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210 results for “Bayesian inference”
Supplementary data: The added value of Bayesian inference for estimating biotransformation rates of organic contaminants in aquatic invertebrates.
<p>Supporting information for the article "<strong>The added value of Bayesian inference for estimating biotransformation rates of organic contaminants in aquatic invertebrates.</strong>"</p> <p>This provides all the R script and .csv files for each dataset. </p>
Supplement to "Proof of concept for Bayesian inference of dynamic rating curve uncertainty" (v3)
<div>This deposit contains part of the updated supplement to “Proof of concept for Bayesian inference of dynamic rating curve uncertainty” (<a href="https://www.tandfonline.com/doi/full/10.1080/02626667.2024.2401094" target="_blank" rel="noopener">Cornelio et al. 2024, HSJ</a>). This version, in particular, contains two files in which the following changes were made from the earlier version (v2.0.1):</div> <div> <ul> <li><strong><em>250117_Lbn_RC_new.R</em></strong> is the updated R code. The argument for the random number generator (RNG) kind is defined for the set.seed() functions used in the script. </li> <li><strong><em>Lbn-DMs-csv0.csv</em></strong> is the updated input file containing the stage-discharge gaugings. The column for the stage values has been renamed to "H_rec" (instead of "H_m" as in the original CSV) to be consistent with the attribute name used throughout the R code.</li> </ul> <p>Except for the above files, all the input and output files in <a href="https://zenodo.org/records/12792513" target="_blank" rel="noopener">v2.0.1</a><span> remain unchanged. </span></p> </div> <p><u> </u></p>
Figure 1. Bayesian phylogenetic tree inferred from the 640 in Two new Geoplaninae species (Platyhelminthes: Continenticola) from Southern Brazil based on an integrative taxonomic approach
Figure 1. Bayesian phylogenetic tree inferred from the 640-bp of cytochrome c oxidase subunit I gene under GTR + I + G model of sequence evolution. The two new species are highlighted in light grey (Cratera ochra sp. nov.) and dark grey (Obama maculipunctata sp. nov.). Values indicate support for each node according to the maximum posterior probabilities>70% and bootstrap support values> 70%, respectively.
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
<p>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.</p>
Fig. 11. Bayesian inference trees. A. 16S rRNA dataset. B. Cytochrome oxidase I in Designation of a neotype for Myxicola infundibulum (Montagu, 1808) (Annelida: Sabellidae) and a new species from the UK
Fig. 11. Bayesian inference trees. A. 16S rRNA dataset. B. Cytochrome oxidase I gene dataset. The first value at each node represents maximum likelihood bootstrap support, the second the Bayesian posterior probabilities and the third the maximum parsimony bootstrap support.
Fig. 2. Bayesian consensus tree generated from partial 28S in Relationships Of The Heteronchocleidids (Heteronchocleidus, Eutrianchoratus And Trianchoratus) As Inferred From Ribosomal Dna Nucleotide Sequence Data
Fig. 2. Bayesian consensus tree generated from partial 28S rDNA sequences (D1 domain) with Diplectanum spp. and Gyrodactylus spp. as outgroups. Values shown at each node refer to Bayesian (BI) posterior probabilities/maximum likelihood (ML) percentages of the bootstrap values with 100 replicates. Bootstrap values lower than 50 are given as dashes (-).
Fig. 6. Bayesian inference tree for 5519 in First Record of Poecilobdella nanjingensis (Hirudinida: Arhynchobdellida: Hirudinidae) from Taiwan and its Molecular Phylogenetic Position within the Family
Fig. 6. Bayesian inference tree for 5519 bp alignment positions of nuclear 18S rRNA, 28S rRNA, mitochondrial cytochrome c oxidase subunit I, and 12S rRNA markers. Numbers on nodes indicate bootstrap values for maximum likelihood and Bayesian inference posterior probabilities.
Supplementary Data to *Robust adaptive distance functions for approximate Bayesian inference on outlier-corrupted data*
<p>Supplementary code and data to <strong>Robust adaptive distance functions for approximate Bayesian inference on outlier-corrupted data</strong> by <strong>Y. Schaelte et al., 2021</strong>.</p> <p>The archive contains a <strong>README.rst </strong>for information on what is where and how to execute the study and generate the figures. The underlying code without the data can be found at the repository https://github.com/yannikschaelte/study_abc_rad, of which this archive is a snapshot.</p> <p> </p>
Figure 5. Bayesian Inference tree calculated with complete cox1 in Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species
Figure 5. Bayesian Inference tree calculated with complete cox1 (1428 bp), cox3 (753 bp), and cytb (1127 bp) sequences of haemosporidian parasites and Klossiella equi (MH203050) and Klossia razorbacki (MT084562) as the outgroup. Bayesian posterior probabilities and Maximum Likelihood bootstrap values are indicated at most nodes. The scale bar indicates the expected number of substitutions per site according to the model of sequence evolution applied.
FIGURE 3 in Bayesian inference reveals a complex evolutionary history of belemnites
FIGURE 3. Cladogram showing the here suggested systematics of the Belemnitida based on the Bayesian tip-dated analysis. Sketches show the general outer morphological features of a typical representative of the groups in either dorsal (d), ventral (v), or lateral (l) view.
FIGURE 2 in Bayesian inference reveals a complex evolutionary history of belemnites
FIGURE 2. Maximum clade credibility tree of the Bayesian tip-dated analysis. Numbers at nodes represent posterior probability, while the blue bars indicate the 95% highest posterior density interval of the divergence time estimates. The small black dot represents the constrained clade. Tips with zero-length branches represent sampled ancestors.
◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West) in Bumps on the back: An unusual morphology in phylogenetically distinct Peridinium aff. cinctum (= Peridinium tuberosum; Peridiniales, Dinophyceae)
◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West)
◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae) in Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy
◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae)
Fig. 1. Circular Bayesian tree inferred from mtDNA cox-2 in Temporal stability of parasite distribution and genetic variability values of Contracaecum osculatum sp. D and C. osculatum sp. E (Nematoda: Anisakidae) from fish of the Ross Sea (Antarctica)
Fig. 1. Circular Bayesian tree inferred from mtDNA cox-2 sequences obtained from specimens of C. osculatum sp. D and C. osculatum sp. E analysed in the present study, based on Bayesian Inference (BI) method using MrBayes v3.2.2 (Ronquist et al., 2012). Evolutionary distance was estimated using the TrN + G (G = 0.60) substitution model as implemented in jModeltest (Posada, 2008), with the AIC approach (Posada and Buckley, 2004). Posterior probability values are the result of 1.000000 of runs and are reported at the nodes. The coloured icons correspond to the two species considered in this study (red = C. osculatum sp. D and blue = C. osculatum sp. E).
Towards identifying the optimal datasize for lexically-based Bayesian inference of linguistic phylogenies
<p>This repository contains the nexus files and MrBayes command files needed for running the experiments to determine the optimal word list size required for inferring the best phylogenies.</p> <p>The paper is forthcoming at <strong>The 27th International Conference on Computational Linguistics (COLING 2018), Santa Fe, New-Mexico, USA</strong>.</p>
Figure 4. Phylogeny constructed through Bayesian inference estimated from the 35H in Gene Flow Patterns of the Aedes aegypti (Diptera: Culicidae) Mosquito in Colombia: a Continental Comparison Suggests Multiple Invasion Routes and Gene Exchange
Figure 4. Phylogeny constructed through Bayesian inference estimated from the 35H found of the ND4 gene for the A. aegypti populations in the American continent. The blue horizontal bars above the branches reflect the 95% CI for the branch supports. The color bars (blue, green, and red) on the tree terminals indicate which haplotypes are exclusive for a specific population. The dotted lines on the right side of the tree and numbers I or II indicate to what clade each of the terminals belong. H1-Col (Colombia (Sucre and Quindio), Venezuela, Peru, M-NA, Brasil (MA-O, RBPV, SEBr, BE-L)), H4 (Venezuela, M-NA, Brasil (MA-O, RBPV, BEL)), H3 (Venezuela, M-NA, Brazil (RBPV, SEBr, BE-L)), H2-Col (Colombia (Sucre), Venezuela, Peru, M-NA, Brazil (RBPV, SEBr, BE-L)), H13 (M-NA, Brazil (SEBr)), H8 (Venezuela, Brazil (SEBr)).
Figure 4. Bayesian inference tree for 8103 in A new species of Orobdella (Hirudinida, Arhynchobdellida, Orobdellidae) from the Tsukuba Mountains in Japan
Figure 4. Bayesian inference tree for 8103 bp of nuclear 18S rRNA, 28S rRNA and H3, and mitochondrial COI, tRNACys, tRNAMet, 12S rRNA, tRNAVal, 16S rRNA, tRNALeu and ND1 markers. Numbers on nodes indicate bootstrap (BS) values for maximum likelihood ≥ 50 % and Bayesian posterior probabilities (PP) ≥ 0.90. An asterisk denotes the node with BS = 100 % and PP ≥ 1.0.
Fig. 2. Bayesian Inference tree constructed from Internal transcribed Spacer 2 in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism
Fig. 2. Bayesian Inference tree constructed from Internal transcribed Spacer 2 (non-coding) sequence data. Each specimen is labelled with the species name and location abbreviation as indicated in Table 1. Green text corresponds to European samples of Lucilia bufonivora; red represents Lucilia elongata; purple represents Canadian L. bufonivora; orange represents Lucilia silvarum. Scale bar represents expected changes per site. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Bayesian inference of the dense matter equation of state built upon extended Skyrme interactions [Data Set]
<pre> </pre> <p>We provide the posterior distributions of the input parameters of the five main runs considered in the article "Bayesian inference of the dense matter equation of state built upon extended Skyrme interactions" (accepted to Phys. Rev. C, arXiv: 2403.19325).</p> <p>Each row in each file corresponds to one equation of state. It contains 13 input parameters of the extend Skyrme interaction that define the effective interaction and that can be used in order to construct equations of state. The input parameters (columns, from left to right) and their dimensions are: </p> <p>C_0 (MeV*fm^3); D_0 (MeV*fm^3); C_3 (MeV*fm^{3+3*sigma}); D_3 (MeV*fm^{3+3*sigma}); C_eff (MeV*fm^5); D_eff (MeV*fm^5); t_4 (MeV*fm^{5+3*beta}); t_5 (MeV*fm^{5+3*gamma}); x_4; x_5; sigma; beta; gamma.</p> <p>See the article for more details.</p>
FIG. 3. — Bayesian consensus tree inferred from concatenated chloroplast rps4 in Pterygoneurum sampaianum (Guim.) Guim.: range extension to Africa, first mentions in France, confirmation of specific status and improved morphological circumscription
FIG. 3. — Bayesian consensus tree inferred from concatenated chloroplast rps4-trnS and trnM-trnV sequence data of the analysed dataset of Pottiaceae subfam. Pottioideae, partitioned between DNA sequence and indel data. Posterior probability from BI is displayed above the branches; bootstrap support (656 replications) from ML analysis is displayed below the branches.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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
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