by Affine Recombination' which was submitted to PPSN 2022.</p> <p>We show all recombinations that include the unshifted two-dimensional sphere function paired with every other two-dimensional BBOB function. </p>
High dimensionality of stoichiometric niches in soil fauna
The ecological niche is a fundamental concept to understand species coexistence in natural communities. The recently developed framework of the multidimensional stoichiometric niche (MSN) characterizes species niches using chemical elements in living organisms. Despite the fact that living organisms are composed by multiple elements, stoichiometric studies have so far mostly focused on carbon (C), nitrogen (N), and phosphorus (P), and therefore a quantitative analysis of the dimensionality of the MSN in living organisms is still lacking, particularly for animals. Here we quantified ten elements composing the biomass of nine soil animal taxa (958 individuals) from three trophic groups. We found that all ten elements exhibited large variation among taxa, which was partially explained by their phylogeny. Overlaps of MSNs among the nine soil animal taxa were relatively smaller based on ten elements, compared with those based on only C, N, and P. Discriminant analysis using all ten elements successfully differentiated among the nine taxa (accuracy: 90%), whereas that using only C, N, and P resulted in a lower accuracy (60%). Our findings provide new evidence for MSN differentiation in soil fauna and demonstrate the high dimensionality of organismal stoichiometric niches beyond C, N, and P.
Supplementary material for "A collection of Constraint Programming models for the three-dimensional stable matching problem with cyclic preferences"
<p>No external dependency is needed to compile the code, but MiniZinc is required to run it. Running the code without any argument will give the instructions.</p>
Precessional dynamics of geometrically scaled magnetostatic spin waves in two-dimensional magnonic fractals
<p>Open data for "Precessional dynamics of geometrically scaled magnetostatic spin waves in two-dimensional magnonic fractals" published in PRB <strong>105</strong>, 174415 (2022)</p>
Datasets of the manuscript "Optical manipulation of Rashba-split 2-Dimensional Electron Gas"
<p>You can find here the two TimeResolved ARPES datasets used in the paper titled "Optical manipulation of Rashba-split 2-Dimensional Electron Gas". </p> <p>https://www.nature.com/articles/s41467-022-30742-5</p> <p>Data are in Igor Pro binary format.</p> <p>RawData_1 is the dataset used in Fig.3. The x scaling has been converted from angle to momentum and the energy is rescaled with respect to the chemical potential at negative delays. The Time Delay scaling is found in timewave_1.</p> <p>Similarly, RawData_2, RawData_20 and timewave_2 are the datasets used in Fig.2 of the paper. This x scale in both datasets has been converted from angle to momentum. The y-axes in RawData_20 is the kinetic energy. The y-axes in RawData_2 is the energy rescaled to the chemical potential at each time delay. The chemical potential is obtained by fitting the topological surface state around its Fermi momentum. </p> <p> </p>
Embedding obtained in the paper "Two-dimensional visualization of large document libraries using t-SNE"
<p>Embedding obtained in the paper "Two-dimensional visualization of large document libraries using t-SNE" (<a href="https://openreview.net/forum?id=Hebl3EZ16lq">https://openreview.net/forum?id=Hebl3EZ16lq</a>, <a href="https://github.com/berenslab/pubmed-tsne-iclr">https://github.com/berenslab/pubmed-tsne-iclr</a>).</p> <p>The paper used the PubMed 2020 baseline originally obtained from <a href="https://www.nlm.nih.gov/databases/download/pubmed_medline.html">https://www.nlm.nih.gov/databases/download/pubmed_medline.html</a>, courtesy of the U.S. National Library of Medicine. That exact dataset is not available anymore. Now (June 2022) one can access the 2021 baseline, which includes our data and new works published in 2021, plus some revised and deleted citations. </p> <p>The dataset provided here includes:</p> <p>- from the PubMed database: article title, journal, PMID, and publication year.</p> <p>- produced by us: t-SNE embedding X and Y coordinates, label, and color.</p>
From Networked to Isolated: Observing Water Hydrogen Bonds in Concentrated Electrolytes with Two Dimensional Infrared Spectroscopy
<p>The files contain the data that are shown in the figures of the Main Text and of the Supplementary Materials of the research article:</p> <p>From Networked to Isolated: Observing Water Hydrogen Bonds in Concentrated Electrolytes with Two Dimensional Infrared Spectroscopy</p> <p>Nicholas H. C. Lewis, Bogdan Dereka, Yong Zhang, Edward J. Maginn, and Andrei Tokmakoff</p> <p>J. Phys. Chem. B, (2022)</p>
Nonunique fraction of Fock exchange for defects in two-dimensional materials
<p>This dataset contains the input and output files for the defect calculations as described in the paper "Nonunique fraction of Fock exchange for defects in two-dimensional materials".</p> <ol> <li>ws2.tar.gz: PBE and PBE0, monolayer WS<sub>2</sub></li> <li>ws2_bulk.tar.gz: PBE and PBE0, bulk WS<sub>2</sub></li> <li>ws2_bgw.tar.gz: G<sub>0</sub>W<sub>0</sub>, monolayer WS<sub>2</sub></li> </ol> <p> </p>
Data and code from: A spectral three-dimensional color space model of tree crown health
<p>Protecting the future of forests in the United States and other countries depends in part on our ability to monitor and map forest health conditions in a timely fashion to facilitate management of emerging threats and disturbances over a multitude of spatial scales. Remote sensing data and technologies have contributed to our ability to meet these needs, but existing methods relying on supervised classification are often limited to specific areas by the availability of imagery or training data, as well as model transferability. Scaling up and operationalizing these methods for general broadscale monitoring and mapping may be promoted by using simple models that are easily trained and projected across space and time with widely available imagery. Here, we describe a new model that classifies high resolution (~1 m<sup>2</sup>) 3-band red, green, blue (RGB) imagery from a single point in time into one of four color classes corresponding to tree crown condition or health: green healthy crowns, red damaged or dying crowns, gray damaged or dead crowns, and shadowed crowns where the condition status is unknown. These Tree Crown Health (TCH) models trained on data from the United States (US) Department of Agriculture, National Agriculture Imagery Program (NAIP), for all 48 States in the contiguous US and spanning years 2012 to 2019, exhibited high measures of model performance and transferability when evaluated using randomly withheld testing data (<em>n</em> = 122 NAIP state x year combinations; median overall accuracy 0.89-0.90; median Kappa 0.85-0.86). We present examples of how TCH models can detect and map individual tree mortality resulting from a variety of nationally significant native and invasive forest insects and diseases in the US. We conclude with discussion of opportunities and challenges for extending and implementing TCH models in support of broadscale monitoring and mapping of forest health.</p>
Experimental data for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels
<p>Experimental data set for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels. Provides all raw data needed to reproduce experimental graphs presented within the paper.</p>
ScienceDex guides
Understand access before you commit
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.