Find research datasets worth reusing

opencc-zeroMay 2023View details →

Social network and fitness data from age-structured populations of forked fungus beetles

We investigated the relationships between age, social behavior, and fitness at three levels of organization: the individual, the local social environment, and the population. Replicate groups of forked fungus beetles (Bolitotherus cornutus) were engineered to have either young- or old- biased age structures, and both social and reproductive behaviors were recorded.

Data of "Multilayer spintronic neural networks with radio-frequency connections"

This dataset corresponds to the open data of the publication "Multilayer spintronic neural networks with radio-frequency connections".

Rogues, villains, and eccentrics - network analysis dataset

The dataset used for the study: Rogues, villains, and eccentrics – network analysis of schizotypy indicators.

Repositiry for the article: "Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection" by Alain Mbebi & Zoran Nikoloski

This is the repository for the manuscript "Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection" by Alain J. Mbebi & Zoran Nikoloski. Organisation <ol> <li>The folder Codes contains the following R scripts with the K-folds cross-validation option to learn the hyperparameters:</li> </ol> <ul> <li>Mixed_L1L21_GRN.R which computes L1L21-solution</li> <li>Mixed_L1L21G_GRN.R which computes L1L21G-solution</li> <li>Mixed_L2L21_GRN.R which computes L2L21-solution</li> <li>Mixed_L2L21G_GRN.R which computes L2L21G-solution</li> <li>L1L21_Dream5_Scerevisiae_example_run.R is an example run using the L1L21-solution with S. cerevisiae data (Network 4 in DREAM5 challenge) All files needed to successfully run "L1L21_Dream5_Scerevisiae_example_run" are locaded in the folder Codes.</li> </ul> 2. The folder Figures contains all figures in the manuscript. 3. The folder Inferred-networks contains all network objects for each dataset and each inference methods in the comparative analysis. Dependencies and required packages The following packages are required for the contending approaches in the comparative analysis: "devtools", "foreach", "plyr", "glmnet" and "randomForest". GENIE3 The GENIE3 package can be installed from: <a href="http://bioconductor.org/packages/release/bioc/html/GENIE3.html">http://bioconductor.org/packages/release/bioc/html/GENIE3.html</a> TIGRESS The TIGRESS repository can be obtained from: <a href="https://github.com/jpvert/tigress">https://github.com/jpvert/tigress</a> ENNET The ENNET repository can be obtained from: <a href="https://github.com/slawekj/ennet">https://github.com/slawekj/ennet</a> PLSNET The Matlab source code of PLSNET can be obtained from: <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1398-6#Sec17">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1398-6#Sec17</a> PORTIA The PORTIA repository can be obtained from: <a href="https://github.com/AntoinePassemiers/PORTIA">https://github.com/AntoinePassemiers/PORTIA</a> D3GRN The Matlab source code of D3GRN can be obtained from: <a href="https://github.com/chenxofhit/D3GRN">https://github.com/chenxofhit/D3GRN</a> Fused-LASSO The fused-LASSO repository can be obtained from: <a href="https://github.com/omranian/inference-of-GRN-using-Fused-LASSO">https://github.com/omranian/inference-of-GRN-using-Fused-LASSO</a> ANOVerence Because of some technical issues (e.g code's accessibility: <a href="http://www2.bio.ifi.lmu.de/%CB%9Ckueffner/anova.tar.gz">http://www2.bio.ifi.lmu.de/&tilde;kueffner/anova.tar.gz</a>), we were not able to reproduce ANOVerence results and used the inferred network from DREAM5 challenge instead. 4. Although the codes here were tested on Fedora 29 (Workstation Edition) using R (version 4.2.2), they can run under any Linux or Windows OS distributions, as long as all the required packages are compatible with the desired R version.

Alkane dataset for reactive chemistry neural network potentials at DFT and CASPT2 level

datasets used for training and evaluating neural networks in the following work: Neural Network Potentials for Reactive Chemistry: CASPT2 Quality Potential Energy Surfaces for Bond Breaking <a href="https://doi.org/10.26434/chemrxiv-2023-13cv6">https://doi.org/10.26434/chemrxiv-2023-13cv6</a>

opencc-zeroMay 2023View details →

Cactus height increases the modularity of a plant-frugivore network in the Caatinga dry forest

Cacti fruits are key resources to many frugivorous animals in Neotropical arid and semiarid regions. However, most studies have focused on a particular animal group or cacti species, but few have explored the overall interactions of such species at the community level. Here we monitored frugivory on five cacti species using camera traps that sampled diurnal and nocturnal interactions. We investigated the structure of interactions with bird, mammal, and reptile frugivores in the Brazilian Caatinga dry forest. We hypothesized that the height of cacti limit interactions with different types of frugivores, which would result in highly structured and modular interaction networks. In 2,929 camera-days, we recorded 23 vertebrate species feeding on cacti fruits, including seven new records, all determined to be primary seed dispersers. As predicted, the cacti-frugivore network was modular and non-nested, with the two shortest cacti species grouped in a module dominated by interactions with reptiles and non-flying mammals. The tallest cacti species were dominated by frugivory interactions with birds and had comparatively less interaction diversity than shorter cacti species. Our results support the contention that cacti are keystone species in semiarid ecosystems where they produce small-seeded fleshy fruits year-round.

Reproducibility Package for Predictive Limitations of Physics-Informed Neural Networks in Vortex Shedding

This archive contains the repro-pack for the paper at <a href="http://github.com/barbagroup/jcs_paper_pinn">https://github.com/barbagroup/jcs_paper_pinn</a>.

Reproducibility Package (Raw Data) for Predictive Limitations of Physics-Informed Neural Networks in Vortex Shedding

Raw data results from the simulations using PINN methods and PetIBM for the paper at: https://github.com/barbagroup/jcs_paper_pinn

Supplementary material for: Accounting for within-species variation in continuous trait evolution on a phylogenetic network

This supplementary material contains data and scripts for (1) a simulation study assessing the performance of our phylogenetic comparative method on trait data generated using an actual species network, and (2) a comparative analysis of how Polemonium leaflet size covaries with geographical predictors, assuming either a reticulate or non-reticulate time-calibrated phylogeny, accounting for or ignoring within-species variation. There are two top-level folders: (1) simulations: contains scripts to replicate the simulation study and associated figures in the subfolder "scripts", and results from the simulations in the subfolder "data". (2) polemonium: contains uncalibrated/calibrated species phylogenies (.tre), gene trees (.t, .tre) and genetic distance estimates (.csv) used for calibration, morphological and geographical data for Polemonium (.csv), and model estimates (.csv) in the subfolder "data"; and scripts to do calibration, preprocess the trait data, fit models and save estimates, and recreate figures from the article in the subfolder "scripts". The archive and each top-level folder contain their own README file with more detailed information.

opencc-by-4.0Jul 2023View details →

Data for GECCO2023 Paper "Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness"

Data for Paper "Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness" <ul> <li>instances.tar.xz contains 𝜌mnk-landscape instances</li> <li>metrics.csv contains the (C)PLOS-net metric-values</li> <li>performance.csv contains the performance of the different algorithms on each instance</li> <li>merged.csv contains the merged data from the 2 csv files above</li> </ul> Reference Arnaud Liefooghe, Gabriela Ochoa, Sébastien Verel, and Bilel Derbel. 2023. Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness. In Genetic and Evolutionary Computation Conference (GECCO ’23), July 15–19, 2023, Lisbon, Portugal. ACM, New York, NY, USA, 9 pages. <a href="https://doi.org/10.1145/3583131.3590474">https://doi.org/10.1145/3583131.3590474</a> Abstract The structure of local optima in multi-objective combinatorial optimization and their impact on algorithm performance are not yet properly understood. In this paper, we are interested in the representation of multi-objective landscapes and their multi-modality. More specifically, we revise and extend the network of Pareto local optimal solutions (PLOS-net), inspired by the well-established local optima network from single-objective optimization. We first define a compressed PLOS-net which allows us to enhance its perception while preserving the important notion of connectedness between local optima. We then study an alternative visualization of the (compressed) PLOS-net that focuses on good-quality solutions, improves the distinction between connected components in the network, and generalizes well to landscapes with more than 2 objectives. We finally define a number of network metrics that characterize the PLOS-net, some of them being strongly correlated with search performance. We visualize and experiment with small-size multi-objective nk-landscapes, and we disclose the effect of PLOS-net metrics against well-established multi-objective local search and evolutionary algorithms.

Data for: Capturing synchronization with complexity measure of ordinal pattern transition network constructed by Crossplot

To evaluate the synchronization of bivariate time series has been a hot topic and a number of measures have been proposed. In this work, by introducing the ordinal pattern transition network (OPTN) into the crossplot, a new method for measuring the synchronisation of bivariate time series is proposed. After the crossplot been partitioned and coded, the coded partitions are defined as network nodes and a directed weighted network is constructed based on the temporal adjacency of the nodes. The crossplot transition entropy (CPTE) of the network is proposed as an indicator of the synchronization between two time series. To test the characteristics and performance of the method, it is used to analyse the unidirectional coupled Lorentz model and compared it with existing methods. The results showed the new method had the advantages of easy parameter setting, efficiency, robustness, good consistency and suitable for short time series. Finally, EEG data from auditory evoked potential EEG-Biometric dataset are investigated, and some useful and interesting results are obtained.

Data for: Prediction in cultured cortical neural networks

Theory suggest that networks of neurons may predict their input. Prediction may underlie most aspects of information processing, and is believed to be involved in motor and cognitive control and decision making. Retinal cells have been shown to be capable of predicting visual stimuli, and there is some evidence for prediction of input in the visual cortex and hippocampus. However, there is no proof that the ability to predict is a generic feature of neural networks. We investigated whether random in vitro neuronal networks can predict stimulation, and how prediction is related to short and long-term memory. To answer these questions we applied two different stimulation modalities. Focal electrical stimulation has been shown to induce long term memory traces, whereas global optogenetic stimulation did not. We used mutual information to quantify how much activity recorded from these networks reduces the uncertainty of upcoming stimuli (prediction) or recent past stimuli (short-term memory). Cortical neural networks did predict future stimuli, with the majority of all predictive information provided by the immediate network response to the stimulus. Interestingly, prediction strongly depended on short-term memory of recent sensory inputs during focal as well as global stimulation. However, prediction required less short-term memory during focal stimulation. Furthermore, the dependency on short-term memory decreased during 20h of focal stimulation, when long-term connectivity changes were induced. These changes are fundamental for long-term memory formation, suggesting that besides short-term memory the formation of long-term memory traces may play a role in efficient prediction.

Data Set "Protein network centralities as descriptor for QM region construction in QM/MM simulations of enzymes"

This data set accompanies the publication "Efficient automatic construction of atom-economical QM regions with point-charge variation analysis" by Felix Brandt and Christoph R. Jacob (TU Braunschweig, Germany)  It contains: - PDB files of the starting structures - modified AMBER95 force field file - AMS fragment files for the substrates and ions - AMS input files for all geometry optimizations and single point calculations - Python script for WISP and centrality analysis

Data and code for "Competitive hierarchies in bryozoan assemblages mitigate network instability by keeping short and long feedback loops weak"

This repository contains all scripts and data files to reproduce the analysis of the manuscript "Competitive hierarchies in bryozoan assemblages mitigate network instability by keeping short and long feedback loops weak" Abstract Competitive hierarchies in diverse ecological communities have long been thought to lead to instability and prevent coexistence. However, system stability has never been tested and the relation between hierarchy and instability has never been explained in complex competition networks parameterised with data from direct observation. Here we test model stability of 30 multispecies bryozoan assemblages, using estimates of energy loss from observed interference competition to parameterise both the inter- and intraspecific interactions in the competition networks. We find that all competition networks are unstable. However, instability is mitigated considerably by asymmetries in the energy loss rates brought about by hierarchies of strong and weak competitors. This asymmetric organisation results in asymmetries in the interaction strengths, which reduces instability by keeping the weight of short (positive) and longer (positive and negative) feedback loops low. Our results support the idea that interference competition leads to instability and exclusion but demonstrate that this is not because of, but despite, competitive hierarchy. Data Our data set contains records of overgrowth competition in 30 high-latitude bryozoan assemblages. Rocks were collected by hand from shallow subtidal coastal locations at Rothera Island, West Antarctic Peninsula, Signy Island in the maritime Antarctic and Spitsbergen in the Arctic. For each assemblage, the data set contains one .csv file with abundance per species and one .csv file containing the species-contact-matrix. All bryozoans were identified to species and counted, giving abundance data in colonies per species. Then, all pairwise contests between colonies were classified as win, draw or loss and the results were compiled in the species-contact-matrices. For details, see the methods section of the paper. Analysis The analysis is subdivided into the following sections: <ul> <li>0 Random matrices: Stability of random matrices with symmetric and asymmetric interactions.</li> <li>1 Preparation: Define functions to calculate asymmetry measures and set plotting parameters</li> <li>2 Read and process raw data: Converts raw data to Jacobian matrices</li> <li>3 Analysis of empirical matrices: Calculates stability, asymmetry measures, loop weights of empirical matrices.</li> <li>4 Analysis of randomised matrices: Randomises empirical matrices and analyses the effect on stability, asymmetry measures and loop weights.</li> <li>5 Sensitivity: Effect of model assumptions (cost-values / replacement of missing values) on the results.</li> </ul> Details on how to reproduce the full analysis, including all figures and tables in the manuscript can be found in the ReadMe file.

Data for: Honey bees (Apis mellifera) modify plant-pollinator network structure, but do not alter wild species' interactions

Honey bees (Apis mellifera) are widely used for honey production and crop pollination, raising concern for wild pollinators, as honey bees may compete with wild pollinators for floral resources. The first sign of competition, before changes appear in wild pollinator abundance or diversity, may be changes to wild pollinator interactions with plants. Such changes for a community can be measured by looking at changes to metrics of resource use overlap in plant-pollinator interaction networks. Studies of honey bee effects on plant-pollinator networks have usually not distinguished whether honey bees alter wild pollinator interactions, or if they merely alter total network structure by adding their own interactions. To test this question, we experimentally introduced honey bees to a Canadian grassland and measured plant-pollinator interactions at varying distances from the introduced hives. We found that honey bees increased the network metrics of pollinator and plant functional complementarity and decreased interaction evenness. However, in networks constructed from just wild pollinator interactions, honey bee abundance did not affect any of the metrics calculated. Thus, all network structural changes to the full network (including honey bee interactions) were due only to honey bee-plant interactions, and not to honey bees causing changes in wild pollinator-plant interactions. Given widespread and increasing use of honey bees, it is important to establish whether they affect wild pollinator communities. Our results suggest that honey bees did not alter wild pollinator foraging patterns in this system, even in a year that was drier than the 20-year average.

Data set for Dynamic Service Restoration of Distribution Networks with Volt-Var Devices, Distributed Energy Resources, and Energy Storage Systems

Two power distribution systems are presented. The first system consists of 53 nodes and 61 branches, while the second system consists of 404 buses and 430 branches. Both distribution systems offer extensive applications in problems related to multi-time service restoration, Volt/Var devices, and distributed energy resource operation.

almost 3000 Networks (unweighted, undirected, simple, connected) from Network Repository

Data All networks from <a href="https://networkrepository.com"><code>networkrepository.com</code></a> [1] with at most 1M edges (fall 2020) with the following modifications: <ul> <li>weights and edge directions have been ignored</li> <li>multi-edges and self loops have been removed, i.e., the graphs are simple</li> <li>each graph has been reduced to its largest connected component</li> <li>for isomorphic graphs, only one copy has been kept</li> </ul> [1] Ryan A. Rossi and Nesreen K. Ahmed, The Network Data Repository with Interactive Graph Analytics and Visualization (AAAI 2015) Format The data format is a simple edge list: <ul> <li>each row contains two numbers u and v separated by a space representing an edge {u, v}</li> <li>for a graph with n vertices, the numbers range from 0 to n - 1</li> <li>for each edge {u, v} only one of the pairs u v or v u is present, i.e., if the graph has m edges, the file contains m rows</li> </ul>

Graph database of the urban road network of Modena

The file contains a dump of the neo4j instance of the road network of the city of Modena. The database contains both the primal graph and the dual graph and integrates traffic volume data and Points Of Interest (POI). The database is generated from Open Street Map data exploiting the code in <a href="https://anonymous.4open.science/r/roadRouting-2D96">this</a> git repository. The git repository shows how to employ the graph database for analysis, routing, and the simulation of road closure scenarios.

Results for paper 'The Potential Role of a Hydrogen Network in Europe'

Results and Figures dataset accompanying The Potential Role of a Hydrogen Network in Europe. This dataset includes the main result files and figures.