Find research datasets worth reusing

opencc-by-4.0Dec 2014View details →

Convex inference for community discovery in signed networks (European Parliament Voting Dataset)

This repository contains the necessary tools to reproduce the experiments of the paper <ul> <li>G. Santatmaría, V. Gómez (2015) Convex inference for community discovery in signed networks. NIPS 2015 Workshop: Networks in the Social and Information Sciences</li> </ul> The method first maps the MAP problem on the Potts model as a hinge-loss minimization problem (see the paper for details). To run the code you need to install psl (included here) and if you want to additionally compare with other inference methods, such as max prod belief propagation or junction tree, you need to install the libDAI library (also included here) The directory europeanCongressData/ (~500 Mb) contains the votings of the EU parlament, including 300 votings events from the actual term, from May 2014 to June 2015, obtained from http://www.votewatch.eu/ <ul> <li>data/ : json files with the european votes</li> <li>network.net : signed network built from the votes</li> <li>political_parties.txt : "ground truth" party</li> <li>community_results/ : results for different number of communities and initial vertices</li> <li>dataComputations.py : used to build the signed network</li> <li>dataProcessing.py : used to build the signed network</li> </ul> We would appreciate if you cite the paper after using the data or the code. DEPENDENCIES The code has been tested in Linux Mint 18.1 Serena and Ubuntu 14.04 - For PSL library, you need to have java 1.8 you may need to export JAVAHOME='/usr/lib/jvm/YOURJAVA1.8FOLDER' maven 3.x - For libDAI you will need: make doxygen graphviz libboost-dev libboost-graph-dev libboost-program-options-dev libboost-test-dev libgmp-dev cimg-dev libgmp-dev CODE TO RUN THE FOLLOWING EXPERIMENTS: Compare the performance in terms of structural balance of max prod bp and our method against an exact inference method (junction tree), with different number of communities INSTALL To install the experiments you have to follow the next steps: 1 Build the libdai library by doing: make -B on the folder (libdai) 2 Generate the class path of the groovy project: mvn clean install mvn dependency:build-classpath-Dmdep.outputFile=classpath.out on the psl root folder (You need to have java 1.8 and maven 3.x installed) 3 Grant exec permissions to the run.sh script Options The main python file to run the experiments is evaluatebalanceon_sn.py. It accepts the following parameters: 1 (Int) Nodes of the graph. In order to run the junction tree we recommend to set this paremeter to 150 or less 2 (Int) The number of underlying communities 3 (Float) The maximum amount of unbalance for the experiments. We recommend 0.45 4 (Bool) Whether to use an heuristic to find the initial node for each community or to use directly random nodes from the ground truth communities. This heuristic looks alternatively for the nodes with highest negative degree and highest positive degree. For the case when the number of communities is equal to 2 (Ising Model), the heuristic is used by default. An example of execution would be: python evaluate_balance_on_sn.py 120 3 0.45 True True The results of the experiments are save in the folder results/ Scripts The main script of the hinge-loss method can be found in the folder psl/psl-example/src/main/java/edu/umd/cs/example/PottsCommunities.groovy Authors: Guillermo Santamaria & Vicenc Gomez Mar 5, 2017 For further questions, please contact vicen.gomez@upf.edu

opencc-by-nc-sa-4.0Jun 2023View details →

Data archive: CICT for single cell RNA-seq network inference

This archive contains benchmarking input data and results for using single cell gene expression data to infer gene regulatory networks (GRN) by the Causal Inference with Composition of Transactions (CICT) method and a selected set of published methods. This accompanies the manuscript "Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions" (Shojaee and Huang, Brief in Bioinform 2023. DOI: 10.1093/bib/bbad370). The CICT code is available at the GitHub repo (https://github.com/hlab1/scRNAseqWithCICT/).The original CICT algorithm was described in Shojaee et al. (arXiv:1608.02658, 2016). The benchmarked methods were included in the BEELINE benchmarking pipeline (Pratapa et al., Nat Methods 2020), to which we added DEEPDRIM (Chen et al., Brief Bioinform 2021), SCENIC (Aibar et al., Nat Methods 2017), Inferelator 3.0 (Gibbs et al., Bioinformatics 2022), and CellOracle (Kamimoto et al., Nature 2023). The output directory names are (subdirectories within each dataset):* CICT_ewMIshrink_RFmaxdepth10_RFntrees20/: CICT for simulated data * CICT_v2/: CICT for experimental data * CELLORACLEDB/: CellOracle for experimental data * DEEPDRIM72_ewMIshrink_RFmaxdepth10_RFntrees20/: DEEPDRIM for simulated data * DEEPDRIM72_v2/: DEEPDRIM for experimental data * INFERELATOR38_ewMIshrink_RFmaxdepth10_RFntrees20/: Inferelator-Prior for simulated data * INFERELATOR38_v2/: Inferelator-Prior for experimental data * INFERELATOR34_ewMIshrink_RFmaxdepth10_RFntrees20/: Inferelator-NoPrior for experimental data * INFERELATOR34_v2/: Inferelator-NoPrior for experimental data * GENIE3/: GENIE3 * GRNBOOST2/: GRNBOST2 * LEAP/: LEAP * PIDC/: PIDC * PPCOR/: PPCOR * SCENICDB/: SCENIC for experimental data * SCNS/: SCNS * SCODE/: SCODE * SCRIBE/: SCRIBE * SINCERITIES/: SINCERITIES * SINGE/: SINGE * RANDOM/: RANDOMThe methods were benchmarked against two kinds of scRNA-seq datasets: * Simulated datasets produced by the SERGIO simulator from a synthetic network (Dibaeinia et al., Cell Systems 2020), including complete datasets and datasets with dropouts with shape parameter k=6.5 and rate parameter q=10, 30, 50, 70, 80.  * Experimental datasets compiled by the BEELINE pipeline, evaluated at three different levels L0, L1 and L2, with three types of ground truth networks.     * Evaluation levels:         * L0: 500 highly varying genes plus TFs         * L1: 1000 highly varying genes plus TFs         * L2: 500 highly varying genes, TFs and 500 genes randomly selected that excluded the 1000 highly varying genes from L1.     * Types of ground truths:         * Cell-type-specific ChIP-seq ground truth (L0, L1, L2)         * Non-specific ChIP-seq ground truth (L0_ns, L1_ns, L2_ns)         * Loss-of-function/gain-of-function ground truth (L0_lofgof, L1_lofgof, L2_lofgof)The directory structure is organized in accordance with the BEELINE benchmarking pipeline. For complete details please please see the BEELINE documentation (https://murali-group.github.io/Beeline/) and Github repo (https://github.com/Murali-group/Beeline).

opencc-by-4.0Oct 2024View details →

Processed Data for "Improving Gene Regulatory Network Inference using Dropout Augmentation"

Here are the processed dataset that are used in the manuscript "Improving Gene Regulatory Network Inference using Dropout Augmentation"

opencc-by-4.0Dec 2020View details →

Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Supplementary Tables

This repository contains the Supplementary Tables for  Suriyalaksh et al.  Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive  of novel ageing genes. The list of table files can be found in <a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/Supplementary%20table%20guide.pdf">Supplementary Tables guide.pdf</a> Tables S1, S2 and S3 corresponding to physical gene-gene interaction data are in a separate repository doi:10.5281/zenodo.4382337 Details about some of the Supplementary tables: TableS4_inferred_networks.csv - list of inferred GRNs for specified input combinations (set of input regulators, length of the time sequence, NI tool and prior used). <a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS5_consensus_network_member.xlsx">TableS5_consensus_network_member.xlsx</a> - list of groups of topologically similar GRNs (from Table S4) Table S6: edge lists (source,target) for each one of the three consensus networks selected according to the GS validation metrics: middle PFE/AUFE, max AUFE, max PFE. TableS6a_max_AUFE_GRN.txt - max AUFE; largest network - this is the one we used in the main analysis and discussion TableS6b_max_PFE_GRN.xt - max PFE TableS6c_middle_AUFE_PFE_GRN.txt - middle PFE/AUFE <a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS7_qRTPCR_ddCt_network_accuracy.csv">TableS7_qRTPCR_ddCt_network_accuracy.csv</a> - gene expression count differences for RNAi knockdown GRN validation experiments.  Table S8: Group membership for each one of the nodes in each one of the selected networks according to the SBM that best describes the observed network topology. Each column shows the group membership for each level in a SBM block hierarchy. Our analysis is in the second most coarse-grained level (level 1). TableS8a_max_AUFE_SBM.csv TableS8b_max_PFE_SBM.csv TableS8c_middle_AUFE_PFE_SBM.csv <a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS9_glp_gs_datasets.pdf">TableS9_glp_gs_datasets.pdf</a> - list of datasets used for defining functional clusters. TableS14a_glp_l1_vs_fem_l1_lifespan_assay.xlsx - Day13 survival of fem-3(q20)ts vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1 TableS14b_glp_l1_vs_glp_l4_lifespan_assay.xlsx - Day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L4 vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1 TableS15a_glp1_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of glp-1(e2144)ts;rrf-3(pk1426) TableS15b_fem3_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of fem-3(q20)ts TableS17_input_regulators_annotated.csv - list input regulators used as input for Network Inference Tools annotated by source type (2nd column): GenAge, known transcription factors (TF) and gene with high variability in the gene expression time series (HV). The third column lists whether that regulator has an orthologue in human (y) according to WormBase (v 278). TableS20_epistasis_lifespan_data.xlsx - Epistasis lifespan data of glp-1(e2144)ts All the image (TIF) files represent representative images in the following genetic backgrounds (below) that have been treated  with empty vector (EV) or RNAi against the gene highlighted in the title of the image. See methods section for details.  femliu1:  fem-3(q20)ts.; dhs-3p::dhs-3::gfp femsod3: fem-3(q20)ts.; sod-3p::gfp glp1lgg1: glp-1(e2144); lgg-1p:lgg-1:gfp

opencc-by-4.0Nov 2020View details →

Large-Scale Gravitational Lens Modeling with Bayesian Neural Networks for Accurate and Precise Inference of the Hubble Constant - Datasets, Trained Models, BNN Samples, and MCMC Chains

We publish the training/validation/test datasets, trained model weights, configuration files, Bayesian neural network samples, and MCMC chains used to produce the figures in the LSST DESC paper, "Large-Scale Gravitational Lens Modeling with Bayesian Neural Networks for Accurate and Precise Inference of the Hubble Constant." They are formatted to be used with the DESC package "H0rton" (<a href="https://github.com/jiwoncpark/h0rton">https://github.com/jiwoncpark/h0rton</a>). Additional descriptions can be found in the README. Please contact Ji Won Park (@jiwoncpark) on GitHub or <a href="https://github.com/jiwoncpark/h0rton/issues">make an issue</a> for any questions.

opencc-by-4.0Dec 2020View details →

Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Database of Physical gene-gene Interactions in young adult C.elegans.

This repository contains Supplementary Information for manuscript Suriyalaksh et al Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive  of novel ageing genes corresponding to the curation of physical gene-gene interactions for young adult C elegans worms  We manually curated 239,001 regulatory interactions from 289 young adult wild-type (WT) C.elegans datasets, consisting of 126 genes and 495 unique transcription factors (see TableS1_datasets_for_prior.csv for references).  This repository contains 3 different files: TableS1_datasets_for_prior.csv - contains datasets used as sources for physical gene-gene or TF-gene interactions TableS2_physical_priors.xlsx - contains three tabs: ChIPATAC - contains physical TF-gene interactions from 115 L4 or young-adult ChIP-seq datasets from modERN (Kudron et al., 2018) +  ChIP-seq datasets (GSE28350, GSE81521) from  (Hochbaum et. al, 2011, Li et. al, 2016). eY1HATAC- contains  3,501 TF-gene interactions from eY1H assay by Fuxman Bass et al. (2016). motifATAC - contains 202 unique TF DNA recognition motifs using “direct evidence” option from CiS-BP motif database (Weirauch et al., 2014), obtained through RTFBSDB R package (Wang et al., 2016) - see TableS1 TableS3_WT_functional_priors.csv - contains functional knockdown data that we use as gold standard to validate inferred networks in Suriyalaksh et al. (see TableS1_datasets_for_prior.csv for sources) --- Description of methodology to obtain regulatory interactions in TableS2: Regulatory sequences for each gene were acquired from ENSEMBL (Aken et al., 2017), obtained using biomaRt R package (accessed on 31st Oct 2017). This study used WBcel235/ce11 version of the C. elegans genome, and WormBase WS260 genome annotations. For motifs, TFs whose motifs overlapped with an open ATAC-seq region by at least one base pair were kept. For ChIP-seq, TF binding sites that overlapped with an open ATAC-seq region by at least one base pair were kept using bedtools intersect and bedtools merge commands. An interaction from a TF to a gene was inferred by aligning transcription start sites (TSS) using bedtools window commands with 1000 bp window size to the TF-binding locations from ChIP-seq and motifs. For eY1H data, an interaction is included if the TSS site of the target gene overlaps with an open ATAC-seq region by at least one base pair. For gene-gene interactions, of the 298 studies compiled in WormExp v1.0 database (Yang et al, 2016, updated 27/07/16), 98 studies were included in the database spanning 126 different genes (see Table S1 in this repository).

opencc-by-4.0Nov 2021View details →

Archival Datasets for SuperNova Artificial Inference by Lstm neural networks (SNAIL)

The spectral-observation dataset (enclosed in the file archival_spec_observations.tar.gz) is comprised of 3091 observed spectra from 361 SNe Ia, largely contributed from CfA (Blondin et al. 2012), BSNIP (Silverman et al. 2012), CSP (Folatelli et al. 2013) and Supernova Polarimetry Program (Wang & Wheeler 2008; Cikota et al. 2019a; Yang et al. 2020). The spectral-template dataset (enclosed in the file archival_spec_templates.tar.gz) includes 361 spectral templates, each of them (covering -15 to +33d with wavelength from 3800 to 7200 A) was generated from the available spectroscopic observations of an individual SN via a LSTM neural network model. The auxiliary photometry dataset (enclosed in the file archival_phot_observations.tar.gz) provides the B & V light curves of these SNe (in total, 196 available SNe Ia), that were used to calibrate the synthetic B-V color of the observed spectra. In additional, the two master catalogs give the detailed information about the 361 SNe and their spectroscopic observations, respectively.  These datasets are associated to the paper "Spectroscopic Studies of Type Ia Supernovae Using LSTM Neural Networks" (Hu et al. 2022, ApJ, accepted).

opencc-by-4.0Jan 2022View details →

Identifying strengths and weaknesses of methods for computational network inference from single cell RNA-seq data

These data files contain single-cell RNA-sequencing expression data (expression_data.zip) and pseudotime files (pseudotime.zip) used to conduct comparisons of network inference methods on six published single-cell RNA-sequencing datasets. The resulting networks generated from the network inference methods are also uploaded here (normalized_inferred_networks.zip and imputed_inferred_networks.zip). Finally, the gold standard networks we used as ground truth to measure accuracy of the inferred networks are uploaded here (gold_standard_datasets.zip).

opencc-by-4.0Jun 2022View details →

Combined network file for "FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data"

Combined network from scRNA-seq and proteomics data Given the complementary nature of the networks based on scRNA-seq and proteomics data individually, we decided to combine them into a single network. As the Pearson Correlation Coefficient scores from FAVA cannot be assumed to be directly comparable across the two networks, we converted them to probabilistic scores based on the KEGG benchmarks. These calibrated scores were then combined to produce a single network based on scRNA-seq as well as proteomics data. As should be expected, this network outperforms the individual networks, combining the best aspects of both.

opencc-zeroMay 2024View details →

Benefits and limits of phasing alleles for network inference of allopolyploid complexes

Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared to haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American Dryopteris fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared to using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical non-identifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.

opencc-by-4.0Dec 2015View details →

Fig. 34. Phylogenetic network inferred from 1,476 in Morphology, Ciliary Pattern and Molecular Phylogeny of Trachelophyllum brachypharynx Levander, 1894 (Litostomatea, Haptoria, Spathidiida)

Fig. 34. Phylogenetic network inferred from 1,476 nucleotide characters of 69 litostomatean taxa, using the NeighborNet algorithm and the uncorrected distances. Numbers along the edges indicate bootstrap support values coming from 1,000 replicates. Only bootstraps> 50% and relevant to this study are shown. The scale bar indicates three substitutions per one thousand nucleotide positions.

opencc-by-4.0Oct 2024View details →

Knowledge-inspired fusion strategies for the inference of PM2.5 values with a Neural Network - CAMS data for experiments

Contains data generated by the CAMS model (during a global reanalysis), used to train and evaluate the models presented article "Knowledge-inspired fusion strategies for the inference of PM2.5 values with a Neural Network" - DOI of this article will be provided as soon as it is available. This data can be downloaded from the Copernicus Atmospheric Data Store (https://ads.atmosphere.copernicus.eu/#!/home), and is also hosted by the ICARE Data and Services Center (https://www.icare.univ-lille.fr/). This dataset only contains the specific data collection used for the experiments presented in aforementioned article. It is only a portion of the data available from these two websites.

opencc-by-4.0Mar 2021View details →

FIGURE 3. Haplotype network inferred from A in On the taxonomic identity of Pteronotus davyi incae Smith, 1972 (Chiroptera: Mormoopidae)

FIGURE 3. Haplotype network inferred from A, cyt-b and B, CO1 datasets, highlighting the clusters corresponding to Pteronotus davyi, P. fulvus, and P. gymnonotus. Each circle represents one distinct haplotype (H), whose size is proportional to its frequency in the sample (1 to 6 individuals).

opencc-by-4.0Apr 2023View details →

Data of "Bayesian inference of high-dimensional finite-strain visco-elastic-visco-plastic model parameters for additive manufactured polymers and neural network based material parameters generator"

General Data of <a href="http://doi.org/10.1016/j.ijsolstr.2023.112470">https://doi.org/10.1016/j.ijsolstr.2023.112470</a> related to MOAMMM project. Data related to the publication (we would be grateful if you could cite the paper in the case in which you are using the data): title = "Bayesian inference of high-dimensional finite-strain visco-elastic-visco-plastic model parameters for additive manufactured polymers and neural network based material parameters generator.", journal = "International Journal of Solids and Structures", year = "2023", volume = "283", pages = "112470", doi = "10.1016/j.ijsolstr.2023.112470", author = "Ling Wu, Cyrielle Anglade, Lucia Cobian, Miguel Monclus, Javier Segurado, Fatma Karayagiz, Ubiratan Freitas, and Ludovic Noels" This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862015. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union. Neither the European Union nor the granting authority can be held responsible for them. Description BI code and results of the inference of a pressure-dependent visco-elastic visco-plastic model developed in [NGU16] with a umat implementation in <a href="https://gitlab.uliege.be/moammm/moammmPublic/code/-/tree/main/MaterialModels/FiniteStrain/Finite_VEVP">https://gitlab.uliege.be/moammm/moammmPublic/code/-/tree/main/MaterialModels/FiniteStrain/Finite_VEVP</a>. The BI is described in [WU23] .The experimental results used in the BI are reported in [COB22,COB22b]. To run the BI you need the open source code <a href="https://gitlab.onelab.info/cm3/cm3Libraries">https://gitlab.onelab.info/cm3/cm3Libraries</a> If you use these data or model, we would be grateful if you could cite the related papers. Bibliography <ul> <li>[WU23] L. Wu, C. Anglade, L. Cobian, M. Monclus, J. Segurado, F. Karayagiz, U. Santos Freitas, L. Noels, Bayesian inference of high-dimensional finite-strain visco-elastic-visco-plastic model parameters for additive manufactured polymers and neural network based material parameters generator, International Journal of Solids and Structures (2023) 112470: https://doi.org/10.1016/j.ijsolstr.2023.112470</li> <li>[COB22] L. Cobian, M. Rueda-Ruiz, J.P. Fernandez-Blazquez, V. Martinez, F. Galvez, F. Karayagiz, T. Lück, J. Segurado, M.A. Monclus, Micromechanical characterization of the material response in a PA12-SLS fabricated lattice structure and its correlation with bulk behaviour, Polymer Testing 110 (2022) 107556: https://doi.org/10.1016/j.polymertesting.2022.107556 (in Open access)</li> <li>[COB22b] Data of “. Cobian, M. Rueda-Ruiz, J.P. Fernandez-Blazquez, V. Martinez, F. Galvez, F. Karayagiz, T. Lück, J. Segurado, M.A. Monclus, Micromechanical characterization of the material response in a PA12-SLS fabricated lattice structure and its correlation with bulk behaviour, Polymer Testing 110 (2022) 107556” http://dx.doi.org/10.5281/zenodo.6136935 (in Open access)</li> <li>[NGU16] V. D. Nguyen, F. Lani, T. Pardoen, X. Morelle, L. Noels, A large strain hyperelastic viscoelastic-viscoplastic-damage constitutive model based on a multi-mechanism non-local damage continuum for amorphous glassy polymers. International Journal of Solids and Structures 96 (2016): 192-216; https://dx.doi.org/10.1016/j.ijsolstr.2016.06.008, Open access: https://orbi.uliege.be/handle/2268/197898</li> </ul> Directories All the codes and experimental results are in five directories: <ol> <li>experimentalTests: experimental data, see the README.txt in each subdirectory for details</li> <li>BayesianVE: BI of the visco-elastic parameters <ol> <li>PlotExperimentalCurves: to vizualize the experimental curves and prepare the observations for the BI in the VE range <ol> <li>Loadcase_H.py and Loadcase_V.py read experimental results and create Load_ExpVE_H.dat and Load_ExpVE_V.dat, which keep the experimental observations and loading conditions to perform the BI.</li> <li>PrintDir_H & PrintDir_V subdirectories with the functions called by Loadcase_H.py and Loadcase_V.py</li> <li>Load_ExpVE_H.dat and Load_ExpVE_V.dat created files with the observations and loading conditions to perform the BI</li> </ol> </li> <li>VE_V2Step and VE_H: BI for viscoelastic properties of "V" specimen (VE_V2Step) and "H" specimen (VE_H) <ol> <li>BI_allpos_sequence.py runs the BI using Predict_VETest.py and creates the MCMC_VE_....dat</li> <li>WarmStart = True is used to restart an inference</li> <li>MCMC_VE_....dat in the VE_V2Step and VE_H directories are the BI results</li> <li>When proceeding in two steps in VE_V2Step, a first step generates MCMC_VE_VN8_1st.dat whose posterior is used as prior in the second step to generate MCMC_VE_VN8_2nd.dat</li> </ol> </li> <li>CheckBayRes: to visualize predictions of a BI sample and experimental curves <ol> <li>MCMCRes.py is used to check the numerical predictions of a BI parameter sample (read last sample by default, V or H direction can be selected at line</li> <li>ResKGEmu.py plots the evolution of elastic properties with time</li> <li>uses as input VE_V2Step/MCMC_VE_....dat or VE_H/MCMC_VE_....dat</li> <li>uses local ViscoElasticTest.py, line.geo, line. msh as interface with https://gitlab.onelab.info/cm3/cm3Libraries code</li> <li>uses local functions plotExpLoad_Unload.py, plotExp.py</li> </ol> </li> <li>ViscoElasticTest.py, line.geo, line.msh: interface with <a href="https://gitlab.onelab.info/cm3/cm3Libraries">https://gitlab.onelab.info/cm3/cm3Libraries</a> code used by VE_V2Step and VE_H to call the VEVP model</li> </ol> </li> <li>BayesianVEVP: BI of the visco-elastic and visco-plastic parameters <ol> <li>PlotExperimentalCurves: to vizualize the experimental curves and prepare the observations for the BI in the VE-VP ranges <ol> <li>Loadcase_H.py and Loadcase_V.py read experimental results and create Load_ExpVEVP_H.dat and Load_ExpVEVP_V.dat, which keep the experimental observations and loading conditions to perform BI at the viscoplastic stage.</li> <li>PrintDir_H & PrintDir_V subdirectories with the functions called by Loadcase_H.py and Loadcase_V.py</li> <li>Load_ExpVEVP_H.dat and Load_ExpVEVP_V.dat created files with the observations and loading conditions to perform the BI</li> </ol> </li> <li>VP_V2step and VP_H2step: BI for viscoelastic-viscoplastic properties of "V" specimen (VP_V2Step) and "H" specimen (VP_H2Step) <ol> <li>BI_allpos_sequence.py runs the BI using Predict_VETest.py and creates the MCMC_VP_....dat</li> <li>WarmStart = True is used to restart an inference</li> <li>It starts from the VE prosterior as prior, see point 2, and generates a MCMC_VP_?_1of2Steps.dat (? being H or V)</li> <li>Then using MCMC_VP_?_1of2Steps.dat posterior to get a new prior, it generates MCMC_VP_?_2of2Steps.dat (? being H or V)</li> </ol> </li> <li>CheckBayRes: visualize predictions of a BI sample and experimental curves <ol> <li>MCMCRes.py is used to check the numerical predictions with 3 BI parameter samples ([28000, 45000,70000] by default, V or H direction can be selected at line 12) using the samples of BayesianVEVP/VP_?2step/MCMC_VP_?_2of2Steps.dat (? being H or V)</li> <li>plot_hist.py is used to plot histograms of all the inferred parameters using the samples of BayesianVEVP/VP_?2step/MCMC_VP_?_2of2Steps.dat (? being H or V)</li> <li>Plot_Prop.py plots joints histograms of the inferred parameters using the samples of BayesianVEVP/VP_?2step/MCMC_VP_?_2of2Steps.dat (? being H or V)</li> <li>ResKGEmu.py plots the evolution of elastic properties with time</li> </ol> </li> <li>VEVPTest.py: interface with https://gitlab.onelab.info/cm3/cm3Libraries code used by VP_V2Step and VP_H2Step to call the VEVP model</li> </ol> </li> <li>RandomParametersGenerator: used to generate the parameters from the BI samples, with the same statistical content <ol> <li>Generator <ol> <li>DataProcess.py: creates normalized data for training from final inferred parameters in ../MCMC_ResData and creates ?_dirNormData (? being H or V)</li> <li>KmeanDataProcess.py: performs clustering for the data of H_dirNormDat and creates H_dirNormData_2cluster (no need for V direction because not bimodal)</li> <li>Gan_V.py and Gan_H.py are used to train the random material parameter generators and create the VDir_Gan or HDir_Gan200_0/HDir_Gan200_1</li> <li>GenerateParameters.py generates random parameters using the Gan files VDir_Gan or HDir_Gan200_0/HDir_Gan200_1 and checks the joint histograms of generated parameters, generated parameters are in V_GenData and H_GenData</li> <li>Ganlib.py is used by the generator</li> </ol> </li> <li>CheckRes <ol> <li>GenDataRes.py is used to check the numerical predictions with the generated parameter samples, see point 4) (using V_GenData and H_GenData).</li> <li>Plot_PropGen.py plots joints histograms of the generated parameters using the samples of V_GenData or H_GenData</li> </ol> </li> </ol> </li> <li>MCMC_ResData:All final data used in the paper (they can substitute the ones used here above) <ol> <li>H_direction and V_direction keep the MCMC random walk results of BI.</li> <li>RandomParameterGenerator keeps results of the generator Paper</li> </ol> </li> </ol> Figures of [WU23] <ul> <li>Fig. 5: From directory BayesianVE/PlotExperimentalCurves, run python3 ./PrintDir_V/plotExp_T.py or ./PrintDir_V/plotExp_C.py or ./PrintDir_V/plotExp_R.py</li> <li>Fig. 7: BayesianVEVP/CheckBayRes/Plot_Prop.py with direct = "V" and then with direct = "H" and with Var = [0,1,20,24,28,29,30,31]</li> <li>Fig. 8: BayesianVEVP/CheckBayRes/MCMCRes.py with direct = "V" (requires <a href="https://gitlab.onelab.info/cm3/cm3Libraries">https://gitlab.onelab.info/cm3/cm3Libraries</a> code)</li> <li>Fig. 9: BayesianVEVP/CheckBayRes/MCMCRes.py with direct = "H" (requires<a href="https://gitlab.onelab.info/cm3/cm3Libraries"> https://gitlab.onelab.info/cm3/cm3Libraries</a> code)</li> <li>Fig. 11: RandomParametersGenerator/CheckRes/Plot_PropGen.py with direct = "V" and then with direct = "H" and with Var = [0,1,20,24,28,29,30,31]</li> <li>Fig. 12: RandomParametersGenerator/CheckRes/GenDataRes.py with direct = "V" (requires <a href="https://gitlab.onelab.info/cm3/cm3Libraries">https://gitlab.onelab.info/cm3/cm3Libraries</a> code)</li> <li>Fig. 13: RandomParametersGenerator/CheckRes/GenDataRes.py with direct = "H" (requires <a href="https://gitlab.onelab.info/cm3/cm3Libraries">https://gitlab.onelab.info/cm3/cm3Libraries</a> code)</li> <li>Fig. 14A: From directory BayesianVE/PlotExperimentalCurves, run python3 ./PrintDir_H/plotExp_T.py or ./PrintDir_H/plotExp_C.py or ./PrintDir_H/plotExp_R.py</li> <li>Fig. 15C: BayesianVEVP/CheckBayRes/Plot_Prop.py with direct = "V", Var = [2,3,8,9,14,15,18,19] and [20,21,22,23,24,25,26,27]</li> <li>Fig. 16C: BayesainVEVP/CheckBayRes/plot_hist.py with direct = "V"</li> <li>Fig. 17C: BayesianVEVP/CheckBayRes/plot_hist.py with direct = "V"</li> <li>Fig. 18C: BayesianVEVP/CheckBayRes/Plot_Prop.py with direct = "H", Var = [2,3,8,9,14,15,18,19] and [20,21,22,23,24,25,26,27]</li> <li>Fig. 19C: BayesianVEVP/CheckBayRes/plot_hist.py with direct = "H"</li> <li>Fig. 20C: BayesianVEVP/CheckBayRes/plot_hist.py with direct = "H"</li> <li>Fig. 21D: RandomParametersGenerator/CheckRes/Plot_PropGen.py with direct = "V" , Var = [2,3,8,9,14,15,18,19] and [20,21,22,23,24,25,26,27]</li> <li>Fig. 22D: RandomParametersGenerator/CheckRes/Plot_PropGen.py with direct = "H" , Var = [2,3,8,9,14,15,18,19] and [20,21,22,23,24,25,26,27]</li> </ul>

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