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Dataset results
103 results for “regression modeling”
AMOC reconstruction between 1981 and 2016 from hydrographic data using an empirical linear regression model from Worthington, E. L., Moat, B. I., Smeed, D. A., Mecking, J. V., Marsh, R., and McCarthy, G. D.: A 30-year reconstruction of the Atlantic meridional overturning circulation shows no decline, Ocean Sci., 17, 285–299, https://doi.org/10.5194/os-17-285-2021, 2021.
<p>Dataset used to create Figure 8 in Worthington et al., 2021 (https://doi.org/10.5194/os-17-285-2021). Details of the data and methods can be found in the journal article.<br> <br> Worthington, E. L., Moat, B. I., Smeed, D. A., Mecking, J. V., Marsh, R., and McCarthy, G. D.: A 30-year reconstruction of the Atlantic meridional overturning circulation shows no decline, Ocean Sci., 17, 285–299, <a href="https://doi.org/10.5194/os-17-285-2021">https://doi.org/10.5194/os-17-285-2021</a>, 2021.</p>
Parsimonious Random-Forest-Based Land-Use Regression Model Using Particulate Matter Sensors in Berlin, Germany
<p>The dataset consists of particulate matter pollution concentration, measured in three localities - Hermsdorf, Charlottenburg and Adlershof, in Berlin, Germany.</p> <p><a href="../api/records/10076056/draft/files/pm25_summer_rd_30s.geojson/content" target="_blank" rel="noopener noreferrer">pm25_summer_rd_30s.geojson</a> shows the observed PM2.5 concentration in a 30 second interval.</p> <p><a href="../api/records/10076056/draft/files/pm25_summer.geojson/content" target="_blank" rel="noopener noreferrer">pm25_summer.geojson</a> shows the concentrations shown is the local concentration (observed concentration - background concentration) in a 30 second interval. The background concentration is calculated as the lowest 5 percentile of the measured concentration for each measurement round. </p> <p><a href="../api/records/10076056/draft/files/PM2.5_lc_max.geojson/content" target="_blank" rel="noopener noreferrer">PM2.5_lc_max.geojson</a> contains the information from <a href="../api/records/10076056/draft/files/pm25_summer.geojson/content" target="_blank" rel="noopener noreferrer">pm25_summer.geojson</a> in a 25m resolution. Additionally, it contains the land use information for each coordinate.</p> <p>The original publication providing all necessary background information on study sites, methodology and data processing is the following: Venkatraman Jagatha, J., T. Sauter, C. Schneider (2024): Parsimonious Random-Forest-Based Land-Use Regression Model Using Particulate Matter Sensors in Berlin, Germany. MDPI Sensors, 24(13), 4193, DOI: 10.3390/s24134193. The paper is fully open access and can be downloaded at <a href="https://doi.org/10.3390/s24134193">https://doi.org/10.3390/s24134193</a>.</p> <p>Information on working with geojson file can be found under <a href="https://geojson.readthedocs.io/en/latest/">GeoJSON</a> .</p>
Dataset: The effects of class balance on the training energy consumption of logistic regression models
<p>Two synthetic datasets for binary classification, generated with the Random Radial Basis Function generator from WEKA. They are the same shape and size (104.952 instances, 185 attributes), but the "balanced" dataset has 52,13% of its instances belonging to class c0, while the "unbalanced" one only has 4,04% of its instances belonging to class c0. Therefore, this set of datasets is primarily meant to study how class balance influences the behaviour of a machine learning model.</p>
Convolutional Neural Net (CNN) models for epigenomic landscapes in epidermal differentiation - Basset architecture, classification and regression
<p>Deep learning models trained on epigenomic landscapes in keratinocyte differentiation. The models are Basset convolutional neural networks (Kelley, et al 2016). The dataset used to train these models can be found at https://doi.org/10.5281/zenodo.4062509. The file `nn.ggr.models.basset.clf.tar.gz` contains 10 cross-validated models that were pretrained using ENCODE-Roadmap trained model weights as initialization weights and also 10 cross-validated models that were initialized with random weights. Similarly, the file `nn.ggr.models.basset.regr.tar.gz` contains 10 cross-validated models that were pretrained using the classification model weights as initialization weights and also 10 cross-validated models that were initialized with random weights.</p>
GNN Models and results for the paper "Band-gap regression with architecture-optimized message-passing neural networks"
<p>Contains files with model parameters for random search and reference models, as well as the converted AFLOW dataset, in graphs form. Corresponds to results in <a href="https://arxiv.org/pdf/2309.06348.pdf">https://arxiv.org/pdf/2309.06348.pdf</a>.</p> <p>Model predictions along with AUID identifiers are located in result_combined.zip, band gap (egap) and formation energy (ef) predictions are from the PaiNN ensemble, band gap classification is done by MPEU model.</p> <p>New results include PaiNN NAS models.</p> <p>Compatible source code can be found at <a href="https://github.com/tisabe/jraph_MPEU/tree/v1.0.0">jraph_MPEU GitHub repository</a>.</p>
Code and Data to "Quantile regression for temporal streamflow modeling"
<p>This is the accompanying code to "Quantile regression for temporal streamflow modeling", which is part of the manuscript "The Role of Process Heterogeneity in Statistical Modeling", which was submitted to the Austrian Journal of Statistics. </p> <p> </p> <p>The data used in this publication is fully accessible through the <a href="https://doi.org/10.5194/essd-13-4529-2021" target="_blank" rel="noopener">LamaH-CE</a> dataset. The two scripts "functions_create_data.R" and "create_data.R" will create the final dataset used for modelling. </p> <p>"functions_modelling.R" provide the functions for tuning the XGBoost model and computing the SHAP values. An example script is also attached (calc_predictions_shap.R). "analyzing_results.R" and "error_metrics.R" will produce the final output used in the manuscript. Finally, two plots produced in the script are added as pdf. </p> <p>All data analysis was performed in R, and we want to acknowledge the following packages: <a href="https://dplyr.tidyverse.org/">dplyr</a>, <a href="https://tidyr.tidyverse.org/">tidyr</a>, <a href="https://www.jstatsoft.org/v40/i03/">lubridate</a>, <a href="https://purrr.tidyverse.org/">purrr</a>, <a href="https://doi.org/10.18637/jss.v033.i01">glmnet</a>, <a href="https://cran.r-project.org/web/packages/xgboost/index.html">xgboost</a>, <a href="https://CRAN.R-project.org/package=shapr">shapr</a>, <a href="https://CRAN.R-project.org/package=Metrics">Metrics</a>, <a href="https://CRAN.R-project.org/package=gridExtra" target="_blank" rel="noopener">gridExtra</a>, <a href="https://doi.org/10.18637/jss.v014.i06">zoo</a> and <a href="https://CRAN.R-project.org/package=wesanderson">wesanderson</a>. </p> <p> </p>
Association of Body Index with Fecal Microbiome in Children Cohorts with Ethnic-Geographic Factor Interaction: Accurately Using a Bayesian Zero-inflated Negative Binomial Regression Model
<p>this dataset are “ssociation of Body Index with Fecal Microbiome in Children Cohorts with Ethnic-Geographic Factor Interaction: Accurately Using a Bayesian Zero-inflated Negative Binomial Regression Model” Supplementary Material.</p>
Fig. 2. Linear regression models showing the relationship between Aphis citricola and Harmonia axyridis abundance. A in Behavioral responses of Aphis citricola (Hemiptera: Aphididae) and its natural enemy Harmonia axyridis (Coleoptera: Coccinellidae) to non-host plant volatiles
Fig. 2. Linear regression models showing the relationship between Aphis citricola and Harmonia axyridis abundance. A: Catnip (Nepeta cataria) + French marigold (Tagetes patula), B: ageratum (Ageratum houstonianum) + French marigold, C: catnip + ageratum, and D: native vegetation.
Stable Modeling on Resource Usage Parameters of MapReduce Application-Figure 6. RSE and R2 of regression models of MapReduce applications
<p>Figure 6 shows the fit quality of regression models. It is following.The left panel and the right panel of figure 6 show the residual standard error (RSE) distribution and R2 distribution of each application. The good fit quality corresponds to a taller R2 bar and a shorter RSE bar. The R2 almost 1 and small RSE show the best fit quality of the regression models on memory usage as the response. The overall higher RSE and lower R2 of regression models on CPU as the response show the worse quality of fitting goodness. The regression models on read rate as the response also show a moderate fitting quality. For the regression models on write rate as the response, Terasort application exhibits the best quality and Teragen application as well. Others show the worse fitting quality. The results show that the regression models on intensive usage parameters as response exhibit the good fitting quality.</p>
Stable Modeling on Resource Usage Parameters of MapReduce Application-Figure 2. ACF plot of Residuals of Regression Model of Terasort
<p>, are uncorrelated. If the error term is uncorrelated, it proves that there exists strong randomness in residuals of the model and provides the evidence for the unbiased estimate for the true standard error. The autocorrelation plot is used to check this assumption. Figure 2 shows the autocorrelation plot of residuals of regression models of TeraSort application. In Figure 2, the horizontal axis represents lag time and the vertical axis indicates the autocorrelation between residual at time t and residual at other lag time. At lag 0, autocorrelation is always equal to 1 and represents time series itself. Most of the autocorrelation at other lag time fall into the 95% confidence interval, only few of them violate the dashed line. Such a shape of ACF plot proves that residuals are uncorrelated and respects to the independent assumption of the linear regression model residuals.</p>
Regression models generated by APRANK (computational prioritization of antigenic proteins and peptides from complete pathogen proteomes)
<p>Availability of highly parallelized immunoassays has renewed interest in the discovery of serology-based biomarkers for infectious diseases. Protein and peptide microarrays now provide a high-throughput platform for immunological screening of potential antigens and B-cell epitopes. However, there is still a need to prioritize relevant probes when designing these arrays. In this work we describe a computational method called APRANK (Antigenic Protein and Peptide Ranker) which integrates multiple molecular features to prioritize antigenic targets starting from a given pathogen proteome. These features include subcellular localization, presence of repetitive motifs, natively disordered regions, secondary structure, transmembrane spans and predicted interaction with the immune system. We applied this method to the prioritization of potential diagnostic antigens and peptides in a number of pathogen proteomes and human diseases: Borrelia burgdorferi (Lyme disease), Brucella melitensis (Brucellosis), Coxiella burnetii (Q fever), Escherichia coli (Gastroenteritis), Francisella tularensis (Tularemia), Leishmania braziliensis (Leishmaniasis), Leptospira interrogans (Leptospirosis), Mycobacterium leprae (Leprae), Mycobacterium tuberculosis (Tuberculosis), Plasmodium falciparum (Malaria), Porphyromonas gingivalis (Periodontal disease), Staphylococcus aureus (Bacteremia), Streptococcus pyogenes (Group A Streptococcal infections), Toxoplasma gondii (Toxoplasmosis) and Trypanosoma cruzi (Chagas Disease). After training a linear regression model the method achieves good to excellent performance on most species, measured by the enrichment of validated antigens at the top of the ranking. An unbiased validation using independent data sets shows APRANK is successful in predicting antigenicity for all pathogen species tested. We make APRANK available to facilitate the identification of novel diagnostic antigens in infectious diseases.</p>
Regression Model to Predict the Higher Heating Value of Poultry Waste from Proximate Analysis.
<p>The response variable is High Heating Values (HHV), while the independent variables are Fixed Carbon (FC), Volatile Matter (VM), and Ash (A). </p>
Text-fig. 5. Macroevolutionary trends related to the IC model in the first three teeth of the six families of extinct sloths, as well as specimens of the "basal Megatherioidea", Pseudoglyptodon, and Bradypus. Dashed line (- -) shows the regression including all data; solid line shows the regression after the exclusion of Octodontotherium (shown in the plot as a filled triangle). in Unexpected Inhibitory Cascade In The Molariforms Of Sloths (Folivora, Xenarthra): A Case Study In Xenarthrans Honouring Gerhard Storch'S Open-Mindedness
Text-fig. 5. Macroevolutionary trends related to the IC model in the first three teeth of the six families of extinct sloths, as well as specimens of the "basal Megatherioidea", Pseudoglyptodon, and Bradypus. Dashed line (- -) shows the regression including all data; solid line shows the regression after the exclusion of Octodontotherium (shown in the plot as a filled triangle).
Text-fig. 4. Macroevolutionary trends related to the IC model in the last three teeth of the six families of extinct sloths, as well as specimens of the "basal Megatherioidea", Pseudoglyptodon, and Bradypus. Dash-dot line (-.-) shows the regression including all data; solid line shows the regression after the exclusion of Octodontotherium (shown in the plot as a filled triangle). in Unexpected Inhibitory Cascade In The Molariforms Of Sloths (Folivora, Xenarthra): A Case Study In Xenarthrans Honouring Gerhard Storch'S Open-Mindedness
Text-fig. 4. Macroevolutionary trends related to the IC model in the last three teeth of the six families of extinct sloths, as well as specimens of the "basal Megatherioidea", Pseudoglyptodon, and Bradypus. Dash-dot line (-.-) shows the regression including all data; solid line shows the regression after the exclusion of Octodontotherium (shown in the plot as a filled triangle).
Videos of Functional Regression Model for the Antarctic Sea Ice Edge
<p><a href="https://zenodo.org/api/files/198831a6-6078-449d-a532-8564977b425c/ObservedConcentration.mp4">ObservedConcentration.mp4</a> - Daily observed Antarctic sea ice concentration as provided by NSIDC</p> <p><a href="https://zenodo.org/api/files/198831a6-6078-449d-a532-8564977b425c/ObservedOutlines.mp4">ObservedOutlines.mp4</a> - Daily observed Antarctic sea ice edge based on the above concentrations. The edge is defined as the 15% sea ice concentration isoline</p> <p><a href="https://zenodo.org/api/files/198831a6-6078-449d-a532-8564977b425c/model_outline_daily_lon_lat.mp4">model_outline_daily_lon_lat.mp4</a> - Daily observed Antarctic sea ice edge (black) with modeled sea ice edge (blue) and 95% prediction intervals (dashed lines) in geographic projection</p> <p><a href="https://zenodo.org/api/files/198831a6-6078-449d-a532-8564977b425c/model_outline_daily_stereographic.mp4">model_outline_daily_stereographic.mp4</a> - Daily observed Antarctic sea ice edge (black) with modeled sea ice edge (blue) and 95% prediction intervals (dashed lines) in stereographic projection</p> <p> </p>
Supplementary tables for: Dependent variable selection in phylogenetic generalized least squares regression analysis under Pagel's lambda model
<p class="MsoNormal"><span>Phylogenetic generalized least squares (PGLS) regression is widely used to detect evolutionary correlations. In contrast to the equal treatment of analyzed traits in conventional correlation methods such as Pearson and Spearman's rank tests, we must designate one trait as the independent variable and the other as the dependent variable. However, in our PGLS regression analyses (using Pagel's <em>λ</em> model) of both empirical and simulated datasets, switching independent and dependent variables yielded many conflicting results. A serious problem with PGLS regression that has not been noticed before is that selecting an inappropriate trait as the dependent variable will often result in an error. To assess correlations in simulated data, we established a gold standard by analyzing changes in traits along phylogenetic branches. Next, we tested seven potential criteria for dependent variable selection: log-likelihood, Akaike information criterion, <em>R</em><sup>2</sup>, <em>p</em>-value, Pagel's <em>λ</em>, Blomberg et al.'s <em>K</em>, and the estimated <em>λ</em> in <a name="_Hlk136010442"></a>Pagel's <em>λ</em> model. We determined that the last three criteria performed equally well in selecting the dependent variable and were superior to the other four. For practicality, we suggest using the trait with a higher <em>λ</em></span><span> or <em>K</em> </span><span>value as the dependent variable in future PGLS regressions. In analyzing the evolutionary relationship between two traits, we should designate the trait with a stronger phylogenetic signal as the dependent variable even if it could logically assume the cause in the relationship.</span></p>
Factors Associated with Scientific Production Citations in Dentistry: Zero-inflated Negative Binomial Regression and Hurdle Modelling
<p><strong>Abstract:</strong> The global scientific literature in dentistry has shown important advances in the field, with major contributions ranging from the analysis of the basic epidemiological aspects of prevention to specialised results in the field of dental treatments. The present investigation aims to analyse the current state of the scientific literature on dentistry hosted in the Web of Science database. The methodology includes two phases in the analysis of articles and indexed reviews in all thematic areas. During the first phase, the following variables are analysed: scientific production by the publisher, the evolution of scientific output published by publishers, the factors associated with the impact of scientific production, and the modelling of the impact of scientific production on dentistry. During the second phase, associations, evolutions, and trends in the use of main keywords in the scientific literature in dentistry are analysed. In conclusion, the study shows that the most studied topics include the association of dental education and the curriculum, the association of pediatric dentistry with oral health, and dental care. The findings show that more recently emphasised topics also stand out, such as evidence-based dentistry, the pandemic, infection control, and endodontics, as well as the need for future research to expand current knowledge based on emerging topics in the scientific literature on dentistry.</p>
Evidence of absence regression: a binomial N-mixture model for estimating fatalities at wind power facilities
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Supplementary tables for: Dependent variable selection in phylogenetic generalized least squares regression analysis under Pagel’s lambda model
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Empirical data for: Extending phylogenetic regression models for comparing within-species patterns across the Tree of Life
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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.