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921 results for “Neural Network”
Ensemble Ecological Niche Models and Biodiversity Index for 2019 of 96 European Marine Species based on Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, AquaMaps, and Support Vector Machines at 0.1° Resolution
<p>Ensemble Ecological Niche Models for 2019 of 96 European marine species of particular commercial and conservation interest, based on Ecological Niche Models developed with (i) Artificial Neural Networks, (ii) Maximum Entropy, (iii) Support Vector Machines, and (iv) AquaMaps at 0.1° Resolution. The data report, for each 0.1° cell, how many models (from 0 to 4) overcome a model-specific decision threshold to assess species presence in the cell. A Biodiversity Index is also provided as the count of the number of species (among the 96) potentially present in each 0.1° cell according to the ensemble models. For each ensemble model, a threshold of at least 3 models agreeing on species presence in the cell was used to indicate species presence.</p>
Guinea baboon vocalizations dataset automatically extracted with a deep neural network from natural audio recordings
<p><strong>Abstract</strong></p> <p>The data collection process consisted of continuously recording during one month a group of Guinea baboons living in semi-liberty at the CNRS primatology center in Rousset-sur-Arc (France). Two microphones we placed nearby their enclosure to continuously record the sounds produced by the group. A convolutional neural network (CNN) was used on these large and noisy audio recordings to automatically extract segments of sound containing a baboon vocal production by following the method of <a href="https://arxiv.org/abs/2302.07640">Bonafos et al. (2023)</a>. The resulting dataset consists of one-second to several-minute wav files of automatically detected vocalizations segments. The dataset thus provides a wide range of baboon vocalizations produced at all times of the day. It can be used to study vocal productions of non-human primates, their repertoire, their distribution over the day, their frequency, and their heterogeneity. In addition to the analysis of animal communication, the dataset can also be used as a learning base for sound classification models.</p> <p> </p> <p><strong>Data acquisition</strong></p> <p>The data are audio recordings of baboons. The recordings were made with a H6 Zoom recorder, using the included XYH-6 stereo microphone. The sample size is 44100 Hertz, 16 bits. The microphones were placed in the vicinity of the enclosure for one month and recorded continuously on a PC computer. A CNN passed over the data with a sliding window of 1 second and an overlap of 80% to detect the vocal productions of the baboons. The dataset consists of the segments predicted by the CNN to contain a baboon vocalization. Windows containing signal less than one second apart were merged into a single vocalization.</p> <p> </p> <p><strong>Data source location</strong></p> <ul> <li>Institution: CNRS, Primate Facility</li> <li> <p>City/Town/Region: Rousset-sur-Arc</p> </li> <li> <p>Country: France</p> </li> <li> <p>Latitude and longitude for collected samples/data: 43.47033535251509, 5.6514732876668905</p> </li> </ul> <p> </p> <p><strong>Value of the data</strong></p> <ul> <li> <p>This dataset is relatively unique in terms of the quantity of vocalizations available.</p> </li> <li> <p>This massive dataset can be very useful to two types of scientific communities: experts in primatology who study the vocal productions of non-human primates, and experts in data science and audio signal processing.</p> </li> <li> <p>The machine learning research community has at its disposal a database of several dozen hours of animal vocalizations, which will make it possible to build up a large learning base, very useful for Environemental Sound Recognition tasks, for example.</p> </li> </ul> <p> </p> <p><strong>Objective</strong></p> <p>This dataset is a follow-up of two studies on the vocal productions of Guinea baboons (Papio papio) in which we carried out analyses of their vocal productions on the basis of a relatively large vocalization sample containing around 1300 vocalizations (<a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169321">Boë, Berthommier, Legou, Captier, Kemp, Sawallis, Becker, Rey, & Fagot, 2017</a>; <a href="https://hal.science/hal-01649539">Kemp, Rey, Legou, Boë, Berthommier, Becker, & Fagot, 2017</a>). The aim was to collect a larger database using the technique of deep convolutional neural networks in order to 1) automatically detect vocal productions in a large continuous audio recording and 2) perform a categorization of these vocalizations on a more massive sample. A description of the pipeline that enabled these automatic detections and categorizations is given in <a href="https://arxiv.org/abs/2302.07640">Bonafos, Pudlo, Freyermuth, Legou, Fagot, Tronçon, & Rey (2023)</a>.</p> <p> </p> <p><strong>Data description</strong></p> <p>The data is a set of audio files in wav format. They are at least one second long (the size of the window), up to several minutes, if several windows are consecutively predicted as containing signal. Moreover, we add the labeled data we used to train the CNN which did the prediction. We also provide two hours of the continuous recordings to have an idea of the continuous recordings and test the code of the paper provided on <a href="https://gitlab.com/papers4375727/detection-and-classification-of-vocal-productions">gitlab</a>.</p> <p>In addition, there is a database in csv format listing all the vocalizations, the day and time of their production, and the prediction probabilities of the model.</p> <p> </p> <p><strong>Experimental design, materials and methods</strong></p> <p>The original recordings represent one month of continuous audio recording. Seven hours of this month were manually labelled. They were segmented and labelled according to whether or not there was a monkey vocalization (i.e., noise or vocalization) and, if there was a vocalization, according to the type of vocalization (6 possible classes: bark, copulation grunt, grunt, scream, yak, wahoo). These manually labelled data were used as a training set for a CNN, which was automatically trained following the pipeline of Bonafos et al. (2023). This model was then used to automatically detect and classify vocalization during the whole month of audio recording. It processes the data in the same way when predicting new data as it does when training. It uses a sliding window of one second with an overlap of 80%. It does not take into account information from previous predictions, but calculates the probability of a vocalization in each one-second window independently. It then iterates through the month. For each window, the model predicts two outputs: the probability that there is a vocalization and the probability of each class of vocalization.</p> <p>For the purpose of generating the wav files, if a window has a probability of a vocalization greater than 0.5, it is considered to contain a vocalization. If it is the first one, a vocalization is started at that moment. If the time windows that follow a vocalization also contain a vocalization, then the signal they contain is added to the first segment for which a vocalization has been detected. As soon as a one-second segment no longer contains a signal corresponding to a vocalization, the wav file is closed. If windows are predicted to contain no vocalizations, but are between two windows that contain vocalizations within 1 second of each other, then all windows are merged.</p>
Trained convolutional neural network for the identification of long-duration mixed precipitation in Montréal (Canada)
<p>In this dataset the trained convolutional neural network is published that accompanies the paper "A deep learning approach for the identification of long-duration mixed precipitation in Montréal (Canada)" submitted to the special issue on "Machine-Learning Applications in the Atmospheric and Oceanic Sciences" by the journal Atmosphere&Ocean.</p> <p>The files were created using tensorflow in python. The trained network is available in .h5-format the history as numpy-file (npy).</p>
NoSyms: A neural network approach to detecting data structures in raw memory
<p>This data was used for a experiments with graph convolutional neural networks for memory forensics as part of a bachelor thesis (included as pdf).<br> <br> Abstract:<br> <br> This work presents a neural network based approach for data structure detection in raw memory that does not require an entirely matching description of the target data structure. Instead, it’s merely necessary to provide multiple descriptions of data structures similar to the target as training data in the form of debugging symbols. The core contribution of this work is a formal description and implementation of encoding data structure definitions as well as raw memory contents such that they can be processed by graph convolutional neural networks. A description and implementation of a neural network meant to detect data structures in the memory contents of a Linux Kernel demonstrates the practical applicability of the described approach.<br> <br> The Code is available on GitHub <a href="https://github.com/NiklasBeierl/nosyms">https://github.com/NiklasBeierl/nosyms</a>.<br> <br> nokaslr_dump is the qemu memory snapshot used to test the model.<br> nokaslr.raw is the "raw" form of the snapshot as produced by Volatility 3's layerwriter plugin.<br> symbols-training-data contains the Volatility symbol JSON files from which training data was derived.<br> nokaslr_pointers.csv lists the kernel space pointers in the snapshot and<br> nokaslr_tasks.csv lists task structs in the snapshot. Both were extracted via a Volatility plugins that are included in the GitHub Repo.<br> vmlinux-5.4.0-58-generic.json is the symbol file for the kernel the snapshot was taken from.<br> other-symbols.zip contains symbol files I generated vor various other kernels but did not end up using, use at your own discretion.</p>
Dataset of 'Complete flow characterization from snapshot PIV, fast probes and physics-informed neural networks'
<p>Dataset of the article 'Complete flow characterization from snapshot PIV, fast probes and physics-informed neural networks' (https://doi.org/10.1016/j.cma.2023.116652). The codes processing data here are on https://github.com/AlvaroMS90/Complete-flow-characterization-from-snapshot-PIV-fast-probes-and-physics-informed-neural-networks.</p> <p>This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 949085) and by MCIN/AEI /10.13039/501100011033 and the European Union ‘NextGenerationEU/PRTR’ as part of the grant FJC2020-044342-I.</p>
Data release for "OrchID: a Generalized Framework for Taxonomic Classification of Images Using Evolved Artificial Neural Networks"
<p><strong>Abstract</strong></p> <p>Taxonomic expertise for the identification of species is rare and costly. On-going advances in computer vision and machine learning have led to the development of numerous semi- and fully automated species identification systems. However, these systems are rarely agnostic to specific morphology, rarely can perform taxonomic “approximation” (by which we mean partial identification at least to higher taxonomic level if not to species), and frequently rely on costly scientific imaging technologies.</p> <p>We present a generic, hierarchical identification system for automated taxonomic approximation of organisms from images. We assessed the effectiveness of this system using photographs of slipper orchids (Cypripedioideae), for which we implemented image pre-processing, segmentation, and colour and shape feature extraction algorithms to obtain digital phenotypes for 116 species. The identification system trained on these digital phenotypes uses a nested hierarchy of artificial neural networks for pattern recognition and automated classification that mirrors the Linnean taxonomy, such that user-submitted photos can be assigned a genus, section, and species classification by traversing this hierarchy.</p> <p>Performance of the identification system varied depending on photo quality, number of species included for training, and desired taxonomic level for identification. High quality photos were scarce for some taxa and were under-represented in the training set, resulting in imbalanced network training. The image features used for training were sufficient to reliably identify photos to the correct genus but less so to the correct section and species.</p> <p>The outcomes of this project include a library of feature extraction algorithms called <em>ImgPheno</em>, a collection of scripts for neural network training called <em>NBClassify</em>, a library for evolutionary optimization of artificial neural network construction called <em>AI::FANN::Evolving</em> and a planned web application called <em>OrchID</em> for identification of user-submitted images. All project outcomes are open source and freely available.</p> <p><strong>About this release</strong></p> <p>This release corresponds belongs with our response to the reviewers of PLoS One. At this stage of the review cycle the manuscript is assessed as 'minor revision'. Consequently, we don't anticipate making more releases until publication.</p>
Robustness assessment of a C++ implementation of a quantized (int8) version of the LeNet-5 convolutional neural network
<p>The architecture of the LeNet-5 convolutional neural network (CNN) was defined by LeCun in its paper "Gradient-based learning applied to document recognition" (<a href="https://ieeexplore.ieee.org/document/726791">https://ieeexplore.ieee.org/document/726791</a>) to classify images of hand written digits (MNIST dataset).</p><p>This architecture has been customized to use Rectified Linear Unit (ReLU) as activation functions instead of Sigmoid, and 8-bit integers for weights and activations instead of floating-point.</p><p>It consists of the following layers:</p><ul><li><strong>conv1</strong>: Convolution 2D, 1 input channel (28x28), 3 output channels (28x28), kernel size 5, stride 1, padding 2.</li><li><strong>relu1</strong>: Rectified Linear Unit (3@28x28).</li><li><strong>max1</strong>: Subsampling buy max pooling (3@14x14).</li><li><strong>conv2</strong>: Convolution 2D, 3 input channels (14x14), 6 output channels (14x14), kernel size 5, stride 1, padding 2.</li><li><i><strong>relu2</strong></i>: Rectified Linear Unit (6@14x14).</li><li>max2: Subsampling buy max pooling (6@7x7).</li><li><i><strong>fc1</strong></i>: Fully connected (294, 147)</li><li><i><strong>fc2</strong></i>: Fully connected (147, 10)</li></ul><p>The fault hypotheses for this work include the occurrence of:</p><ul><li><strong>BF</strong>: single, double-adjacent and triple-adjacent bit-flip faults</li><li><strong>S0</strong>: single, double-adjacent and triple-adjacent stuck-at-0 faults</li><li><strong>S1</strong>: single, double-adjacent and triple-adjacent stuck-at-1 faults</li></ul><p>In the memory cells containing all the parameters of the CNN: </p><ul><li><strong>w</strong>: weights (int8)</li><li><strong>zw</strong>: zero point of the weights (int8)</li><li><strong>b</strong>: biases (int32)</li><li><strong>z</strong>: zero point (int8)</li><li><strong>m</strong>: m (int32)</li></ul><p>Images 200 to 249 from the MNIST dataset have been used as workload.</p><p>This dataset contains the raw data obtained from running exhaustive fault injection campaigns for all considered fault models, targeting all considered locations and for all the images in the workload.</p><p>In addition, the raw data have been lightly processed to obtain global data related to the particular bits and parameters affected by the faults, and the obtained failure modes.</p><h3>Files information</h3><ul><li><i>golden_run.csv</i>: Prediction obtained for all the images considered in the workload in the absence of faults (Golden Run). This is intended to act as oracle to determine the impact of injected faults. </li><li><i>single_faults/bit_flip</i> folder: Prediction obtained for all the images considered in the workload in presence of single bit-flip faults. There is one file for each parameter of each layer.</li><li><i>single_faults/stuck_at_0</i> folder: Prediction obtained for all the images considered in the workload in presence of single stuck-at-0 faults. There is one file for each parameter of each layer.</li><li><i>single_faults/stuck_at_1</i> folder: Prediction obtained for all the images considered in the workload in presence of single stuck-at-1 faults. There is one file for each parameter of each layer.</li><li><i>double_adjacent_faults/bit_flip</i> folder: Prediction obtained for all the images considered in the workload in presence of double adjacent bit-flip faults. There is one file for each parameter of each layer.</li><li><i>double_adjacent_faults/stuck_at_0</i> folder: Prediction obtained for all the images considered in the workload in presence of double adjacent stuck-at-0 faults. There is one file for each parameter of each layer.</li><li><i>double_adjacent_faults/stuck_at_1</i> folder: Prediction obtained for all the images considered in the workload in presence of double adjacent stuck-at-1 faults. There is one file for each parameter of each layer.</li><li><i>triple_adjacent_faults/bit_flip</i> folder: Prediction obtained for all the images considered in the workload in presence of triple adjacent bit-flip faults. There is one file for each parameter of each layer.</li><li><i>triple_adjacent_faults/stuck_at_0</i> folder: Prediction obtained for all the images considered in the workload in presence of triple adjacent stuck-at-0 faults. There is one file for each parameter of each layer.</li><li><i>triple_adjacent_faults/stuck_at_1</i> folder: Prediction obtained for all the images considered in the workload in presence of triple adjacent stuck-at-1 faults. There is one file for each parameter of each layer.</li></ul><h3>Methodology information</h3><p>First, the CNN was used to classify all the images of the workload in the absence of faults to get a reference to determine the impact of faults. This is golden_run.csv file.</p><p>After that, one fault injection experiment was executed for each bit of each element of each parameter of the CNN.</p><p>Each experiment consisted in:</p><ul><li>Affecting the bits (inverting it in case of bit-flip faults, setting it to 0 or 1 in case of stuck-at-0 or atuck-at-1 faults) identified by the mask.</li><li>Classifying all the images of the workload in the presence of this fault. The obtained output was stored in a given .csv file.</li><li>Removing the fault from the CNN by restoring the affected bits to its previous value.</li></ul><h3>List of variables (Name : Description (Possible values))</h3><ul><li><strong>IMGID</strong>: Integer number identifying the considered image (200-249).</li><li><strong>TENSORID</strong>: Integer number identiying the parameter affected by the fault (0 - No fault, 1 - conv1.w, 2 - conv1.zw, 3 - conv1.m, 4 - conv1.b, 5 - conv1.z, 6 - conv2.w, 7 - conv2.zw, 8 - conv2.m, 9 - conv2.b, 10 - conv2.z, 11 - fc1.w, 12 - fc1.zw, 13 - fc1.m, 14 - fc.b, 15 - fc1.z, 16 - fc2.w, 17 - fc2.zw, 18 - fc2.m, 19 - fc2.b, 20 - fc2.z)</li><li><strong>ELEMID</strong>: Integer number identiying the element of the parameter affected by the fault (-1 - No fault, [0-2] - {conv1.b, conv1.m, conv1.zw}, [0-74] - conv1.w, 0 - conv1.z, [0-5] - {conv2.b, conv2.m, conv2.zw}, [0-149] - conv2.w, 0 - {conv1.z, conv2.z, fc1.z, fc2.z}, [0-146] - {fc1.b, fc1.m, fc1.zw}, [0-43217] - fc1.w, [0-9] - {fc2.b, fc2.m, fc2.zw}, [0-1469] - fc2.w)</li><li><strong>MASK</strong>: 8-digit hexadecimal number identifying those bits affected by the fault ([00000000 - No fault, FFFFFFFF - all 32 bits faulty])</li><li><strong>FAULT</strong>: String identiying the type of fault (NF - No fault, BF - bit-flip, S0 - Stuck-at-0, S1 - Stuck-at-1)</li><li><strong>OUTPUT</strong>: 10 integer numbers provided by the CNN as output after processing the image. The highest value identifies the selected category for classification.</li><li><strong>SOFTMAX</strong>: 10 decimal numbers obtained after applying the softmax function to the provided output. They represent the probability of the image of belonging to the corresponding category for classification.</li><li><strong>PRED</strong>: Integer number representing the category predicted for the processed image.</li><li><strong>LABEL</strong>: integer number representing the actual category for the processed image.</li></ul>
Artificial Neural Networks-generated Dataset: pH, Total Alkalinity, and Hydrogen Ion Concentration in Ría de Vigo (NW Spain), 1995–2020
<p>This dataset comprises input data from INTECMAR and the predicted outcomes. The variables and their units are as follows:</p> <p>station: 'Station ID [1-6]'</p> <p>year: 'Year [1995-2020]'</p> <p>month: 'Month [1-12]'</p> <p>day: 'Day'</p> <p>latitude: 'Latitude (decimal degrees)'</p> <p>longitude: 'Longitude (decimal degrees)'</p> <p>depth: 'Depth (meters)'</p> <p>temperature: 'Temperature (degrees Celsius)'</p> <p>salinity: 'Salinity (psu)'</p> <p>phosphate: 'Phosphate (umol/kg)'</p> <p>nitrate: 'Nitrate (umol/kg)'</p> <p>silicate: 'Silicate (umol/kg)'</p> <p>cweek: 'Cosine week'</p> <p>sweek: 'Sine week'</p> <p>TA: 'Total Alkalinity predicted (umol/kg)'</p> <p>NTA: 'Normalized Total Alkalinity (umol/kg)'</p> <p>NAT_st: 'Normalized per station Total Alkalinity (umol/kg)'</p> <p>NTA_gl: 'Normalized globally Total Alkalinity (umol/kg)'</p> <p>pHTS_insitu: 'pH insitu (pH units)'</p> <p>HT: 'Hydrogen ion concentration predicted (nmol/kg)'</p> <p> </p> <p>The authors gratefully acknowledge the financial support by the Programa de axudas á etapa predoutoral da Xunta de Galicia (Axencia Galega de Innovación) (Grant nº IN606A-2022/025). F.F.P. and A.V. were supported by REDEIRA (TED2021-132188B-I00) project, funded by MCIN/AEI/10.13039/501100011033. The authors also express their gratitude to the Instituto Tecnolóxico para o Control do Medio Mariño de Galicia (INTECMAR), for the analyses and production of the database used to make predictions.</p>
Dataset and neural network weights to the paper: "Generative diffusion for regional surrogate models from sea-ice simulations"
<p>All the needed code and data to reproduce the results from the paper: "Generative diffusion for regional surrogate models from sea-ice simulations".<br>While most of the code is a frozen clone of the original <a href="https://github.com/cerea-daml/diffusion-nextsim-regional">Repository</a>, this capsule also includes the dataset and neural network weights to train and apply the surrogate models.</p> <p>The <strong>dataset</strong> for training and evaluation can be found at <em>data/nextsim</em>, which includes three different Zarr folders for training/validation/testing. The dataset is based on neXtSIM simulation data and ERA5 forcing data and extracted from the <a href="https://ige-meom-opendap.univ-grenoble-alpes.fr/thredds/catalog/meomopendap/extract/catalog.html">SASIP shared data OpenDAP server</a>:</p> <ul> <li>The neXtSIM simulations were performed by Gauillaume Boutin and published in the paper "<a href="https://doi.org/10.5194/tc-17-617-2023">Arctic sea ice mass balance in a new coupled ice–ocean model using a brittle rheology framework</a>" (Boutin et al., 2023) and available as Zenodo <a href="../records/7277523">dataset</a> (Boutin et al., 2022).</li> <li>The forcing data is based on the ERA5 reanalysis dataset published in the paper: "<a href="https://doi.org/10.1002/qj.3803">The ERA5 global reanalysis</a>" (Hersbach et al., 2020) and available as dataset from the Copernicus Climate Change Service (C3S, Copernicus Climate Change Service, 2023). The here used forcing data is based on the <a href="https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels">hourly reanalysis data on single levels</a> and interpolated with nearest neighbors to the curvilinear grid as used in the output from the neXtSIM simulations. <strong>Disclaimer:</strong> The results contain modified Copernicus Climate Change Service information, 2023. Neither the European Commission nor ECMWF is responsible for any use that may be made of the Copernicus information or data it contains.</li> </ul> <p>The <strong>neural network weights</strong> are included under <em>data/models </em>and split into weights for the deterministic models and the diffusion models.<br>These neural network weights have been used to generate the results presented in the paper.</p> <p>In this capsule, the <em>notebooks</em> folder includes also the figures used within the paper and additional trajectory data used in the qualitative analysis of the paper.</p> <p>Generally, we recommend to just download the <em>data.tar.gz </em>file and use otherwise the original <a href="https://github.com/cerea-daml/diffusion-nextsim-regional">Repository</a>, since the here included code can be outdated. We further refer to the repository for additional information.</p> <p> </p> <p>Contained in this capsule:</p> <ul> <li>configs.tar.gz: The configuration files for the experiments.</li> <li>data.tar.gz: The dataset and neural network weights.</li> <li>diffusion_nextsim.tar.gz: The main code for the neural network etc.</li> <li>environment.yaml: The anaconda environment file, can be used to install the needed packages.</li> <li>notebooks.tar.gz: The notebooks that were used to create the figures in the paper. The figures from the paper and the data from the qualitative analysis are included as well.</li> <li>readme.md: The readme file from the repository.</li> <li>scripts.tar.gz: The scripts used for the experiments.</li> <li>setup.py: the file to install the <em>diffusion_nextsim</em> package in a python environment.</li> </ul> <p>References:</p> <p>Guillaume Boutin, Heather Regan, Einar Ólason, Laurent Brodeau, Claude Talandier, Camille Lique, & Pierre Rampal. (2022). Data accompanying the article "Arctic sea ice mass balance in a new coupled ice-ocean model using a brittle rheology framework" (1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7277523</p> <p>Boutin, G., Ólason, E., Rampal, P., Regan, H., Lique, C., Talandier, C., Brodeau, L., and Ricker, R.: Arctic sea ice mass balance in a new coupled ice–ocean model using a brittle rheology framework, The Cryosphere, 17, 617–638, https://doi.org/10.5194/tc-17-617-2023, 2023.</p> <p>Copernicus Climate Change Service (2023): ERA5 hourly data on single levels from 1940 to present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS), DOI: <a href="https://doi.org/10.24381/cds.adbb2d47">10.24381/cds.adbb2d47</a>.</p> <p>Hersbach H, Bell B, Berrisford P, et al. The ERA5 global reanalysis. <em>Q J R Meteorol Soc</em>. 2020; 146: 1999–2049. <a href="https://doi.org/10.1002/qj.3803">https://doi.org/10.1002/qj.3803</a></p> <p> </p>
scGraph2Vec: a deep generative model for gene embedding augmented by Graph Neural Network and single-cell omics data
<p>This repository contains the training data and source code to reproduce the results of our paper:<br>scGraph2Vec: a deep generative model for gene embedding augmented by Graph Neural Network and single-cell omics data</p> <p>More description can be also found in GitHub (https://github.com/LPH-BIG/scGraph2Vec).</p>
Deep neural networks and humans both benefit from compositional language structure
<p>This dataset holds the results generated in the paper:</p> <p>Deep neural networks and humans both benefit from compositional language structure</p> <p>by L. Galke, Y. Ram, and L. Raviv.</p>
Robust Method for Property Prediction via Artificial Neural Networks: Incorporating Key Structural Features for Carbon Dioxide – Ionic Liquid Mixtures
<p>This Dataset comprises two sub-sets of information:</p> <ul> <li>Database and Results of the work present in the paper "Robust Method for Property Prediction via Artificial Neural Networks: Incorporating Key Structural Features for Carbon Dioxide – Ionic Liquid Mixtures" published in The Journal of Physical Chemistry B (https://doi.org/10.1021/acs.jpcb.4c04432).</li> <li>Sample of the code used, in order to reproduce any of the results presented above. This can be found in the previous version of this Dataset (v1.0 https://zenodo.org/records/11216901)</li> </ul> <p> </p> <p>Regarding the sample code, an example for all ANN Models used in this work is provided. This includes the three models used:</p> <ol> <li>One based only on Critical Properties of Ionic Liquids (CRT Model)</li> <li>One based only on Structural Properties of Ionic Liquids (STR Model)</li> <li>One combination of the previous models, taking into account both Critical and Structural Properties (COMB Model)</li> </ol> <p>In this manner, it is possible to observe the differences between the performance of the different models, either through statiscal analysis or using graphical representation. This allows for the benchmarking to be done in a more concise way.</p>
Deep learning models predicting gene functions and pathways using public DRKG knowledge graph and graph neural network
<p>The attached dataset contains pretrained link prediction models, as described in our paper 'Morphological Map of Under- and Over-Expression of Genes in Human Cells'.</p>
Self-Supervised Representation Learning on Neural Network Weights for Model Characteristic Prediction - Datasets
<p>Datasets to NeurIPS 2021 accepted paper "Self-Supervised Representation Learning on Neural Network Weights for Model Characteristic Prediction".</p> <p>Datasets are pytorch files containing a dictionary with training, validation and test sets. Train, validation and test sets are custom dataset classes which inherit from the standard torch dataset class. Corresponding code an be found at https://github.com/HSG-AIML/NeurIPS_2021-Weight_Space_Learning.</p> <p>Datasets 41, 42, 43 and 44 are our dataset format wrapped around the zoos from Unterthiner et al, 2020 (https://github.com/google-research/google-research/tree/master/dnn_predict_accuracy)<br> <br> Abstract:<br> Self-Supervised Learning (SSL) has been shown to learn useful and information-preserving representations. Neural Networks (NNs) are widely applied, yet their weight space is still not fully understood. Therefore, we propose to use SSL to learn neural representations of the weights of populations of NNs. To that end, we introduce domain specific data augmentations and an adapted attention architecture. Our empirical evaluation demonstrates that self-supervised representation learning in this domain is able to recover diverse NN model characteristics. Further, we show that the proposed learned representations outperform prior work for predicting hyper-parameters, test accuracy, and generalization gap as well as transfer to out-of-distribution settings.</p>
Data for "Unfolding the structural stability of nanoalloys via symmetry-constrained genetic algorithm and neural network potential"
<p><strong>PtNi_alloy_eam.db</strong> is the dataset (ase.db object) consisting of 55982 intially sampled Pt-Ni alloy structures with EAM energies and forces.</p> <p><strong>PtNi_alloy_dft.db</strong> is the dataset (ase.db object) consisting of the final 6828 resampled Pt-Ni alloy structures with DFT energies and forces calculated by VASP. This is the training set for the NNP, and could be very useful for fitting other machine learning models.</p> <p><strong>PtNi_nanoalloy_vertices_nnp.db</strong> is the dataset (ase.db object) consisting of all the vertices (stable structures) on the convex hulls obtained from NNP-based SCGA runs on 36 Pt-Ni nanoalloy systems. The energies are given by the NNP. Additional information such as mixing energy, motif and symmetry axis are also saved in the dataset and can be queried by the 'data' keyword. An xyz format trajectory of these stable structures is also uploaded.</p> <p>All the input files and scripts for hybrid MC-MD simulations, QBC resampling, DFT calculations, NNP training, NNP-based SCGA runs and convex hull analysis are provided in <strong>inputs_and_scripts.zip</strong>.</p>
Surrogate-based optimization using an artificial neural network for a parameter identification in a 3D marine ecosystem model
<p><strong>Abstract:</strong></p> <p>Parameter identification for marine ecosystem models is important for the assessment and validation of marine ecosystem models against observational data. The surrogate-based optimization (SBO) is a computationally efficient method to optimize complex models. SBO replaces the computationally expensive (high-fidelity) model by a surrogate constructed from a less accurate but computationally cheaper (low-fidelity) model in combination with an appropriate correction approach, which improves the accuracy of the low-fidelity model. To construct a computationally cheap low-fidelity model, we tested three different approaches to compute an approximation of the annually periodic solution (i.e., a steady annual cycle) of a marine ecosystem model: firstly, a reduced number of spin-up iterations (several decades instead of millennia), secondly, an artificial neural network (ANN) approximating the steady annual cycle and, finally, a combination of the both approaches. Except for the low-fidelity model using only the ANN, the SBO yielded a solution close to the target and reduced the computational effort significantly. If an ANN approximating appropriately a marine ecosystem model is available, the SBO using this ANN as low-fidelity model presents a promising and computational efficient method for the validation.</p> <p> </p> <p><strong>Content:</strong></p> <ul> <li>SQLite database including the data of the different optimization runs</li> <li>Structure and weights of the used artificial neural network</li> <li>Tracer concentrations obtain from the high-fidelity model for the different optimization runs</li> </ul>
A Deep Neural Network Based SMAP Soil Moisture Product
<p>The soil moisture datasets here are based on a deep neural network (DNN) that utilizes the merits of a suite of existing satellite and reanalysis products to produce a new SM product with minimum (maximum) bias (correlation) -- using NASA’s Soil Moisture Active Passive (SMAP) data and ERA5 reanalysis. The benchmark of the network is a bias-adjusted SM with maximum correlation with in situ data over each land-cover type. The bias is adjusted to the product that exhibits a minimum bias over each land-cover type. Consistent with the laws of L-band microwave propagation in soil and canopy, the input variables include polarized SMAP brightness temperatures, incidence angles, vegetation scattering albedo, surface roughness parameter, surface water fraction, effective soil temperatures, bulk density, clay fraction, and vegetation optical depth from the normalized difference vegetation index (NDVI) climatology. The DNN is trained and validated using two years (04/2015--03/2017) of global data and deployed for assessment of its performance from 04/2017 to 03/2021. The testing results against in situ measurements demonstrate that the DNN outputs typically exhibit improved error quality metrics over most land cover types and climate regimes and can properly capture SM temporal dynamics, beyond each SMAP product across regional to continental scales.</p>
Generated Data for the Manuscript "Nonideality-Aware Training for Accurate and Robust Low-Power Memristive Neural Networks"
<p>The file contains data generated and referred to in the text and the figures of the manuscript.</p>
A dataset of published journal papers using neural networks for seismological tasks.
<p>This is a dataset of 637 journal papers applying neural networks for various tasks in seismology spanning January 1988 to January 2022. The dataset mainly includes peer reviewed papers and does not contain duplicated works. It follows a hierarchical classification of papers based on seismological tasks (i.e. category, sub_category_I, sub_category_II, task, and sub_task). For each paper following information are provided: 1) first author's last name, 2) publication year, 3) paper's title, 4) journal 's name, 5) machine learning method used, 6) the type of used neural network, 7) the name of neural network architecture, 8) the number of neurons/kernels in each hidden layer, 9) type of training process, i.e. supervised, semi-supervised, etc, 10) input data into the network, 11) output data, 12) data domain, i.e. time, frequency, feature, etc, 13) the type of data used for training, e.g. synthetic or real data, 14) the size of training set, 15) the metrics used to measure the performance, 16) performance scores, 17) the baseline method used for evaluation, and 18) a short note summarizing the paper's objective, its approach, and its significance. </p> <p>An updating version of the dataset can be find from here: https://smousavi05.github.io/dl_seismology/ and here:https://github.com/smousavi05/dl_seismology/tree/main/docs. </p> <p>An updating glossary of seismological tasks and relevant machine learning techniques and papers are provided here: https://smousavi05.gitbook.io/mlseismology/</p>
Neural network dataset, script and model
<p>This data was collected from several sources and compiled into a single text file called NN.txt</p> <p>Ten quiet and five disturbed days in each month from 2009 to 2019 were used to develop the dataset. These days were got from the list of International Q and D days accessed on the website of the World Data Centre of Geomagnetism, Kyoto (<em><a href="https://wdc.kugi.kyoto-u.ac.jp/qddays/index.html">https://wdc.kugi.kyoto-u.ac.jp/qddays/index.html</a>). </em>The dataset has seventeen columns defined as Date, Year (Y), Day of the year (DOY), hour of the day (HH), cosine and sine components of the day of the year for annual variation (DAC and DAS), cosine and sine components of the day of the year for semi-annual variation (DSC and DSS), cosine and sine components of the hour for daily variation (HRC and HRS), geographical coordinates (Lat, Lon), geomagnetic coordinates (Glat, Glon), Dst Index, F10.7 Index, TEC and sunspot number (SSN). The geographical coordinates were converted to geomagnetic coordinates using quasi dipole coordinates (Emmert et al., 2010; Richmond, 1995). Dst index, F10.7 index, and SSN were downloaded from the OmniWeb database (<em>https://omniweb.gsfc.nasa.gov/form/dx1.html</em>). Jason TEC data was downloaded from the FTP access of the CEDAR Madrigal database (<em>http://cedar.openmadrigal.org/ftp/</em>). </p> <p>The data resolution was an 18-second interval. </p> <p>It should be noted that any day that had a missing value was eliminated from the database. The data downloaded from Omni web was on a resolution of 1 hour and it was put at an 18-second interval by repeating the same value. The TEC data from the CEDAR Madrigal database is in a second interval and therefore it was averaged at an 18-second interval. </p> <p>The dataset was trained with MATLAB software, the MATLAB script (NN script) is attached. The output was a Neural network model also attached </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.