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107 results for “integrative learning”
Using machine learning to integrate genetic and environmental data to model genotype-by-environment interactions
<p>Files generated from the study described in <a href="https://doi.org/10.1101/2024.02.08.579534">Fernandes et. al (2024)</a> .</p> <p>The file "cvs_h2s.csv" comprises the coefficient of variation and the Cullis heritability for each environment.</p> <p>The file "all_predictions.csv" contains the predictions from all the models evaluated, in different cross-validation (CV) scenarios.</p> <p>The file "coincidence_index.csv" has the Coincidence Index (CI) for each CV and models evaluated in our study.</p> <p>Our study used the multi-environment maize yield trials data from the Genomes to Fields 2022 initiative (<a href="https://doi.org/10.1186/s13104-023-06421-z">Lima et. al 2024</a>).</p>
Course Materials for Environmental Data Science in R: Introduction to Data Integration and Machine Learning (ENV 730)
In today's world, understanding environmental data and making informed decisions based on it is crucial for addressing complex environmental challenges. Yale School of the Environment's Environmental Data Science in R: Introduction to Data Integration and Machine Learning (ENV 730) course serves as an introduction to the integration of environmental data using R programming language, coupled with machine learning techniques. This dataset contains a zip file with all the data files used in this course, along with a README that has the metadata for those files.
Enhanced Westermo dataset - Transformed and Modified for Test case Selection and Priorotization in the context of Continuous Integration and Reinforcement Learning.
<p><strong>Overview</strong></p> <p>This repository contains a modified version of the existing, recently published dataset, Westermo. The initial dataset was gathered at Westermo Network Technologies AB, located in Västerås, Sweden. It encompasses over <strong>1 Million verdicts</strong> obtained from testing embedded systems, collected over a span of more than <strong>500 consecutive days</strong> of nightly testing. The dataset has been transformed and tailored specifically to cater to the research community, particularly for addressing challenges such as regression test selection, identification of flaky tests, and visualization of test results. The original dataset can be accessed through the reference provided in <strong>[1]</strong>.</p> <p>The Westermo dataset offers valuable historical information regarding the execution of test cases and their corresponding results. It serves as a valuable resource for evaluating and comparing different Test case Selection and Prioritization (TSP) techniques, enabling researchers to identify test cases that are more likely to fail during subsequent executions. Test cases in the dataset are characterized by attributes such as execution duration, previous last execution time, and the results of their recent executions.</p> <p>This dataset offers valuable historical information regarding the execution of test cases and their corresponding results. It serves as a valuable resource for evaluating and comparing different test case prioritization and selection techniques, enabling researchers to identify test cases that are more likely to fail during subsequent executions. Test cases in the dataset are characterized by attributes such as execution duration, previous last execution time, and the results of their recent executions.</p> <table align="left"> <caption><strong>Table 1: Dataset Overview</strong></caption> <tbody> <tr> <td>Test Cases</td> <td>1855</td> </tr> <tr> <td>CI Cycles</td> <td>15,197</td> </tr> <tr> <td>Verdict</td> <td>1,036,818</td> </tr> <tr> <td>Failed</td> <td>5.03%</td> </tr> </tbody> </table> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p>However, the diversity and multitude of the features in the dataset can be irrelevant to some TSP approaches. This led us to perform a dataset conversion, where we customized Westermo to have the same features from Paint Control and IOF/ROL, two widely used datasets in Reinforcement Learning based TSP approaches.</p> <p>This conversion required the combination of multiple variables and generating the target ones. When it comes to generating the “LastResults” and “Cycle” values, further analysis was required and the data handling needed an in-depth understanding of how the nightly testing was conducted. This led us to investigate what a CI cycle is in their context, and we followed their definition of a session, stating that “a session is when we run a suite of tests on one test system with a certain software version and testware version”. When splitting the data according to the 9 different systems used, we were able to generate 9 different sub-sets that fit the CI context.</p> <p> </p> <p><strong>File Format</strong></p> <p>The compressed .zip file contains 9 files, each one corresponding to each of the 9 systems. The datasets are available in CSV format, with the semicolon (;) serving as the delimiter. The columns included are represented in the table below along with their descriptions.</p> <table> <caption><strong>Table 2: Parameters of the dataset</strong></caption> <thead> <tr> <th scope="col">Column Name</th> <th scope="col">Content</th> </tr> </thead> <tbody> <tr> <td>Id</td> <td>Unique numeric identifier of the test execution </td> </tr> <tr> <td>Name</td> <td>Unique numeric identifier of the test case</td> </tr> <tr> <td>Duration</td> <td>Approximated runtime of the test case</td> </tr> <tr> <td>CalcPrio</td> <td>Priority of the test case, calculated by the prioritization algorithm (output column, initially 0)</td> </tr> <tr> <td>LastRun</td> <td>Previous last execution of the test case as date-time-string (Format: <em>YYYY-MM-DD HH:ii </em>)</td> </tr> <tr> <td>LastResults</td> <td>List of previous test results (Failed: 1, Passed: 0), ordered by ascending age. Lists are delimited by [ ].</td> </tr> <tr> <td>Verdict</td> <td> <p>Test verdict of this test execution (Failed: 1, Passed: 0)</p> </td> </tr> <tr> <td>Cycle</td> <td>The number of the CI cycle this test execution belongs to.</td> </tr> </tbody> </table> <p> </p> <p>The implications of this conversion are important as it can help the previous works to re-assess their approaches and have more data for training and testing, as well as opening a broader data spectrum for future researchers in this field to find ready-to-use, rich datasets, on which they could evaluate their approaches and contribute to the TSP community. This also addresses the limitations in the field discussed in the systematic literature review <strong>[2]</strong>, stating that future research on TSP techniques should focus on collecting data from more recent subjects in a CI context with varying failure rates and larger execution times, as reproducible studies with appropriate datasets are needed to develop a usable body of knowledge regarding TSP over time. We believe that this conversion of the Westermo dataset is our contribution to alleviating the gap for the RL-based approaches.</p> <p>The original dataset can be found <a href="https://sites.mdu.se/aidoart/results/open-source/test-results-dataset-westermo">here.</a></p>
Rule based and information integration category learning
<p>The following dataset includes sessions from rats and humans learning and generalizing to Rule-based and Information Integration categories. Here, category exemplars are Gabor patches, which are circular stimuli that contain black and white gratings. Across exemplars, these gratings can change in their spatial frequency and orientation. For Rule-based tasks, only one stimulus dimension (i.e., spatial frequency or orientation) is category-relevant, and the other dimension varies randomly. For Information Integration tasks, both stimulus dimensions (i.e., spatial frequency and orientation) are category-relevant. On each learning trial, participants are presented with a category exemplar and must decide its category membership. Feedback guides learning. Rats are trained using a touchscreen apparatus, whereas humans are trained using a desktop computer. </p>
Dataset for Integrated hydrodynamic and machine learning models
<p>The dataset is the supplement to our publication in <a href="https://www.nonlinear-processes-in-geophysics.net/">Nonlinear Processes in Geophysics</a> (https://doi.org/10.5194/npg-2021-36). To use this data, please give us credit by citing our article.</p>
Integrated Machine Learning model in Early Urban Flooding Warning System - Data
<p>AI_DATA.npy - Inundation data (mm) generated from MIKE+ model that has been converted to numpy array</p> <p>INDEX.npy - The index where inundation is > 0 </p> <p>source.tif - Source tif image for creating map from ML models</p>
Prototyping 3D Virtual Learning Environments with X3D-based Content and Visualization Tools-Figure 7. The HTML source (partial) code, integrating the X3D model
<p>To integrate the model into a web page, a model conversion to X3D format and an X3DOM output under the form of an HTML5 encoded webpage (Figure 7) were needed. Instant Reality distribution provides a command line transcoding tool, named Avalon Optimizer (aopt), that was used to convert a VRML format (wrl extension) of the model to X3D. </p>
Extended data integration of motivational aspects in gamification and game-based learning educational designs
<p>This is the extended data for a systematic review article about the integration of motivational aspects in gamification and game-based learning educational designs related to teacher´s training and teacher´s professional development.</p>
Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning: Cleaned Data
<p>The included files and script are to allow for reconstruction of the data directory and cleaned data used in "Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning" ( https://doi.org/10.1101/2022.07.29.502051 ). Code used is available at 10.5281/zenodo.7401113 .</p> <table> <tbody> <tr> <th>Filename</th> <th>Description</th> </tr> <tr> <td>interim.tar.gz</td> <td>Contains site grouping dictonary</td> </tr> <tr> <td>processed.tar.gz</td> <td>Processed data</td> </tr> <tr> <td>raw.tar.gz</td> <td>Input data</td> </tr> <tr> <td>SetupInstructions.sh</td> <td>Bash script to prepare folders and unzipped data expected by code in 10.5281/zenodo.7401113</td> </tr> <tr> <td>SetupInstructions.txt</td> <td>Instructions for unzipping the data</td> </tr> <tr> <td>Train_Test_Split_Reference_Phenotypes.csv</td> <td>Reference spreadsheet to allow for easily exploring training and test set groupings</td> </tr> </tbody> </table> <ul> </ul> <p>This work was supported through funding from the USDA Agricultural Research Service, ARS project number 5070-21000-041-000-D. Raw data provided by the [Genomes to Field Initiative](https://www.genomes2fields.org/) and the [Daymet database](https://daymet.ornl.gov/).</p>
Data from: Data fusion for integrative species identification using deep learning
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DeepInMiniscope: Deep-learning-powered physics-informed integrated miniscope
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Data from: Integrating deep learning derived morphological traits and molecular data for total-evidence phylogenetics: lessons from digitized collections
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Rule based and information integration category learning
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Datasets from the study Peer learning as a key component of an Integrated Teaching Method in large size classes
<p>The theory and research on learning in higher education are pointing out that active methods are able to improve learners’ performance more than passive ones and to trigger situated and deep learning. However, some factors prevent their spread and trust amongst university instructors, like their complex logistics in large size lectures. Indeed, in academic crowded classes these interactive-engagement methodologies are sporadically employed and seem to be rarely successful. In this context, in the academic years 2017-2018 and 2018-2019 we carried out a quasi-experiment at Politecnico di Milano aimed at investigating the effectiveness of the integration of peer learning activities, strengthened by the use of technology, into traditional Physics lectures as a teaching method in large size classes. Data related to both an experimental and a control group were gathered and analysed through descriptive and inferential statistics; Shapiro-Wilk, Levene, Mann-Whitney U, Wilcoxon signed-rank and Kruskal-Wallis tests were employed. Our combined strategy appears to be effective with relation to learning Physics and more successful than traditional courses centred on academic lectures, regardless of the difficulty of the issues investigated. Furthermore, a threshold for the exposure to peer learning in order for it to be effective has been highlighed.</p> <p>In this page it is shared:</p> <p>1) Dataset with reference to both 2017-2018 and 2018-2019</p> <p>2) R Script with reference to both 2017-2018 and 2018-2019</p>
Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data
<p>The growing availability of genetic datasets, in combination with machine learning frameworks, offer great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What factors determine intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we analyzed repurposed data using machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open-access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow-up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this dataset, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contain lower genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful datasets with greater utility for understanding global biodiversity.</p>
DeepAnnotation: A novel interpretable deep learning-based genomic selection model that integrates comprehensive functional annotations
<p>1. Update package, example dataset, and demo code of DeepAnnotation</p> <p>2. Update the transformed genotype data, the phenotype data, the comprehensive functional annotation data for Duroc prepared by RNAfold, DeepSEA, easyMF models, and the four types of input data for training DeepAnnotation model</p> <p>3. Add the conserved functional annotation</p> <p> </p>
NMDA receptors in visual cortex are necessary for normal visuomotor integration and skill learning
<p>Raw data and Matlab code to generate the figures of the publication "NMDA receptors in visual cortex are necessary for normal visuomotor integration and skill learning" <a href="https://doi.org/10.7554/eLife.71476">https://doi.org/10.7554/eLife.71476</a>. Run generate_NKO_figures.m to produce all figures in the publication. </p>
Learning by Viewing: Generating Test Inputs for Games by Integrating Human Gameplay Traces in Neuroevolution
<p>Replication package for the paper "Learning by Viewing: Generating Test Inputs for Games by Integrating Human Gameplay Traces in Neuroevolution" </p><p> </p><p>Although automated test generation is common in many programming domains, games still challenge test generators due to their heavy randomisation and hard-to-reach program states. Neuroevolution combined with search-based software testing principles has been shown to be a promising approach for testing games, but the co-evolutionary search for optimal network topologies and weights involves unreasonably long search durations. Humans, on the other hand, tend to be quick in picking up basic gameplay. In this paper, we therefore aim to improve the evolutionary search for game input generators by integrating knowledge about human gameplay behaviour. To this end, we propose a novel way of systematically recording human gameplay traces, and integrating these traces into the evolutionary search for networks using traditional gradient descent as a mutation operator. Experiments conducted on eight diverse Scratch games demonstrate that the proposed approach reduces the required search time from five hours down to only 30 minutes on average.</p>
[Data] Real-time monitoring and quality assurance for laser-based directed energy deposition: integrating co-axial imaging and self-supervised deep learning framework
<p>The experimental setup utilized a co-axial color Charged Couple Device (CCD) camera, integrated into the laser deposition head. This camera operates at a frame rate of 30 frames per second and captures the morphology of the process area. The captured images consist of three RGB channels with a 640 × 480 pixels resolution. To enable the camera to capture the radiation from the process zone, a beam splitter is installed on Precitec's laser applicator head. An optical notch filter within the 650–675 nm range also blocks the laser wavelengths.</p> <p>The dataset consists of four categories that covers the process map of DED process [.rar file].<br>The dataset consist of around 48,000 images that are labelled into 4 categories [P1-P2-P3-P4]. The images correspond to DED process zone captured co-axially<br>The categories are function of linear laser energy deposited. The folder is already split into Train and Test.</p>
Aerial Images_Part 2_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria
<p>Aerial Images_Part 2_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria</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.