To create effective data visualizations, it helps to represent data using visual features in intuitive ways. When visualization designs match observer expectations, visualizations are easier to interpret. Prior work suggests that several factors influence such expectations. For example, the dark-is-more bias leads observers to infer that darker colors map to larger quantities, and the opaque-is-more bias leads them to infer that regions appearing more opaque (given the background color) map to larger quantities. Previous work suggested that the background color only plays a role if visualizations appear to vary in opacity. The present study challenges this claim. We hypothesized that the background color modulate inferred mappings for colormaps that should not appear to vary in opacity (by previous measures) if the visualization appeared to have a "hole" that revealed the background behind the map (hole hypothesis). We found that spatial aspects of the map contributed to inferred mappings, though the effects were inconsistent with the hole hypothesis. Our work raises new questions about how spatial distributions of data influence color semantics in colormap data visualizations.
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Factor models are widely used for dimension reduction in the analysis of multivariate data. This is achieved through decomposition of a p x p covariance matrix into the sum of two components. Through a latent factor representation, they can be interpreted as a diagonal matrix of idiosyncratic variances and a shared variation matrix, that is, the product of a p x k factor loadings matrix and its transpose. If k << p, this defines a sparse factorisation of the covariance matrix. Historically, little attention has been paid to incorporating prior information in Bayesian analyses using factor models where, at best, the prior for the factor loadings is order invariant. In this work, a class of structured priors is developed that can encode ideas of dependence structure about the shared variation matrix. The construction allows data-informed shrinkage towards sensible parametric structures while also facilitating inference over the number of factors. Using an unconstrained reparameterisation of stationary vector autoregressions, the methodology is extended to stationary dynamic factor models. For computational inference, parameter-expanded Markov chain Monte Carlo samplers are proposed, including an efficient adaptive Gibbs sampler. Two substantive applications showcase the scope of the methodology and its inferential benefits.
Rational function approximations provide a simple but flexible alternative to polynomial approximation, allowing one to capture complex non-linearities without oscillatory artifacts. However, there have been few attempts to use rational functions on noisy data due to the likelihood of creating spurious singularities. To avoid the creation of singularities, we use Bernstein polynomials and appropriate conditions on their coefficients to force the denominator to be strictly positive. While this reduces the range of rational polynomials that can be expressed, it keeps all the benefits of rational functions while maintaining the robustness of polynomial approximation in noisy data scenarios. Our numerical experiments on noisy data show that existing rational approximation methods continually produce spurious poles inside the approximation domain. This contrasts our method, which cannot create poles in the approximation domain and provides better fits than a polynomial approximation and even penalized splines on functions with multiple variables. Moreover, guaranteeing pole-free in an interval is critical for estimating non-constant coefficients when numerically solving differential equations using spectral methods. This provides a compact representation of the original differential equation, allowing numeric solvers to achieve high accuracy quickly, as seen in our experiments.
In this article, we focus on the error that is committed when computing the matrix logarithm using the Gauss--Legendre quadrature rules. These formulas can be interpreted as Pad\'e approximants of a suitable Gauss hypergeometric function. Empirical observation tells us that the convergence of these quadratures becomes slow when the matrix is not close to the identity matrix, thus suggesting the usage of an inverse scaling and squaring approach for obtaining a matrix with this property. The novelty of this work is the introduction of error estimates that can be used to select a priori both the number of Legendre points needed to obtain a given accuracy and the number of inverse scaling and squaring to be performed. We include some numerical experiments to show the reliability of the estimates introduced.
Covariance matrices of random vectors contain information that is crucial for modelling. Certain structures and patterns of the covariances (or correlations) may be used to justify parametric models, e.g., autoregressive models. Until now, there have been only few approaches for testing such covariance structures systematically and in a unified way. In the present paper, we propose such a unified testing procedure, and we will exemplify the approach with a large variety of covariance structure models. This includes common structures such as diagonal matrices, Toeplitz matrices, and compound symmetry but also the more involved autoregressive matrices. We propose hypothesis tests for these structures, and we use bootstrap techniques for better small-sample approximation. The structures of the proposed tests invite for adaptations to other covariance patterns by choosing the hypothesis matrix appropriately. We prove their correctness for large sample sizes. The proposed methods require only weak assumptions. With the help of a simulation study, we assess the small sample properties of the tests. We also analyze a real data set to illustrate the application of the procedure.
HyperNetX (HNX) is an open source Python library for the analysis and visualization of complex network data modeled as hypergraphs. Initially released in 2019, HNX facilitates exploratory data analysis of complex networks using algebraic topology, combinatorics, and generalized hypergraph and graph theoretical methods on structured data inputs. With its 2023 release, the library supports attaching metadata, numerical and categorical, to nodes (vertices) and hyperedges, as well as to node-hyperedge pairings (incidences). HNX has a customizable Matplotlib-based visualization module as well as HypernetX-Widget, its JavaScript addon for interactive exploration and visualization of hypergraphs within Jupyter Notebooks. Both packages are available on GitHub and PyPI. With a growing community of users and collaborators, HNX has become a preeminent tool for hypergraph analysis.
The proliferation of data generation has spurred advancements in functional data analysis. With the ability to analyze multiple variables simultaneously, the demand for working with multivariate functional data has increased. This study proposes a novel formulation of the epigraph and hypograph indexes, as well as their generalized expressions, specifically tailored for the multivariate functional context. These definitions take into account the interrelations between components. Furthermore, the proposed indexes are employed to cluster multivariate functional data. In the clustering process, the indexes are applied to both the data and their first and second derivatives. This generates a reduced-dimension dataset from the original multivariate functional data, enabling the application of well-established multivariate clustering techniques which have been extensively studied in the literature. This methodology has been tested through simulated and real datasets, performing comparative analyses against state-of-the-art to assess its performance.
We study step-wise time approximations of non-linear hyperbolic initial value problems. The technique used here is a generalization of the minimizing movements method, using two time-scales: one for velocity, the other (potentially much larger) for acceleration. The main applications are from elastodynamics namely so-called generalized solids, undergoing large deformations. The evolution follows an underlying variational structure exploited by step-wise minimisation. We show for a large family of (elastic) energies that the introduced scheme is stable; allowing for non-linearities of highest order. If the highest order can assumed to be linear, we show that the limit solutions are regular and that the minimizing movements scheme converges with optimal linear rate. Thus this work extends numerical time-step minimization methods to the realm of hyperbolic problems.
The Graded of Membership (GoM) model is a powerful tool for inferring latent classes in categorical data, which enables subjects to belong to multiple latent classes. However, its application is limited to categorical data with nonnegative integer responses, making it inappropriate for datasets with continuous or negative responses. To address this limitation, this paper proposes a novel model named the Weighted Grade of Membership (WGoM) model. Compared with GoM, our WGoM relaxes GoM's distribution constraint on the generation of a response matrix and it is more general than GoM. We then propose an algorithm to estimate the latent mixed memberships and the other WGoM parameters. We derive the error bounds of the estimated parameters and show that the algorithm is statistically consistent. The algorithmic performance is validated in both synthetic and real-world datasets. The results demonstrate that our algorithm is accurate and efficient, indicating its high potential for practical applications. This paper makes a valuable contribution to the literature by introducing a novel model that extends the applicability of the GoM model and provides a more flexible framework for analyzing categorical data with weighted responses.
Finding the optimal design of experiments in the Bayesian setting typically requires estimation and optimization of the expected information gain functional. This functional consists of one outer and one inner integral, separated by the logarithm function applied to the inner integral. When the mathematical model of the experiment contains uncertainty about the parameters of interest and nuisance uncertainty, (i.e., uncertainty about parameters that affect the model but are not themselves of interest to the experimenter), two inner integrals must be estimated. Thus, the already considerable computational effort required to determine good approximations of the expected information gain is increased further. The Laplace approximation has been applied successfully in the context of experimental design in various ways, and we propose two novel estimators featuring the Laplace approximation to alleviate the computational burden of both inner integrals considerably. The first estimator applies Laplace's method followed by a Laplace approximation, introducing a bias. The second estimator uses two Laplace approximations as importance sampling measures for Monte Carlo approximations of the inner integrals. Both estimators use Monte Carlo approximation for the remaining outer integral estimation. We provide three numerical examples demonstrating the applicability and effectiveness of our proposed estimators.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
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