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Dataset results
414 results for “Generative Model”
Automating pharmacovigilance evidence generation: Using large language models to produce context-aware SQL
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Generation of synthetic whole-slide image tiles of tumours from RNA-sequencing data via cascaded diffusion models
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Leatherback sea turtle (<em>Dermochelys coriacea</em>) presence locations used to generate distribution models in the Northwest Atlantic Ocean
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Data from: GnRH pulse generator activity in mouse models of polycystic ovary syndrome
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Data from: Changing measurements or changing movements? Sampling scale and movement model identifiability across generations of biologging technology
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BEAM input generation and low exposure routing model
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Supplementary Material to Context-tailored Workload Model Generation for Continuous Representative Load Testing
<p>This package contains files and instructions to replicate our experiments on context-tailored workload model generation for continuous representative load testing. Please download and extract the <code>context-tailoring.tar.gz</code> file and view <code>index.html</code> (also contained in the tarball) for further instructions.</p> <p><code>cobra-db.tar.gz </code>is only required for skipping parts of the steps (see the detailed instructions).</p>
Data from: A model-derived short-term estimation method of effective size for small populations with overlapping generations
If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rate increases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasing their risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and therefore of considerable conservation relevance. However, estimators of Ne that account for demographic parameters in species with overlapping generations require sampling of populations across generations, which is often not feasible in long-lived species. We created an individual-based model that allows calculation of Ne based on demographic parameters that can be obtained in a time period much shorter than a generation. It can be adapted to every life-history parameter combination. The model is freely available as an r-package NEff. The model was first used in a simulation experiment observing changes in Ne in response to different degrees of generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosity loss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of different recruitment rates only affected Ne for populations with low generational overlap. The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata. Simulation results were compared to genetic analyses and matched estimates of the real population very well. Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring nor genetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne within short time periods and comparably low costs facilitating the use of Ne in applied conservation and management.
Data from: "Genome-wide microsatellite marker development from next-generation sequencing of two non-model bat species impacted by wind turbine mortality: Lasiurus borealis and L. cinereus (Vespertilionidae)" in Genomic Resources Notes accepted 1 October 2013 to 30 November 2013
Tree-roosting bats in the genus Lasiurus are widespread, migratory species that have not been well characterized for population genetic diversity and structure due to a lack of genetic resources. Generating genetic resources in Lasiurus is made pressing by the need for conservation genetic assessments of demographic trends in this genus, which comprise a large percentage of bat mortalities at wind turbine sites across North America. We report on marker development from whole-genome Illumina sequencing of the red bat (Lasirus borealis) and the hoary bat (L. cinereus). We generated paired-end libraries for a single individual of each species, sequenced on the Illumina HiSeq platform. We mapped a total of 46.6 million reads to the Myotis lucifigus reference genome, and used bioinformatics searches to identify tends of thousands of simple sequence repeats (SSRs) distributed across the bat genome. We selected 48 candidate microsatellite loci to develop cross-species primer sequences for Lasiurus, assembled these into multiplex combinations, and tested for amplification and polymorphism levels in a sample of 23 individuals from each of L. borealis and L. cinereus. In total, we identified 42 highly polymorphic loci that could be robustly amplified and scored, the majority of which (39) were also combinable into highly multiplexed assays of 4-8 loci each. The combination of new genomic sequence assemblies, a large set of highly polymorphic microsatellite loci, and the ability to efficiently multiplex represents a significant contribution to the genetic resources available for population and comparative genetic studies of bats.
Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed.
Dataset for Generative Model of Software Dependency Graphs
<p>Data set for the paper entitled "A Generative Model of Software Dependency Graphs to Better Understand Software Evolution".</p> <p>Available files are:</p> <ul> <li>Sources archives (102 MB),</li> <li>Extracted dependencies (3.5 MB) and</li> <li>Generated graphs (15 MB).</li> </ul>
Text generated by OPUS-MT and T5 models with single-bit errors in the parameters
<h2>Description</h2> <p>The dataset contains text generated using T5 and OPUS-MT model with and with single-bit errors in the parameters of the LLM. The T5 LLM used the <a href="https://huggingface.co/datasets/cnn_dailymail/viewer/3.0.0/test">CNN Daily Mail</a> dataset for summarization and OPUS-MT used the <a href="https://aclanthology.org/2017.iwslt-1.1/">IWSLT2017</a> dataset for Chinese-to-English translation.</p> <p> </p> <p>Folders:</p> <ul> <li>t5_fp32: T5 model with a quantified version of FP32</li> <li>t5_fp16: T5 model with a quantified version of FP16</li> <li>opus_fp32: OPUS-MT model with a quantified version of FP32</li> <li>opus_fp16: OPUS-MT model with a quantified version of FP16</li> </ul> <p>Files:</p> <ul> <li><strong>{cnn/iwslt2017}_input_text.txt</strong>: Input text, that is, text to summarize (cnn and T5) or Chinese text to translate (iwslt2017 and OPUS-MT). For each dataset in total there are <em>number_input_texts.</em></li> <li><strong>{cnn/iwslt2017}_output_reference.txt:</strong> Example of result expected for CNN (T5) and IWSLT2017 (OPUS-MT). For each dataset in total there are <em>number_input_texts.</em></li> <li><strong>{cnn/iwslt2017}_output_predict_fault_free:</strong> Example of predictions without single-bit errors. For each dataset in total there are <em>number_input_texts.</em></li> <li><strong>{cnn/iwslt2017}_output_predict_single_fi_bit_100times:</strong> Example of predictions with 100 different single-bit error. In each dataset in total there are <em>100*number input texts</em>.</li> </ul> <h2>Paper</h2> <ul> <li>Paper: <a href="https://doi.org/10.48550/arXiv.2403.16393">Concurrent Linguistic Error Detection (CLED) for Large Language Models</a></li> <li>Cite:</li> </ul> <p><code>@misc{zhu2024concurrent,</code><br><code> title={Concurrent Linguistic Error Detection (CLED) for Large Language Models}, </code><br><code> author={Jinhua Zhu and Javier Conde and Zhen Gao and Pedro Reviriego and Shanshan Liu and Fabrizio Lombardi},</code><br><code> year={2024},</code><br><code> eprint={2403.16393},</code><br><code> archivePrefix={arXiv},</code><br><code> primaryClass={cs.AI}</code><br><code>}</code></p> <p> </p>
Controllable velocity synthesis using generative diffusion models
<div> <p><span>We presented a controllable velocity synthesis framework using diffusion models, </span><span>yielding a high-diversity and high-quality velocity synthesis. Here</span> we present the relevant dataset to the paper. </p> </div>
Input files and movie visualizations for convection models discussed in Becker and Fuchs, "Generation of evolving plate boundaries and toroidal flow from visco-plastic damage-rheology mantle convection and continents", manuscript revised for G-Cubed
<p>These input files are for the CitcomS software as available on github.com/geodynamics/citcoms and used in the version under commit 2bda530. They can be used to recreate the models discussed in Becker and Fuchs (revised manuscript submitted to G-Cubed, 11/2023), with model codes discussed and listed in Table 1 of the preprint as provided here. We also provide selected animations of the time dependence of model output, referenced to the same model names.</p>
DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model.
<p>test and training data.</p>
Replication Package of the Paper: "Using Large Language Models for Commit Message Generation: A Preliminary Study"
<p>This replication package contains the evaluation data and script files used in the paper "Using Large Language Models for Commit Message Generation: A Preliminary Study". We provide below a brief description of each folder:</p><ul><li><strong>experiment_data/human_evaluation</strong>: Human evaluation results from two participants.</li><li><strong>experiment_data/msg</strong>: Generated commit messages of each method (baselines & LLMs) and human-written commit messages.</li><li><strong>script</strong>: Evaluation metric script, parallel inference script (for using OpenAI API).</li></ul>
Databases generated for Manuscript titled "Quantifying downward radiative fluxes from nighttime Martian water ice clouds: Applications to thermal modeling of surface temperatures"
<p>Databases generated for manuscript "<strong>Quantifying downward radiative fluxes from nighttime Martian water ice clouds: Applications to thermal modeling of surface temperatures</strong>"</p> <p>There are two zip files containing generated databases:</p> <p>The zip file titled "database.zip" contains generated database for calculated fluxes using the methodology mentioned in the manuscript. The database spans calculated fluxes in one degree bins for latitudes spanning 30° to -10° N and longitudes spanning 0° to 360°. There are 14760 separate .csv files that are for each one by one degree bin. The title of each file contains its coordinates in the format XXXNXXXEtb.csv (e.g. 000N000Etb.csv for 0°N, 0°E). Each .csv file contains four separate columns and variable rows. The columns have headers corresponding to specific values. "ls" corresponds to solar longitude or date based on Mars' orbit around the Sun. "Flux" corresponds to calculated flux based on the methodology presented on the manuscript. "Delta-T" is the difference in temperature comparing modeled temperature compared to Thermal Emission Spectrometer (TES) measured temperature. "Tau" corresponds to calculated Dust visible opacities using the methodology presented in this work. The rows in each file vary based on the temporal observations from TES at each location. </p> <p>The zip file titled "fitdatabase.zip" contains generated database for fitted fluxes using the methodology mentioned in the manuscript. The database spans calculated fluxes in one degree bins for latitudes spanning 30° to -10° N and longitudes spanning 0° to 360°. There are 14760 separate .csv files that are for each one by one degree bin. The title of each file contains its coordinates in the format XXXNXXXEtbf.csv (e.g. 000N000Etbf.csv for 0°N, 0°E). Each .csv file contains six separate columns and three hundred and sixty rows. The columns have headers corresponding to specific values. "ls" corresponds to solar longitude or date based on Mars' orbit around the Sun. "Flux" corresponds to calculated flux based on the methodology presented on the manuscript. "Delta-T" is the difference in temperature comparing modeled temperature compared to measured temperature. The fitting algorithm interpolates points between values in the calculated flux database and applies a rolling mean fit with a window spanning ten degrees in solar longitude centered at each calculated flux point. "FLAG" indicates the amount of points of calculated flux points that exist within the ten degree window centered at each flux point to demonstrate to the user how much data had to be fitted. "From Ls" shows the leftmost edge of the rolling mean fit window. "To Ls" shows the rightmost edge of the rolling mean fit window. The rows in each file correspond to one degree of solar longitude the fitting algorithm was designed to cover each solar longitude bin. </p> <p> </p>
A comparison of model-based and model-free agents in solving semi-automatically generated PPDDL problems - Plots
<p>A collection of all plots generated for deriving the conclusions seen in "<span><span>A comparison of model-based and model-free agents in solving semi-automatically generated PPDDL problems</span></span>".</p>
Leveraging basecaller's move table to generate a lightweight k-mer model
<p>The ONT RNA004 dataset that is used to create a 5-mer model using the basecaller's movetable.</p> <p>The dataset is a sub-sample extracted from a dataset that sequenced Universal Human Reference RNA.</p> <p>The specification of the bio sample is here</p> <p>https://www.agilent.com/cs/library/usermanuals/public/740000.pdf</p>
Raw datasets for mechnaical results and code generation for modelling the strength characteristics of TBC incorporating VPA and CP
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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.