arXiv subjects

David Gunawan

Publications and source records attributed to David Gunawan.

At least 37 records · Page 2Linked to original sources

arXiv2023

Flexible Variational Bayes based on a Copula of a Mixture

Variational Bayes methods approximate the posterior density by a family of tractable distributions whose parameters are estimated by optimisation. Variational approximation is useful when exact inference is intractable or very costly. Our article develops a flexible variational approximation based on a copula of a mixture, which is implemented by combining boosting, natural gradient, and a variance reduction method. The efficacy of the approach is illustrated by using simulated and real datasets to approximate multimodal, skewed and heavy-tailed posterior distributions, including an application to Bayesian deep feedforward neural network regression models.

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arXiv2023

The Correlated Particle Hybrid Sampler for State Space Models

Particle Markov Chain Monte Carlo (PMCMC) is a general computational approach to Bayesian inference for general state space models. Our article scales up PMCMC in terms of the number of observations and parameters by generating the parameters that are highly correlated with the states \lq integrated out\rq{} in a pseudo marginal step; the rest of the parameters are generated conditional on the states. The novel contribution of our article is to make the pseudo-marginal step much more efficient by positively correlating the numerator and denominator in the Metropolis-Hastings acceptance probability. This is done in a novel way by expressing the target density of the PMCMC in terms of the basic uniform or normal random numbers used in the sequential Monte Carlo algorithm instead of the standard way in terms of state particles. We also show that the new sampler combines and generalizes two separate particle MCMC approaches: particle Gibbs and the correlated pseudo marginal Metropolis-Hastings. We investigate the performance of the hybrid sampler empirically by applying it to univariate and multivariate stochastic volatility models having both a large number of parameters and a large number of latent states and show that it is much more efficient than competing PMCMC methods.

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arXiv2023

Bayesian Inference for Evidence Accumulation Models with Regressors

Evidence accumulation models (EAMs) are an important class of cognitive models used to analyze both response time and response choice data recorded from decision-making tasks. Developments in estimation procedures have helped EAMs become important both in basic scientific applications and solution-focussed applied work. Hierarchical Bayesian estimation frameworks for the linear ballistic accumulator model (LBA) and the diffusion decision model (DDM) have been widely used, but still suffer from some key limitations, particularly for large sample sizes, for models with many parameters, and when linking decision-relevant covariates to model parameters. We extend upon previous work with methods for estimating the LBA and DDM in hierarchical Bayesian frameworks that include random effects which are correlated between people, and include regression-model links between decision-relevant covariates and model parameters. Our methods work equally well in cases where the covariates are measured once per person (e.g., personality traits or psychological tests) or once per decision (e.g., neural or physiological data). We provide methods for exact Bayesian inference, using particle-based MCMC, and also approximate methods based on variational Bayesian (VB) inference. The VB methods are sufficiently fast and efficient that they can address large-scale estimation problems, such as with very large data sets. We evaluate the performance of these methods in applications to data from three existing experiments. Detailed algorithmic implementations and code are freely available for all methods.

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arXiv2023

The Block-Correlated Pseudo Marginal Sampler for State Space Models

Particle Marginal Metropolis-Hastings (PMMH) is a general approach to Bayesian inference when the likelihood is intractable, but can be estimated unbiasedly. Our article develops an efficient PMMH method that scales up better to higher dimensional state vectors than previous approaches. The improvement is achieved by the following innovations. First, the trimmed mean of the unbiased likelihood estimates of the multiple particle filters is used. Second, a novel block version of PMMH that works with multiple particle filters is proposed. Third, the article develops an efficient auxiliary disturbance particle filter, which is necessary when the bootstrap disturbance filter is inefficient, but the state transition density cannot be expressed in closed form. Fourth, a novel sorting algorithm, which is as effective as previous approaches but significantly faster than them, is developed to preserve the correlation between the logs of the likelihood estimates at the current and proposed parameter values. The performance of the sampler is investigated empirically by applying it to non-linear Dynamic Stochastic General Equilibrium models with relatively high state dimensions and with intractable state transition densities and to multivariate stochastic volatility in the mean models. Although our focus is on applying the method to state space models, the approach will be useful in a wide range of applications such as large panel data models and stochastic differential equation models with mixed effects.

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arXiv2023

Reliable Bayesian Inference in Misspecified Models

We provide a general solution to a fundamental open problem in Bayesian inference, namely poor uncertainty quantification, from a frequency standpoint, of Bayesian methods in misspecified models. While existing solutions are based on explicit Gaussian approximations of the posterior, or computationally onerous post-processing procedures, we demonstrate that correct uncertainty quantification can be achieved by replacing the usual posterior with an intuitive approximate posterior. Critically, our solution is applicable to likelihood-based, and generalized, posteriors as well as cases where the likelihood is intractable and must be estimated. We formally demonstrate the reliable uncertainty quantification of our proposed approach, and show that valid uncertainty quantification is not an asymptotic result but occurs even in small samples. We illustrate this approach through a range of examples, including linear, and generalized, mixed effects models.

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arXiv2022

Robust Particle Density Tempering for State Space Models

Density tempering (also called density annealing) is a sequential Monte Carlo approach to Bayesian inference for general state models; it is an alternative to Markov chain Monte Carlo. When applied to state space models, it moves a collection of parameters and latent states (which are called particles) through a number of stages, with each stage having its own target distribution. The particles are initially generated from a distribution that is easy to sample from, e.g. the prior; the target at the final stage is the posterior distribution. Tempering is usually carried out either in batch mode, involving all the data at each stage, or sequentially with observations added at each stage, which is called data tempering. Our paper proposes efficient Markov moves for generating the parameters and states for each stage of particle based density tempering. This allows the proposed SMC methods to increase (scale up) the number of parameters and states that can be handled. Most of the current literature uses a pseudo-marginal Markov move step with the states integrated out, and the parameters generated by a random walk proposal; although this strategy is general, it is very inefficient when the states or parameters are high dimensional. We also build on the work of Dufays (2016) and make data tempering more robust to outliers and structural changes for models with intractable likelihoods by adding batch tempering at each stage. The performance of the proposed methods is evaluated using univariate stochastic volatility models with outliers and structural breaks and high dimensional factor stochastic volatility models having both many parameters and many latent states.

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arXiv2022

A Statistical Recurrent Stochastic Volatility Model for Stock Markets

The Stochastic Volatility (SV) model and its variants are widely used in the financial sector while recurrent neural network (RNN) models are successfully used in many large-scale industrial applications of Deep Learning. Our article combines these two methods in a non-trivial way and proposes a model, which we call the Statistical Recurrent Stochastic Volatility (SR-SV) model, to capture the dynamics of stochastic volatility. The proposed model is able to capture complex volatility effects (e.g., non-linearity and long-memory auto-dependence) overlooked by the conventional SV models, is statistically interpretable and has an impressive out-of-sample forecast performance. These properties are carefully discussed and illustrated through extensive simulation studies and applications to five international stock index datasets: The German stock index DAX30, the Hong Kong stock index HSI50, the France market index CAC40, the US stock market index SP500 and the Canada market index TSX250. An user-friendly software package together with the examples reported in the paper are available at \url{https://github.com/vbayeslab}.

econ.EM↗

arXiv2021

Time-evolving psychological processes over repeated decisions

Many psychological experiments have subjects repeat a task to gain the statistical precision required to test quantitative theories of psychological performance. In such experiments, time-on-task can have sizable effects on performance, changing the psychological processes under investigation. Most research has either ignored these changes, treating the underlying process as static, or sacrificed some psychological content of the models for statistical simplicity. We use particle Markov chain Monte-Carlo methods to study psychologically plausible time-varying changes in model parameters. Using data from three highly-cited experiments we find strong evidence in favor of a hidden Markov switching process as an explanation of time-varying effects. This embodies the psychological assumption of "regime switching", with subjects alternating between different cognitive states representing different modes of decision-making. The switching model explains key long- and short-term dynamic effects in the data. The central idea of our approach can be applied quite generally to quantitative psychological theories, beyond the models and data sets that we investigate.

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arXiv2021

Efficient Selection Between Hierarchical Cognitive Models: Cross-validation With Variational Bayes

Model comparison is the cornerstone of theoretical progress in psychological research. Common practice overwhelmingly relies on tools that evaluate competing models by balancing in-sample descriptive adequacy against model flexibility, with modern approaches advocating the use of marginal likelihood for hierarchical cognitive models. Cross-validation is another popular approach but its implementation has remained out of reach for cognitive models evaluated in a Bayesian hierarchical framework, with the major hurdle being prohibitive computational cost. To address this issue, we develop novel algorithms that make variational Bayes (VB) inference for hierarchical models feasible and computationally efficient for complex cognitive models of substantive theoretical interest. It is well known that VB produces good estimates of the first moments of the parameters which gives good predictive densities estimates. We thus develop a novel VB algorithm with Bayesian prediction as a tool to perform model comparison by cross-validation, which we refer to as CVVB. In particular, the CVVB can be used as a model screening device that quickly identifies bad models. We demonstrate the utility of CVVB by revisiting a classic question in decision making research: what latent components of processing drive the ubiquitous speed-accuracy tradeoff? We demonstrate that CVVB strongly agrees with model comparison via marginal likelihood yet achieves the outcome in much less time. Our approach brings cross-validation within reach of theoretically important psychological models, and makes it feasible to compare much larger families of hierarchically specified cognitive models than has previously been possible.

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arXiv2021

Inequality in Education: A Comparison of Australian Indigenous and Nonindigenous Populations

Educational achievement distributions for Australian indigenous and nonindigenous populations in the years 2001, 2006, 2014 and 2017 are considered. Bayesian inference is used to analyse how these ordinal categorical distributions have changed over time and to compare indigenous and nonindigenous distributions. Both the level of educational achievement and inequality in educational achievement are considered. To compare changes in levels over time, as well as inequality between the two populations, first order stochastic dominance and an index of educational poverty are used. To examine changes in inequality over time, two inequality indices and generalised Lorenz dominance are considered. Results are presented in terms of posterior densities for the indices and posterior probabilities for dominance for the dominance comparisons. We find some evidence of improvement over time, especially in the lower parts of the indigenous distribution and that inequality has significantly increased from 2001 to 2017.

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arXiv2021

Posterior Probabilities for Lorenz and Stochastic Dominance of Australian Income Distributions

Using HILDA data for the years 2001, 2006, 2010, 2014 and 2017, we compute posterior probabilities for dominance for all pairwise comparisons of income distributions in these years. The dominance criteria considered are Lorenz dominance and first and second order stochastic dominance. The income distributions are estimated using an infinite mixture of gamma density functions, with posterior probabilities computed as the proportion of Markov chain Monte Carlo draws that satisfy the inequalities that define the dominance criteria. We find welfare improvements from 2001 to 2006 and qualified improvements from 2006 to the later three years. Evidence of an ordering between 2010, 2014 and 2017 cannot be established.

econ.EM↗

arXiv2021

Comparisons of Australian Mental Health Distributions

Bayesian nonparametric estimates of Australian mental health distributions are obtained to assess how the mental health status of the population has changed over time and to compare the mental health status of female/male and indigenous/non-indigenous population subgroups. First- and second-order stochastic dominance are used to compare distributions, with results presented in terms of the posterior probability of dominance and the posterior probability of no dominance. Our results suggest mental health has deteriorated in recent years, that males mental health status is better than that of females, and non-indigenous health status is better than that of the indigenous population.

econ.EM↗

arXiv2021

Variational Approximation of Factor Stochastic Volatility Models

Estimation and prediction in high dimensional multivariate factor stochastic volatility models is an important and active research area because such models allow a parsimonious representation of multivariate stochastic volatility. Bayesian inference for factor stochastic volatility models is usually done by Markov chain Monte Carlo methods, often by particle Markov chain Monte Carlo, which are usually slow for high dimensional or long time series because of the large number of parameters and latent states involved. Our article makes two contributions. The first is to propose fast and accurate variational Bayes methods to approximate the posterior distribution of the states and parameters in factor stochastic volatility models. The second contribution is to extend this batch methodology to develop fast sequential variational updates for prediction as new observations arrive. The methods are applied to simulated and real datasets and shown to produce good approximate inference and prediction compared to the latest particle Markov chain Monte Carlo approaches, but are much faster.

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arXiv2020

The Interaction Between Credit Constraints and Uncertainty Shocks

Can uncertainty about credit availability trigger a slowdown in real activity? This question is answered by using a novel method to identify shocks to uncertainty in access to credit. Time-variation in uncertainty about credit availability is estimated using particle Markov Chain Monte Carlo. We extract shocks to time-varying credit uncertainty and decompose it into two parts: the first captures the "pure" effect of a shock to the second moment; the second captures total effects of uncertainty including effects on the first moment. Using state-dependent local projections, we find that the "pure" effect by itself generates a sharp slowdown in real activity and the effects are largely countercyclical. We feed the estimated shocks into a flexible price real business cycle model with a collateral constraint and show that when the collateral constraint binds, an uncertainty shock about credit access is recessionary leading to a simultaneous decline in consumption, investment, and output.

econ.EM↗

arXiv2020

Identifying relationships between cognitive processes across tasks, contexts, and time

It is commonly assumed that a specific testing occasion (task, design, procedure, etc.) provides insights that generalise beyond that occasion. This assumption is infrequently carefully tested in data. We develop a statistically principled method to directly estimate the correlation between latent components of cognitive processing across tasks, contexts, and time. This method simultaneously estimates individual-participant parameters of a cognitive model at each testing occasion, group-level parameters representing across-participant parameter averages and variances, and across-task correlations. The approach provides a natural way to "borrow" strength across testing occasions, which can increase the precision of parameter estimates across all testing occasions. Two example applications demonstrate that the method is practical in standard designs. The examples, and a simulation study, also provide evidence about the reliability and validity of parameter estimates from the linear ballistic accumulator model. We conclude by highlighting the potential of the parameter-correlation method to provide an "assumption-light" tool for estimating the relatedness of cognitive processes across tasks, contexts, and time.

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arXiv2020

Subsampling Sequential Monte Carlo for Static Bayesian Models

We show how to speed up Sequential Monte Carlo (SMC) for Bayesian inference in large data problems by data subsampling. SMC sequentially updates a cloud of particles through a sequence of distributions, beginning with a distribution that is easy to sample from such as the prior and ending with the posterior distribution. Each update of the particle cloud consists of three steps: reweighting, resampling, and moving. In the move step, each particle is moved using a Markov kernel; this is typically the most computationally expensive part, particularly when the dataset is large. It is crucial to have an efficient move step to ensure particle diversity. Our article makes two important contributions. First, in order to speed up the SMC computation, we use an approximately unbiased and efficient annealed likelihood estimator based on data subsampling. The subsampling approach is more memory efficient than the corresponding full data SMC, which is an advantage for parallel computation. Second, we use a Metropolis within Gibbs kernel with two conditional updates. A Hamiltonian Monte Carlo update makes distant moves for the model parameters, and a block pseudo-marginal proposal is used for the particles corresponding to the auxiliary variables for the data subsampling. We demonstrate both the usefulness and limitations of the methodology for estimating four generalized linear models and a generalized additive model with large datasets.

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arXiv2020

New Estimation Approaches for the Hierarchical Linear Ballistic Accumulator Model

The Linear Ballistic Accumulator (Brown & Heathcote, 2008) model is used as a measurement tool to answer questions about applied psychology. The analyses based on this model depend upon the model selected and its estimated parameters. Modern approaches use hierarchical Bayesian models and Markov chain Monte-Carlo (MCMC) methods to estimate the posterior distribution of the parameters. Although there are several approaches available for model selection, they are all based on the posterior samples produced via MCMC, which means that the model selection inference inherits the properties of the MCMC sampler. To improve on current approaches to LBA inference we propose two methods that are based on recent advances in particle MCMC methodology; they are qualitatively different from existing approaches as well as from each other. The first approach is particle Metropolis-within-Gibbs; the second approach is density tempered sequential Monte Carlo. Both new approaches provide very efficient sampling and can be applied to estimate the marginal likelihood, which provides Bayes factors for model selection. The first approach is usually faster. The second approach provides a direct estimate of the marginal likelihood, uses the first approach in its Markov move step and is very efficient to parallelize on high performance computers. The new methods are illustrated by applying them to simulated and real data, and through pseudo code. The code implementing the methods is freely available.

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arXiv2019

Robustly estimating the marginal likelihood for cognitive models via importance sampling

Recent advances in Markov chain Monte Carlo (MCMC) extend the scope of Bayesian inference to models for which the likelihood function is intractable. Although these developments allow us to estimate model parameters, other basic problems such as estimating the marginal likelihood, a fundamental tool in Bayesian model selection, remain challenging. This is an important scientific limitation because testing psychological hypotheses with hierarchical models has proven difficult with current model selection methods. We propose an efficient method for estimating the marginal likelihood for models where the likelihood is intractable, but can be estimated unbiasedly. It is based on first running a sampling method such as MCMC to obtain samples for the model parameters, and then using these samples to construct the proposal density in an importance sampling (IS) framework with an unbiased estimate of the likelihood. Our method has several attractive properties: it generates an unbiased estimate of the marginal likelihood, it is robust to the quality and target of the sampling method used to form the IS proposals, and it is computationally cheap to estimate the variance of the marginal likelihood estimator. We also obtain the convergence properties of the method and provide guidelines on maximizing computational efficiency. The method is illustrated in two challenging cases involving hierarchical models: identifying the form of individual differences in an applied choice scenario, and evaluating the best parameterization of a cognitive model in a speeded decision making context. Freely available code to implement the methods is provided. Extensions to posterior moment estimation and parallelization are also discussed.

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