cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1603543
title: Sliced Full Factorial-Based Latin Hypercube Designs as a Framework for a Batch Sequential Design Algorithm

description: When fitting complex models, such as finite element or discrete event simulations, the experiment design should exhibit desirable properties of both projectivity and orthogonality. To reduce experimental effort, sequential design strategies allow experimenters to collect data only until some measure of prediction precision is reached. In this article, we present a batch sequential experiment design method that uses sliced full factorial-based Latin hypercube designs (sFFLHDs), which are an extension to the concept of sliced orthogonal array-based Latin hypercube designs (OALHDs). At all stages of the sequential design, good univariate stratification is achieved. The structure of the FFLHDs also tends to produce uniformity in higher dimensions, especially at certain stages of the design. We show that our batch sequential design approach has good sampling and fitting qualities through both empirical studies and theoretical arguments. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.1603544
title: Particle pollution estimation based on image analysis

description: Beijing data acquirement
DOI: 10.6084/m9.figshare.1603546.v1
title: U–Pb zircon age of the Walloon Coal Measures in the Surat Basin, southeast Queensland: implications for paleogeography and basin subsidence

description: The Jurassic Walloon Coal Measures of the Surat Basin were previously estimated to be of Middle Jurassic age, ranging from Aalenian to Callovian, based on an uncalibrated eastern Australian biostratigraphic framework. New U–Pb dates of 162.55 ± 0.05 Ma and 158.86 ± 0.04 Ma obtained from zircons in ash-fall volcanic tuffs now place the Walloon Coal Measures of the Surat Basin in the Upper Jurassic Oxfordian. The new dates have several implications for the interpretation of the Jurassic strata in the Surat Basin. First-order subsidence rates of 61 m/Myr for the Walloon Coal Measures are more akin to those of foreland basins than the previously assumed intracratonic setting. The dates also imply deposition of the Walloon coals in substantially higher latitudes than previously assumed and that they accumulated as peats in mires that experienced more than three months’ continual darkness each winter. Zircon dating of tuffs and associated geochemistry should assist with the correlation of the laterally impersistent coals, fluvial sandstone and mudstone of the Walloon Coal Measures, which are currently difficult to correlate over distances of more than a few kilometres. Dating of the palynostratigraphic zones APJ4.2 to APJ5 (<i>Aequitriradites norrisii</i> Association Zone to <i>Murospora florida</i> Association Zone) will also need to be recalibrated.
DOI: 10.6084/m9.figshare.1603543.v1
title: Sliced Full Factorial-Based Latin Hypercube Designs as a Framework for a Batch Sequential Design Algorithm

description: When fitting complex models, such as finite element or discrete event simulations, the experiment design should exhibit desirable properties of both projectivity and orthogonality. To reduce experimental effort, sequential design strategies allow experimenters to collect data only until some measure of prediction precision is reached. In this article, we present a batch sequential experiment design method that uses sliced full factorial-based Latin hypercube designs (sFFLHDs), which are an extension to the concept of sliced orthogonal array-based Latin hypercube designs (OALHDs). At all stages of the sequential design, good univariate stratification is achieved. The structure of the FFLHDs also tends to produce uniformity in higher dimensions, especially at certain stages of the design. We show that our batch sequential design approach has good sampling and fitting qualities through both empirical studies and theoretical arguments. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.1603884.v3
title: Cuando SEC Data

description: SEC data used to build Cuando archive.
DOI: 10.6084/m9.figshare.1603542
title: Monotonic Metamodels for Deterministic Computer Experiments

description: In deterministic computer experiments, it is often known that the output is a monotonic function of some of the inputs. In these cases, a monotonic metamodel will tend to give more accurate and interpretable predictions with less prediction uncertainty than a nonmonotonic metamodel. The widely used Gaussian process (GP) models are not monotonic. A recent article in <i>Biometrika</i> offers a modification that projects GP sample paths onto the cone of monotonic functions. However, their approach does not account for the fact that the GP model is more informative about the true function at locations near design points than at locations far away. Moreover, a grid-based method is used, which is memory intensive and gives predictions only at grid points. This article proposes the weighted projection approach that more effectively uses information in the GP model together with two computational implementations. The first is isotonic regression on a grid while the second is projection onto a cone of monotone splines, which alleviates problems faced by a grid-based approach. Simulations show that the monotone B-spline metamodel gives particularly good results. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1603544.v1
title: Particle pollution estimation based on image analysis

description: Beijing data acquirement
DOI: 10.6084/m9.figshare.1603884.v6
title: Cuando SEC Data

description: SEC data used to build Cuando archive.
DOI: 10.6084/m9.figshare.1603542.v1
title: Monotonic Metamodels for Deterministic Computer Experiments

description: In deterministic computer experiments, it is often known that the output is a monotonic function of some of the inputs. In these cases, a monotonic metamodel will tend to give more accurate and interpretable predictions with less prediction uncertainty than a nonmonotonic metamodel. The widely used Gaussian process (GP) models are not monotonic. A recent article in <i>Biometrika</i> offers a modification that projects GP sample paths onto the cone of monotonic functions. However, their approach does not account for the fact that the GP model is more informative about the true function at locations near design points than at locations far away. Moreover, a grid-based method is used, which is memory intensive and gives predictions only at grid points. This article proposes the weighted projection approach that more effectively uses information in the GP model together with two computational implementations. The first is isotonic regression on a grid while the second is projection onto a cone of monotone splines, which alleviates problems faced by a grid-based approach. Simulations show that the monotone B-spline metamodel gives particularly good results. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1603884.v5
title: Cuando SEC Data

description: SEC data used to build Cuando archive.
DOI: 10.6084/m9.figshare.1603545.v1
title: AARE 2015

description: Papers and media from our symposium presentation at the Australian Association for Reserch in Education (AARE) conference 2015, Freemantle, WA.
DOI: 10.6084/m9.figshare.1603537
title: cytokines

description: not real data!
DOI: 10.6084/m9.figshare.1603538
title: Three-dimensional visualisation of brooding behaviour in two distantly related brittle stars from South African waters

description: Brooding in ophiuroids (Echinodermata: Ophiuroidea) is a highly-developed reproduction strategy and has evolved independently several times. In South African waters, brooding occurs both in the very small amphiurid <i>Amphipholis squamata</i>, which is hermaphroditic, and in the large ophiodermatid <i>Ophioderma wahlbergii</i>, which is gonochoric. For the first time, microcomputed tomography was applied to visualise and compare brooding and brooded young of these two brittle star species from two distantly related families. The scanned <i>A. squamata</i> brooded six young, whereas <i>O. wahlbergii</i> brooded 13 young. Volume measurements of the adults revealed that <i>A. squamata</i> dedicated about 25% of its disc volume to brooding and <i>O. wahlbergii</i> about 14%. Although the brooded young of <i>O. wahlbergii</i> are thought to be among the largest of all known ophiuroids, young of <i>A. squamata</i> were four times larger in relation to adult body disc volume. Other than differences in the sizes of brooded young, these distantly related species have evolved very similar brooding adaptations. All juveniles were found lying with the mouth upward, pressed against the mother's bursal wall, strengthening the hypothesis that the bursal wall acts as a nutritive organ. In both species, the large size of the young can only be explained by maternal nutrient supply. Both brittle star species, therefore, are regarded as truly viviparous.
DOI: 10.6084/m9.figshare.1603538.v1
title: Three-dimensional visualisation of brooding behaviour in two distantly related brittle stars from South African waters

description: Brooding in ophiuroids (Echinodermata: Ophiuroidea) is a highly-developed reproduction strategy and has evolved independently several times. In South African waters, brooding occurs both in the very small amphiurid <i>Amphipholis squamata</i>, which is hermaphroditic, and in the large ophiodermatid <i>Ophioderma wahlbergii</i>, which is gonochoric. For the first time, microcomputed tomography was applied to visualise and compare brooding and brooded young of these two brittle star species from two distantly related families. The scanned <i>A. squamata</i> brooded six young, whereas <i>O. wahlbergii</i> brooded 13 young. Volume measurements of the adults revealed that <i>A. squamata</i> dedicated about 25% of its disc volume to brooding and <i>O. wahlbergii</i> about 14%. Although the brooded young of <i>O. wahlbergii</i> are thought to be among the largest of all known ophiuroids, young of <i>A. squamata</i> were four times larger in relation to adult body disc volume. Other than differences in the sizes of brooded young, these distantly related species have evolved very similar brooding adaptations. All juveniles were found lying with the mouth upward, pressed against the mother's bursal wall, strengthening the hypothesis that the bursal wall acts as a nutritive organ. In both species, the large size of the young can only be explained by maternal nutrient supply. Both brittle star species, therefore, are regarded as truly viviparous.
DOI: 10.6084/m9.figshare.1603545.v2
title: AARE 2015

description: Papers and media from our symposium presentation at the Australian Association for Reserch in Education (AARE) conference 2015, Freemantle, WA.
DOI: 10.6084/m9.figshare.1603533
title: The longitudinal cerebrospinal fluid metabolomic profile of amyotrophic lateral sclerosis

description: Neurochemical biomarkers are urgently sought in ALS. Metabolomic analysis of cerebrospinal fluid (CSF) using proton nuclear magnetic resonance (<sup>1</sup>H-NMR) spectroscopy is a highly sensitive method capable of revealing nervous system cellular pathology. The <sup>1</sup>H-NMR CSF metabolomic signature of ALS was sought in a longitudinal cohort. Six-monthly serial collection was performed in ALS patients across a range of clinical sub-types (<i>n = </i>41) for up to two years, and in healthy controls at a single time-point (<i>n = </i>14). A multivariate statistical approach, partial least squares discriminant analysis, was used to determine differences between the NMR spectra from patients and controls. Significantly predictive models were found using those patients with at least one year's interval between recruitment and the second sample. Glucose, lactate, citric acid and, unexpectedly, ethanol were the discriminating metabolites elevated in ALS. It is concluded that <sup>1</sup>H-NMR captured the CSF metabolomic signature associated with derangements in cellular energy utilization connected with ALS, and was most prominent in comparisons using patients with longer disease duration. The specific metabolites identified support the concept of a hypercatabolic state, possibly involving mitochondrial dysfunction specifically. Endogenous ethanol in the CSF may be an unrecognized novel marker of neuronal tissue injury in ALS.
DOI: 10.6084/m9.figshare.1603531
title: cytokines

description: Demo data. Not real!
DOI: 10.6084/m9.figshare.1603545.v3
title: AARE 2015

description: Papers and media from our symposium presentation at the Australian Association for Reserch in Education (AARE) conference 2015, Freemantle, WA.
DOI: 10.6084/m9.figshare.1603533.v2
title: The longitudinal cerebrospinal fluid metabolomic profile of amyotrophic lateral sclerosis

description: Neurochemical biomarkers are urgently sought in ALS. Metabolomic analysis of cerebrospinal fluid (CSF) using proton nuclear magnetic resonance (<sup>1</sup>H-NMR) spectroscopy is a highly sensitive method capable of revealing nervous system cellular pathology. The <sup>1</sup>H-NMR CSF metabolomic signature of ALS was sought in a longitudinal cohort. Six-monthly serial collection was performed in ALS patients across a range of clinical sub-types (<i>n = </i>41) for up to two years, and in healthy controls at a single time-point (<i>n = </i>14). A multivariate statistical approach, partial least squares discriminant analysis, was used to determine differences between the NMR spectra from patients and controls. Significantly predictive models were found using those patients with at least one year's interval between recruitment and the second sample. Glucose, lactate, citric acid and, unexpectedly, ethanol were the discriminating metabolites elevated in ALS. It is concluded that <sup>1</sup>H-NMR captured the CSF metabolomic signature associated with derangements in cellular energy utilization connected with ALS, and was most prominent in comparisons using patients with longer disease duration. The specific metabolites identified support the concept of a hypercatabolic state, possibly involving mitochondrial dysfunction specifically. Endogenous ethanol in the CSF may be an unrecognized novel marker of neuronal tissue injury in ALS.
DOI: 10.6084/m9.figshare.1603531.v1
title: Cytokines

description: Demo data. Not real!
DOI: 10.6084/m9.figshare.1603533.v1
title: The longitudinal cerebrospinal fluid metabolomic profile of amyotrophic lateral sclerosis

description: Neurochemical biomarkers are urgently sought in ALS. Metabolomic analysis of cerebrospinal fluid (CSF) using proton nuclear magnetic resonance (<sup>1</sup>H-NMR) spectroscopy is a highly sensitive method capable of revealing nervous system cellular pathology. The <sup>1</sup>H-NMR CSF metabolomic signature of ALS was sought in a longitudinal cohort. Six-monthly serial collection was performed in ALS patients across a range of clinical sub-types (<i>n = </i>41) for up to two years, and in healthy controls at a single time-point (<i>n = </i>14). A multivariate statistical approach, partial least squares discriminant analysis, was used to determine differences between the NMR spectra from patients and controls. Significantly predictive models were found using those patients with at least one year's interval between recruitment and the second sample. Glucose, lactate, citric acid and, unexpectedly, ethanol were the discriminating metabolites elevated in ALS. It is concluded that <sup>1</sup>H-NMR captured the CSF metabolomic signature associated with derangements in cellular energy utilization connected with ALS, and was most prominent in comparisons using patients with longer disease duration. The specific metabolites identified support the concept of a hypercatabolic state, possibly involving mitochondrial dysfunction specifically. Endogenous ethanol in the CSF may be an unrecognized novel marker of neuronal tissue injury in ALS.
DOI: 10.6084/m9.figshare.1603545.v4
title: AARE 2015

description: Papers and media from our symposium presentation at the Australian Association for Reserch in Education (AARE) conference 2015, Freemantle, WA.
DOI: 10.6084/m9.figshare.1603527
title: Design and Analysis of Experiments on Nonconvex Regions

description: Modeling a response over a nonconvex design region is a common problem in diverse areas such as engineering and geophysics. The tools available to model and design for such responses are limited and have received little attention. We propose a new method for selecting design points over nonconvex regions that is based on the application of multidimensional scaling to the geodesic distance. Optimal designs for prediction are described, with special emphasis on Gaussian process models, followed by a simulation study and an application in glaciology. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1603528
title: High-Performance Kernel Machines With Implicit Distributed Optimization and Randomization

description: We propose a framework for massive-scale training of kernel-based statistical models, based on combining distributed convex optimization with randomization techniques. Our approach is based on a block-splitting variant of the alternating directions method of multipliers, carefully reconfigured to handle very large random feature matrices under memory constraints, while exploiting hybrid parallelism typically found in modern clusters of multicore machines. Our high-performance implementation supports a variety of statistical learning tasks by enabling several loss functions, regularization schemes, kernels, and layers of randomized approximations for both dense and sparse datasets, in an extensible framework. We evaluate our implementation on large-scale model construction tasks and provide a comparison against existing sequential and parallel libraries. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1603545.v6
title: AARE 2015

description: Papers and media from our symposium presentation at the Australian Association for Reserch in Education (AARE) conference 2015, Freemantle, WA.
DOI: 10.6084/m9.figshare.1603531.v2
title: Cytokines

description: Demo data. Not real!
DOI: 10.6084/m9.figshare.1603525
title: Joint Identification of Location and Dispersion Effects in Unreplicated Two-Level Factorials

description: Most procedures that have been proposed to identify dispersion effects in unreplicated factorial designs assume that location effects have been identified correctly. Incorrect identification of location effects may impair subsequent identification of dispersion effects. We develop a method for joint identification of location and dispersion effects that can reliably identify active effects of both types. A normal-based model containing parameters for effects in both the mean and variance is used. Parameters are estimated using maximum likelihood, and subsequent effect selection is done using a specially derived information criterion. An exhaustive search through a limited version of the space of possible models is conducted. Both a single-model output and model averaging are considered. The method is shown to be capable of identifying sensible location-dispersion models that are missed by methods that rely on sequential estimation of location and dispersion effects. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1603545.v5
title: AARE 2015

description: Papers and media from our symposium presentation at the Australian Association for Reserch in Education (AARE) conference 2015, Freemantle, WA.
DOI: 10.6084/m9.figshare.1603527.v2
title: Design and Analysis of Experiments on Nonconvex Regions

description: Modeling a response over a nonconvex design region is a common problem in diverse areas such as engineering and geophysics. The tools available to model and design for such responses are limited and have received little attention. We propose a new method for selecting design points over nonconvex regions that is based on the application of multidimensional scaling to the geodesic distance. Optimal designs for prediction are described, with special emphasis on Gaussian process models, followed by a simulation study and an application in glaciology. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1603525.v1
title: Joint Identification of Location and Dispersion Effects in Unreplicated Two-Level Factorials

description: Most procedures that have been proposed to identify dispersion effects in unreplicated factorial designs assume that location effects have been identified correctly. Incorrect identification of location effects may impair subsequent identification of dispersion effects. We develop a method for joint identification of location and dispersion effects that can reliably identify active effects of both types. A normal-based model containing parameters for effects in both the mean and variance is used. Parameters are estimated using maximum likelihood, and subsequent effect selection is done using a specially derived information criterion. An exhaustive search through a limited version of the space of possible models is conducted. Both a single-model output and model averaging are considered. The method is shown to be capable of identifying sensible location-dispersion models that are missed by methods that rely on sequential estimation of location and dispersion effects. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1603527.v1
title: Design and Analysis of Experiments on Non-Convex Regions

description: Modeling a response over a non-convex design region is a common problem in diverse areas such as engineering and geophysics. The tools available to model and design for such responses are limited and have received little attention. We propose a new method for selecting design points over non-convex regions that is based on the application of multidimensional scaling to the geodesic distance. Optimal designs for prediction are described, with special emphasis on Gaussian process models, followed by a simulation study and an application in glaciology.
DOI: 10.6084/m9.figshare.1603528.v2
title: High-Performance Kernel Machines With Implicit Distributed Optimization and Randomization

description: We propose a framework for massive-scale training of kernel-based statistical models, based on combining distributed convex optimization with randomization techniques. Our approach is based on a block-splitting variant of the alternating directions method of multipliers, carefully reconfigured to handle very large random feature matrices under memory constraints, while exploiting hybrid parallelism typically found in modern clusters of multicore machines. Our high-performance implementation supports a variety of statistical learning tasks by enabling several loss functions, regularization schemes, kernels, and layers of randomized approximations for both dense and sparse datasets, in an extensible framework. We evaluate our implementation on large-scale model construction tasks and provide a comparison against existing sequential and parallel libraries. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1603512
title: Data for anvio pangenome example

description: This archive contains anvi'o files for two pangenomes described here: http://merenlab.org/2015/11/14/pangenomics/