arXiv subjects

Tomoyuki Nakagawa

Publications and source records attributed to Tomoyuki Nakagawa.

At least 19 recordsLinked to original sources

arXiv2026

Edgeworth expansions in sphericity testing under high-dimensional two-step monotone incomplete data and their computable error bounds

In this paper, we consider the sphericity test for a one-sample problem under high-dimensional two-step monotone incomplete data. Existing asymptotic expansions for the null distributions of the likelihood ratio test (LRT) statistic and modified LRT statistic deteriorate in high-dimensional settings. Therefore, we derive an Edgeworth expansion for the null distribution of the LRT statistic in such settings and obtain its computable error bounds. Furthermore, we demonstrate that our proposed Edgeworth expansion provide better approximation accuracy than the existing asymptotic expansion. We also conduct numerical experiments using Monte Carlo simulations to evaluate the maximum absolute error between the distribution function of the standardized test statistic and the Edgeworth expansion for the null distribution of the LRT statistic, as well as to assess the performance of the computable error bounds. Finally, by deriving a Cornish-Fisher expansion for the null distribution of the LRT statistic in high-dimensional settings, we evaluate the empirical Type I error rates via Monte Carlo simulations.

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arXiv2026

Semiparametric Copula Estimation for Spatially Correlated Multivariate Mixed Outcomes: Analyzing Visual Sightings of Fin Whales from a Line Transect Survey

For marine biologists, ascertaining the dependence structures between marine species and marine environments, such as sea surface temperature and ocean depth, is imperative for defining ecosystem functioning and providing insights into the dynamics of marine ecosystems. However, obtained data include not only continuous but also discrete data, such as binaries and counts (referred to as mixed outcomes), as well as spatial correlations, both of which make conventional multivariate analysis tools impractical. To solve this issue, we propose semiparametric Bayesian inference and develop an efficient algorithm for computing the posterior of the dependence structure based on the rank likelihood under a latent multivariate spatial Gaussian process using the Markov chain Monte Carlo method. To alleviate the computational intractability caused by the Gaussian process, we also provide a scalable implementation that leverages the nearest-neighbor Gaussian process. Extensive numerical experiments reveal that the proposed method reliably infers the dependence structures of spatially correlated mixed outcomes. Finally, we apply the proposed method to a dataset collected during an international synoptic krill survey in the Scotia Sea of the Antarctic Peninsula to infer the dependence structure between fin whales (Balaenoptera physalus), krill biomass, and relevant oceanographic data.

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arXiv2026

The Covariate-Assisted Bayesian Intransitive Bradley-Terry Model via Combinatorial Hodge Theory

Pairwise comparison data are widely used to recover latent rankings, yet the models in dominant use assume stochastic transitivity. When preferences are in fact intransitive, a single scalar strength conflates genuine hierarchy with cycle-induced structure, biasing both the recovered ranking and any covariate effects attributed to it. To address this limitation, we propose the Covariate-Assisted Bayesian Intransitive Bradley-Terry (CA-BIBT) model, which uses a combinatorial Hodge decomposition to resolve the latent match-up into identifiable and mutually orthogonal flows, attributing the component lying in the covariate-induced subspace to observed covariates and assigning the remaining components to the residuals. A global-local shrinkage prior on the residual cycle-induced flow adapts the model from transitive to intransitive regimes without prespecifying the regime, and a Gibbs sampler yields, as posterior byproducts, calibrated uncertainty for each flow, the posterior probability of the level at which the entities are rankable, and two complementary decision summaries that remain well-defined under intransitivity. In simulations, the CA-BIBT model recovers all flow components accurately with near-nominal coverage, and in applications to two animal dominance datasets, it distinguishes covariate-induced from residual cyclic dominance while quantifying posterior uncertainty, and demonstrates the practical utility of two complementary decision summaries.

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arXiv2026

Convergence fragility in probit Bayesian kernel machine regression implemented in the bkmr R package for binary-outcome environmental mixture analyses: a simulation study

Background. Bayesian kernel machine regression (BKMR) is widely used for exposure-mixture analyses with binary outcomes through a probit extension. Because a bkmr fit can complete without providing adequate effective posterior information, simulation studies should separate execution success from MCMC convergence diagnostics. Methods. We evaluated the public bkmr probit workflow using bkmr::SimData() for data generation, bkmr::kmbayes() for model fitting, and posterior for convergence diagnostics. The balanced generator used family = "binomial", hfun = 2, beta.true = 0.5, ind = 1:2, and M = 4. SimData() generated the covariate as X = 3*cos(z1) + 2*rnorm(n). Four chains were initialized with chain-specific randomized starting values generated reproducibly from the fixed initial-value base seed 20260621. These values affected only the initial state of the sampler and did not alter the BKMR model, default priors, or Metropolis-Hastings proposals. Results. Of 431 prespecified tasks, 430 returned fitted objects and one task had a numerical non-completion. Diagnostic adequacy was limited: rank-normalized R-hat <= 1.01 threshold was achieved in 55/431 tasks, bulk-ESS >= 400 in 85/431, tail-ESS >= 400 in 44/431, and both ESS criteria in 44/431. The primary diagnostic criterion, R-hat at or below the 1.01 threshold with both bulk-ESS and tail-ESS >= 400, was met in 30/431 prespecified tasks, corresponding to 30/430 completed fits. Conclusions. Completion of probit BKMR fits in bkmr should not be equated with convergence of the retained MCMC draws. Applied analyses should report the number of chains, warmup and retained iterations, rank-normalized R-hat, bulk-ESS, and tail-ESS rather than rely on a fixed iteration count or on fit completion alone.

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arXiv2026

Robust estimation via $γ$-divergence for diffusion processes

This paper deals with the problem of outliers in high frequency observation data from diffusion processes. Robust estimation methods are needed because the inclusion of outliers can lead to incorrect statistical inference even in the diffusion process. To construct a robust estimator, we first approximate the transition density of the diffusion process to the Gaussian density by using Kessler's approach and then employ two types of minimum robust divergence estimation methods. In this paper, we provide the asymptotic properties of the robust estimator using $γ$-divergence. Furthermore, we derive the conditional influence functions of the estimation using divergences and discuss its boundness.

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arXiv2025

Divergence-based Robust Generalised Bayesian Inference for Directional Data via von Mises-Fisher models

This paper focusses on robust estimation of location and concentration parameters of the von Mises-Fisher distribution in the Bayesian framework. The von Mises-Fisher (or Langevin) distribution has played a central role in directional statistics. Directional data have been investigated for many decades, and more recently, they have gained increasing attention in diverse areas such as bioinformatics and text data analysis. Although outliers can significantly affect the estimation results even for directional data, the treatment of outliers remains an unresolved and challenging problem. In the frequentist framework, numerous studies have developed robust estimation methods for directional data with outliers, but, in contrast, only a few robust estimation methods have been proposed in the Bayesian framework. In this paper, we propose Bayesian inference based on the density power divergence and the $γ$-divergence and establish their asymptotic properties and robustness. In addition, the Bayesian approach naturally provides a way to assess estimation uncertainty through the posterior distribution, which is particularly useful for small samples. Furthermore, to carry out the posterior computation, we develop the posterior computation algorithm based on the weighted Bayesian bootstrap for estimating parameters. The effectiveness of the proposed methods is demonstrated through simulation studies. Using two real datasets, we further show that the proposed method provides reliable and robust estimation even in the presence of outliers or data contamination.

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arXiv2025

Sampling from density power divergence-based generalized posterior distribution via stochastic optimization

Robust Bayesian inference using density power divergence (DPD) has emerged as a promising approach for handling outliers in statistical estimation. Although the DPD-based posterior offers theoretical guarantees of robustness, its practical implementation faces significant computational challenges, particularly for general parametric models with intractable integral terms. These challenges are specifically pronounced in high-dimensional settings, where traditional numerical integration methods are inadequate and computationally expensive. Herein, we propose a novel {approximate} sampling methodology that addresses these limitations by integrating the loss-likelihood bootstrap with a stochastic gradient descent algorithm specifically designed for DPD-based estimation. Our approach enables efficient and scalable sampling from DPD-based posteriors for a broad class of parametric models, including those with intractable integrals. We further extend it to accommodate generalized linear models. Through comprehensive simulation studies, we demonstrate that our method efficiently samples from DPD-based posteriors, offering superior computational scalability compared to conventional methods, specifically in high-dimensional settings. The results also highlight its ability to handle complex parametric models with intractable integral terms.

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arXiv2025

Robust Spatio-Temporal Distributional Regression

Motivated by investigating spatio-temporal patterns of the distribution of continuous variables, we consider describing the conditional distribution function of the response variable incorporating spatio-temporal components given predictors. In many applications, continuous variables are observed only as threshold-categorized data due to measurement constraints. For instance, ecological measurements often categorize sizes into intervals rather than recording exact values due to practical limitations. To recover the conditional distribution function of the underlying continuous variables, we consider a distribution regression employing models for binomial data obtained at each threshold value. However, depending on spatio-temporal conditions and predictors, the distribution function may frequently exhibit boundary values (zero or one), which can occur either structurally or randomly. This makes standard binomial models inadequate, requiring more flexible modeling approaches. To address this issue, we propose a boundary-inflated binomial model incorporating spatio-temporal components. The model is a three-component mixture of the binomial model and two Dirac measures at zero and one. We develop a computationally efficient Bayesian inference algorithm using Pólya-Gamma data augmentation and dynamic Gaussian predictive processes. Extensive simulation experiments demonstrate that our procedure significantly outperforms distribution regression methods based on standard binomial models across various scenarios.

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arXiv2025

Quasi-symmetry and geometric marginal homogeneity: A simplicial approach to square contingency tables

Square contingency tables are traditionally analyzed with a focus on the symmetric structure of the corresponding probability tables. We view probability tables as elements of a simplex equipped with the Aitchison geometry. This perspective allows us to present a novel approach to analyzing symmetric structure using a compositionally coherent framework. We present a geometric interpretation of quasi-symmetry as an e-flat subspace and introduce a new concept called geometric marginal homogeneity, which is also characterized as an e-flat structure. We prove that both quasi-symmetric tables and geometric marginal homogeneous tables form subspaces in the simplex, and demonstrate that the measure of skew-symmetry in Aitchison geometry can be orthogonally decomposed into measures of departure from quasi-symmetry and geometric marginal homogeneity. We illustrate the application and effectiveness of our proposed methodology using data on unaided distance vision from a sample of women.

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arXiv2025

General Bayesian inference for causal effects using covariate balancing procedure

In observational studies, the propensity score plays a central role in estimating causal effects of interest. The inverse probability weighting (IPW) estimator is commonly used for this purpose. However, if the propensity score model is misspecified, the IPW estimator may produce biased estimates of causal effects. Previous studies have proposed some robust propensity score estimation procedures. However, these methods require considering parameters that dominate the uncertainty of sampling and treatment allocation. This study proposes a novel Bayesian estimating procedure that necessitates probabilistically deciding the parameter, rather than deterministically. Since the IPW estimator and propensity score estimator can be derived as solutions to certain loss functions, the general Bayesian paradigm, which does not require the considering the full likelihood, can be applied. Therefore, our proposed method only requires the same level of assumptions as ordinary causal inference contexts. The proposed Bayesian method demonstrates equal or superior results compared to some previous methods in simulation experimentss, and is also applied to real data, namely the Whitehall dataset.

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arXiv2024

A measure of departure from symmetry via the Fisher-Rao distance for contingency tables

A measure of asymmetry is a quantification method that allows for the comparison of categorical evaluations before and after treatment effects or among different target populations, irrespective of sample size. We focus on square contingency tables that summarize survey results between two time points or cohorts, represented by the same categorical variables. We propose a measure to evaluate the degree of departure from a symmetry model using cosine similarity. This proposal is based on the Fisher-Rao distance, allowing asymmetry to be interpreted as a geodesic distance between two distributions. Various measures of asymmetry have been proposed, but visualizing the relationship of these quantification methods on a two-dimensional plane demonstrates that the proposed measure provides the geometrically simplest and most natural quantification. Moreover, the visualized figure indicates that the proposed method for measuring departures from symmetry is less affected by very few cells with extreme asymmetry. A simulation study shows that for square contingency tables with an underlying asymmetry model, our method can directly extract and quantify only the asymmetric structure of the model, and can more sensitively detect departures from symmetry than divergence-type measures.

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arXiv2024

Nonparametric Bayesian Adjustment of Unmeasured Confounders in Cox Proportional Hazards Models

In observational studies, unmeasured confounders present a crucial challenge in accurately estimating desired causal effects. To calculate the hazard ratio (HR) in Cox proportional hazard models for time-to-event outcomes, two-stage residual inclusion and limited information maximum likelihood are typically employed. However, these methods are known to entail difficulty in terms of potential bias of HR estimates and parameter identification. This study introduces a novel nonparametric Bayesian method designed to estimate an unbiased HR, addressing concerns that previous research methods have had. Our proposed method consists of two phases: 1) detecting clusters based on the likelihood of the exposure and outcome variables, and 2) estimating the hazard ratio within each cluster. Although it is implicitly assumed that unmeasured confounders affect outcomes through cluster effects, our algorithm is well-suited for such data structures. The proposed Bayesian estimator has good performance compared with some competitors.

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arXiv2024

Visualization for departures from symmetry with the power-divergence-type measure in two-way contingency tables

When the row and column variables consist of the same category in a two-way contingency table, it is specifically called a square contingency table. Since it is clear that the square contingency tables have an association structure, a primary objective is to examine symmetric relationships and transitions between variables. While various models and measures have been proposed to analyze these structures understanding changes between two variables in behavior at two-time points or cohorts, it is also necessary to require a detailed investigation of individual categories and their interrelationships, such as shifts in brand preferences. This paper proposes a novel approach to correspondence analysis (CA) for evaluating departures from symmetry in square contingency tables with nominal categories, using a power-divergence-type measure. The approach ensures that well-known divergences can also be visualized and, regardless of the divergence used, the CA plot consists of two principal axes with equal contribution rates. Additionally, the scaling is independent of sample size, making it well-suited for comparing departures from symmetry across multiple contingency tables. Confidence regions are also constructed to enhance the accuracy of the CA plot.

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arXiv2023

Improving the accuracy of estimating indexes in contingency tables using Bayesian estimators

In contingency table analysis, one is interested in testing whether a model of interest (e.g., the independent or symmetry model) holds using goodness-of-fit tests. When the null hypothesis where the model is true is rejected, the interest turns to the degree to which the probability structure of the contingency table deviates from the model. Many indexes have been studied to measure the degree of the departure, such as the Yule coefficient and Cramér coefficient for the independence model, and Tomizawa's symmetry index for the symmetry model. The inference of these indexes is performed using sample proportions, which are estimates of cell probabilities, but it is well-known that the bias and mean square error (MSE) values become large without a sufficient number of samples. To address the problem, this study proposes a new estimator for indexes using Bayesian estimators of cell probabilities. Assuming the Dirichlet distribution for the prior of cell probabilities, we asymptotically evaluate the value of MSE when plugging the posterior means of cell probabilities into the index, and propose an estimator of the index using the Dirichlet hyperparameter that minimizes the value. Numerical experiments show that when the number of samples per cell is small, the proposed method has smaller values of bias and MSE than other methods of correcting estimation accuracy. We also show that the values of bias and MSE are smaller than those obtained by using the uniform and Jeffreys priors.

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arXiv2023

Generalized Cramér's coefficient via $f$-divergence for contingency tables

Various measures in two-way contingency table analysis have been proposed to express the strength of association between row and column variables in contingency tables. Tomizawa et al. (2004) proposed more general measures, including Cramér's coefficient, using the power-divergence. In this paper, we propose measures using the $f$-divergence that has a wider class than the power-divergence. Unlike statistical hypothesis tests, these measures provide quantification of the association structure in contingency tables. The contribution of our study is proving that a measure applying a function that satisfies the condition of the $f$-divergence has desirable properties for measuring the strength of association in contingency tables. With this contribution, we can easily construct a new measure using a divergence that has essential properties for the analyst. For example, we conducted numerical experiments with a measure applying the $θ$-divergence. Furthermore, we can give further interpretation of the association between the row and column variables in the contingency table, which could not be obtained with the conventional one. We also show a relationship between our proposed measures and the correlation coefficient in the bivariate normal distribution of latent variables in the contingency tables.

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arXiv2023

Geometric Mean Type of Proportional Reduction in Variation Measure for Two-Way Contingency Tables

In a two-way contingency table analysis with explanatory and response variables, the analyst is interested in the independence of the two variables. However, if the test of independence does not show independence or clearly shows a relationship, the analyst is interested in the degree of their association. Various measures have been proposed to calculate the degree of their association, one of which is the proportional reduction in variation (PRV) measure which describes the PRV from the marginal distribution to the conditional distribution of the response. The conventional PRV measures can assess the association of the entire contingency table, but they can not accurately assess the association for each explanatory variable. In this paper, we propose a geometric mean type of PRV (geoPRV) measure that aims to sensitively capture the association of each explanatory variable to the response variable by using a geometric mean, and it enables analysis without underestimation when there is partial bias in cells of the contingency table. Furthermore, the geoPRV measure is constructed by using any functions that satisfy specific conditions, which has application advantages and makes it possible to express conventional PRV measures as geometric mean types in special cases.

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arXiv2023

Robustness of Bayesian ordinal response model against outliers via divergence approach

Ordinal response model is a popular and commonly used regression for ordered categorical data in a wide range of fields such as medicine and social sciences. However, it is empirically known that the existence of ``outliers'', combinations of the ordered categorical response and covariates that are heterogeneous compared to other pairs, makes the inference with the ordinal response model unreliable. In this article, we prove that the posterior distribution in the ordinal response model does not satisfy the posterior robustness with any link functions, i.e., the posterior cannot ignore the influence of large outliers. Furthermore, to achieve robust Bayesian inference in the ordinal response model, this article defines general posteriors in the ordinal response model with two robust divergences (the density-power and $γ$-divergences) based on the framework of the general posterior inference. We also provide an algorithm for generating posterior samples from the proposed posteriors. The robustness of the proposed methods against outliers is clarified from the posterior robustness and the index of robustness based on the Fisher-Rao metric. Through numerical experiments on artificial data and two real datasets, we show that the proposed methods perform better than the ordinary bayesian methods with and without outliers in the data for various link functions.

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arXiv2022

Robustness against outliers in ordinal response model via divergence approach

This study deals with the problem of outliers in ordinal response model, which is a regression on ordered categorical data as the response variable. ``Outlier" means that the combination of ordered categorical data and its covariates is heterogeneous compared to other pairs. Although the ordinal response model is important for data analysis in various fields such as medicine and social sciences, it is known that the maximum likelihood method with probit, logit, log-log and complementary log-log link functions, which are often used, is strongly affected by outliers, and statistical analysts are forced to limit their analysis when there may be outliers in the data. To solve this problem, this paper provides inference methods with two robust divergences (the density-power and $γ$-divergences). We also derive influence functions for the proposed methods and show conditions on the link function for them to be bounded and to redescendence. Since the commonly used link functions satisfy these conditions, the analyst can perform robust and flexible analysis with our methods. In addition, and this is a result that further highlights our contributions, we show that the influence function in the maximum likelihood method does not have redescendence for any link function in the ordinal response model. Through numerical experiments using artificial and two real data, we show that the proposed methods perform better than the maximum likelihood method with and without outliers in the data for various link functions.

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