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Methodology (stat.ME)

Wed, 30 Aug 2023

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1.Semiparametric inference of effective reproduction number dynamics from wastewater pathogen surveillance data

Authors:Isaac H. Goldstein, Daniel M. Parker, Sunny Jiang, Volodymyr M. Minin

Abstract: Concentrations of pathogen genomes measured in wastewater have recently become available as a new data source to use when modeling the spread of infectious diseases. One promising use for this data source is inference of the effective reproduction number, the average number of individuals a newly infected person will infect. We propose a model where new infections arrive according to a time-varying immigration rate which can be interpreted as a compound parameter equal to the product of the proportion of susceptibles in the population and the transmission rate. This model allows us to estimate the effective reproduction number from concentrations of pathogen genomes while avoiding difficult to verify assumptions about the dynamics of the susceptible population. As a byproduct of our primary goal, we also produce a new model for estimating the effective reproduction number from case data using the same framework. We test this modeling framework in an agent-based simulation study with a realistic data generating mechanism which accounts for the time-varying dynamics of pathogen shedding. Finally, we apply our new model to estimating the effective reproduction number of SARS-CoV-2 in Los Angeles, California, using pathogen RNA concentrations collected from a large wastewater treatment facility.

2.Sequential Bayesian Predictive Synthesis

Authors:Riku Masuda, Kaoru Irie

Abstract: Dynamic Bayesian predictive synthesis is a formal approach to coherently synthesizing multiple predictive distributions into a single distribution. In sequential analysis, the computation of the synthesized predictive distribution has heavily relied on the repeated use of the Markov chain Monte Carlo method. The sequential Monte Carlo method in this problem has also been studied but is limited to a subclass of linear synthesis with weight constraint but no intercept. In this study, we provide a custom, Rao-Blackwellized particle filter for the linear and Gaussian synthesis, supplemented by timely interventions by the MCMC method to avoid the problem of particle degeneracy. In an example of predicting US inflation rate, where a sudden burst is observed in 2020-2022, we confirm the slow adaptation of the predictive distribution. To overcome this problem, we propose the estimation/averaging of parameters called discount factors based on the power-discounted likelihoods, which becomes feasible due to the fast computation by the proposed method.

3.Sensitivity Analysis for Causal Effects in Observational Studies with Multivalued Treatments

Authors:Md Abdul Basit, Mahbub A. H. M. Latif, Abdus S Wahed

Abstract: One of the fundamental challenges in drawing causal inferences from observational studies is that the assumption of no unmeasured confounding is not testable from observed data. Therefore, assessing sensitivity to this assumption's violation is important to obtain valid causal conclusions in observational studies. Although several sensitivity analysis frameworks are available in the casual inference literature, none of them are applicable to observational studies with multivalued treatments. To address this issue, we propose a sensitivity analysis framework for performing sensitivity analysis in multivalued treatment settings. Within this framework, a general class of additive causal estimands has been proposed. We demonstrate that the estimation of the causal estimands under the proposed sensitivity model can be performed very efficiently. Simulation results show that the proposed framework performs well in terms of bias of the point estimates and coverage of the confidence intervals when there is sufficient overlap in the covariate distributions. We illustrate the application of our proposed method by conducting an observational study that estimates the causal effect of fish consumption on blood mercury levels.

4.A Classification of Observation-Driven State-Space Count Models for Panel Data

Authors:Jae Youn Ahn, Himchan Jeong, Yang Lu, Mario V. Wüthrich

Abstract: State-space models are widely used in many applications. In the domain of count data, one such example is the model proposed by Harvey and Fernandes (1989). Unlike many of its parameter-driven alternatives, this model is observation-driven, leading to closed-form expressions for the predictive density. In this paper, we demonstrate the need to extend the model of Harvey and Fernandes (1989) by showing that their model is not variance stationary. Our extension can accommodate for a wide range of variance processes that are either increasing, decreasing, or stationary, while keeping the tractability of the original model. Simulation and numerical studies are included to illustrate the performance of our method.

5.Likelihood-based inference and forecasting for trawl processes: a stochastic optimization approach

Authors:Dan Leonte, Almut E. D. Veraart

Abstract: We consider trawl processes, which are stationary and infinitely divisible stochastic processes and can describe a wide range of statistical properties, such as heavy tails and long memory. In this paper, we develop the first likelihood-based methodology for the inference of real-valued trawl processes and introduce novel deterministic and probabilistic forecasting methods. Being non-Markovian, with a highly intractable likelihood function, trawl processes require the use of composite likelihood functions to parsimoniously capture their statistical properties. We formulate the composite likelihood estimation as a stochastic optimization problem for which it is feasible to implement iterative gradient descent methods. We derive novel gradient estimators with variances that are reduced by several orders of magnitude. We analyze both the theoretical properties and practical implementation details of these estimators and release a Python library which can be used to fit a large class of trawl processes. In a simulation study, we demonstrate that our estimators outperform the generalized method of moments estimators in terms of both parameter estimation error and out-of-sample forecasting error. Finally, we formalize a stochastic chain rule for our gradient estimators. We apply the new theory to trawl processes and provide a unified likelihood-based methodology for the inference of both real-valued and integer-valued trawl processes.

6.Temporal-spatial model via Trend Filtering

Authors:Carlos Misael Madrid Padilla, Oscar Hernan Madrid Padilla, Daren Wang

Abstract: This research focuses on the estimation of a non-parametric regression function designed for data with simultaneous time and space dependencies. In such a context, we study the Trend Filtering, a nonparametric estimator introduced by \cite{mammen1997locally} and \cite{rudin1992nonlinear}. For univariate settings, the signals we consider are assumed to have a kth weak derivative with bounded total variation, allowing for a general degree of smoothness. In the multivariate scenario, we study a $K$-Nearest Neighbor fused lasso estimator as in \cite{padilla2018adaptive}, employing an ADMM algorithm, suitable for signals with bounded variation that adhere to a piecewise Lipschitz continuity criterion. By aligning with lower bounds, the minimax optimality of our estimators is validated. A unique phase transition phenomenon, previously uncharted in Trend Filtering studies, emerges through our analysis. Both Simulation studies and real data applications underscore the superior performance of our method when compared with established techniques in the existing literature.