arXiv subjects

Edward L. Ionides

Publications and source records attributed to Edward L. Ionides.

At least 19 recordsLinked to original sources

arXiv2026

Exact phylodynamic likelihood via structured Markov genealogy processes

We show that each member of a broad class of Markovian population models induces a unique stochastic process on the space of genealogies. We construct this genealogy process and derive exact expressions for the likelihood of an observed genealogy in terms of a filter equation, the structure of which is completely determined by the population model. We show that existing phylodynamic methods based on the coalescent and linear birth-death processes are special cases. We derive some properties of filter equations and describe a class of algorithms that can be used to numerically solve them. Importantly, because these algorithms rely only on simulation of the population model, they retain the plug-and-play property upon which simulation-based inference depends. Our results open the door to statistically efficient likelihood-based phylodynamic inference for a much wider class of models than has been possible.

q-bio.QM↗

arXiv2026

Jagged AI in Scientific Peer Review: Evidence from POMP Data Analysis

Despite their growing use in academic writing and statistical analysis, the performance of artificial intelligence (AI) tools in scientific peer review remains a largely unexplored area. A key challenge is jagged AI, a phenomenon where AI exhibits strong ability spikes in some domains while remaining deficient in others. To study this jaggedness in a practical data science context, we considered the task of reviewing partially observed Markov process (POMP) data analyses. POMP models, also known as state-space models or hidden Markov models, are used to fit mechanistic dynamic models to time series data in diverse applications including disease transmission, ecological dynamics, and financial risk assessment. High-quality peer review in this area entails assessment of scientific context, identification of errors in implementing complex algorithms, and decisions concerning methodological best practices. We studied 72 POMP projects from four semesters of a University of Michigan graduate time series course for which the project reports, the source code, and student peer reviews are anonymized and open-access. We compared the human reviews with four AI reviewing agents, using Claude Code with differing instructions implemented as skill files. We found that AI reviewers exhibited a jagged capability profile, proficiently catching human-overlooked technical errors and invalid inference methodology, while failing to match human standards in checking interpretive errors, narrative coherence, and domain-informed model critique. The jaggedness was found to be similar for all agents, consistent with it being primarily a property of the underlying AI model rather than the specific instructions. Skill file configuration shifted which weaknesses agents emphasized, without removing the jaggedness.

stat.AP↗

arXiv2025

Iterating marginalized Bayes maps for likelihood maximization with application to nonlinear panel models

Complex dynamic systems can be investigated by fitting mechanistic stochastic dynamic models to time series data. In this context, commonly used Monte Carlo inference procedures for model selection and parameter estimation quickly become computationally unfeasible as the system dimension grows. The increasing prevalence of panel data, characterized by multiple related time series, therefore necessitates the development of inference algorithms that are effective for this class of high-dimensional mechanistic models. Nonlinear, non-Gaussian mechanistic models are routinely fitted to time series data but seldom to panel data, despite its widespread availability, suggesting that the practical difficulties for existing procedures are prohibitive. We investigate the use of iterated filtering algorithms for this purpose. We introduce a novel algorithm that contains a marginalization step that mitigates issues arising from particle filtering in high dimensions. Our approach enables likelihood-based inference for models that were previously considered intractable, thus broadening the scope of dynamic models available for panel data analysis.

stat.ME↗

arXiv2025

Revisiting Inference for ARMA Models: Improved Fits and Superior Confidence Intervals

Autoregressive moving average (ARMA) models are widely used for analyzing time series data. However, standard likelihood-based inference methodology for ARMA models has avoidable limitations. We show that currently accepted standards for ARMA likelihood maximization frequently lead to sub-optimal parameter estimates. Existing algorithms have theoretical support, but can result in parameter estimates that correspond to a local optimum. While this possibility has been previously identified, it remains unknown to most users, and no routinely applicable algorithm has been developed to resolve the issue. We introduce a novel random initialization algorithm, designed to take advantage of the structure of the ARMA likelihood function, which overcomes these optimization problems. Additionally, we show that profile likelihoods provide superior confidence intervals to those based on the Fisher information matrix. The efficacy of the proposed methodology is demonstrated through a data analysis example and a series of simulation studies. This work makes a significant contribution to statistical practice by identifying and resolving under-recognized shortcomings of existing procedures that frequently arise in scientific and industrial applications.

stat.ME↗

arXiv2025

Poisson Approximate Likelihood versus the block particle filter for a spatiotemporal measles model

Filtering algorithms for high-dimensional nonlinear non-Gaussian partially observed stochastic processes provide access to the likelihood function and hence enable likelihood-based or Bayesian inference for this methodologically challenging class of models. A novel Poisson approximate likelihood (PAL) filter was introduced by Whitehouse et al.\ (2023). PAL employs a Poisson approximation to conditional densities, offering a fast approximation to the likelihood function for a certain subset of partially observed Markov process models. PAL was demonstrated on an epidemiological metapopulation model for measles, specifically, a spatiotemporal model for disease transmission within and between cities. At face value, Table\ 3 of Whitehouse et al.\ (2023) suggests that PAL considerably out-performs previous analysis as well as an ARMA benchmark model. We show that PAL does not outperform a block particle filter and that the lookahead component of PAL was implemented in a way that introduces substantial positive bias in the log-likelihood estimates. Therefore, the results of Table\ 3 of Whitehouse et al.\ (2023) do not accurately represent the true capabilities of PAL.

stat.ME↗

arXiv2025

Income, health, and spurious cointegration

Data for many nations show a long-run increase, over many decades, of income, indexed by GDP per capita, and population health, indexed by mortality or life expectancy at birth (LEB). However, the short-run and long-run relationships between these variables have been interpreted in different ways, and many controversies remain open. It has been claimed that population health and income are cointegrated, and that this demonstrates a positive long-run effect of income on population health. We show, however, that an empirically tested cointegration between LEB and GDP per capita is not a sound method to infer a causal link. For a given country it is easy to find computer-generated data or time series of real observations, related or unrelated to the country, that according to standard methods, are also cointegrated with the country's LEB. More generally, given a trending time series, it is easy to find other series, observational or artificial, that appear cointegrated with it. Thus, standard cointegration methodology, often used in empirical investigations, cannot distinguish whether cointegration relationships are spurious or causal.

econ.GN↗

arXiv2025

Mechanistic models for panel data: Analysis of ecological experiments with four interacting species

In an ecological context, panel data arise when time series measurements are made on a collection of ecological processes. Each process may correspond to a spatial location for field data, or to an experimental ecosystem in a designed experiment. Statistical models for ecological panel data should capture the high levels of nonlinearity, stochasticity, and measurement uncertainty inherent in ecological systems. Furthermore, the system dynamics may depend on unobservable variables. This study applies iterated particle filtering techniques to explore new possibilities for likelihood-based statistical analysis of these complex systems. We analyze data from a mesocosm experiment in which two species of the freshwater planktonic crustacean genus, Daphnia, coexist with an alga and a fungal parasite. Time series data were collected on replicated mesocosms under six treatment conditions. Iterated filtering enables maximization of the likelihood for scientifically motivated nonlinear partially observed Markov process models, providing access to standard likelihood-based methods for parameter estimation, confidence intervals, hypothesis testing, model selection and diagnostics. This toolbox allows scientists to propose and evaluate scientifically motivated stochastic dynamic models for panel data, constrained only by the requirement to write code to simulate from the model and to specify a measurement distribution describing how the system state is observed.

stat.AP↗

arXiv2025

panelPomp: Analysis of Panel Data via Partially Observed Markov Processes in R

Panel data arise when time series measurements are collected from multiple, dynamically independent but structurally related systems. Each system's time series can be modeled as a partially observed Markov process (POMP), and the ensemble of these models is called a PanelPOMP. If the time series are relatively short, statistical inference for each time series must draw information from across the entire panel. The component systems in the panel are called units; model parameters may be shared between units or may be unit-specific. Differences between units may be of direct inferential interest or may be a nuisance for studying the commonalities. The R package panelPomp supports analysis of panel data via a general class of PanelPOMP models. This includes a suite of tools for manipulation of models and data that take advantage of the panel structure. The panelPomp package currently highlights recent advances enabling likelihood based inference via simulation based algorithms. However, the general framework provided by panelPomp supports development of additional, new inference methodology for panel data.

stat.ME↗

arXiv2024

Poisson approximate likelihood compared to the particle filter

Filtering algorithms are fundamental for inference on partially observed stochastic dynamic systems, since they provide access to the likelihood function and hence enable likelihood-based or Bayesian inference. A novel Poisson approximate likelihood (PAL) filter was introduced by Whitehouse et al. (2023). PAL employs a Poisson approximation to conditional densities, offering a fast approximation to the likelihood function for a certain subset of partially observed Markov process models. A central piece of evidence for PAL is the comparison in Table 1 of Whitehouse et al. (2023), which claims a large improvement for PAL over a standard particle filter algorithm. This evidence, based on a model and data from a previous scientific study by Stocks et al. (2020), might suggest that researchers confronted with similar models should use PAL rather than particle filter methods. Taken at face value, this evidence also reduces the credibility of Stocks et al. (2020) by indicating a shortcoming with the numerical methods that they used. However, we show that the comparison of log-likelihood values made by Whitehouse et al. (2023) is flawed because their PAL calculations were carried out using a dataset scaled differently from the previous study. If PAL and the particle filter are applied to the same data, the advantage claimed for PAL disappears. On simulations where the model is correctly specified, the particle filter outperforms PAL.

stat.ME↗

arXiv2024

A tutorial on panel data analysis using partially observed Markov processes via the R package panelPomp

The R package panelPomp supports analysis of panel data via a general class of partially observed Markov process models (PanelPOMP). This package tutorial describes how the mathematical concept of a PanelPOMP is represented in the software and demonstrates typical use-cases of panelPomp. Monte Carlo methods used for POMP models require adaptation for PanelPOMP models due to the higher dimensionality of panel data. The package takes advantage of recent advances for PanelPOMP, including an iterated filtering algorithm, Monte Carlo adjusted profile methodology and block optimization methodology to assist with the large parameter spaces that can arise with panel models. In addition, tools for manipulation of models and data are provided that take advantage of the panel structure.

stat.CO↗

arXiv2024

Accelerated Inference for Partially Observed Markov Processes using Automatic Differentiation

Automatic differentiation (AD) has driven recent advances in machine learning, including deep neural networks and Hamiltonian Markov Chain Monte Carlo methods. Partially observed nonlinear stochastic dynamical systems have proved resistant to AD techniques because widely used particle filter algorithms yield an estimated likelihood function that is discontinuous as a function of the model parameters. We show how to embed two existing AD particle filter methods in a theoretical framework that provides an extension to a new class of algorithms. This new class permits a bias/variance tradeoff and hence a mean squared error substantially lower than the existing algorithms. We develop likelihood maximization algorithms suited to the Monte Carlo properties of the AD gradient estimate. Our algorithms require only a differentiable simulator for the latent dynamic system; by contrast, most previous approaches to AD likelihood maximization for particle filters require access to the system's transition probabilities. Numerical results indicate that a hybrid algorithm that uses AD to refine a coarse solution from an iterated filtering algorithm show substantial improvement on current state-of-the-art methods for a challenging scientific benchmark problem.

stat.ME↗

arXiv2024

A tutorial on spatiotemporal partially observed Markov process models via the R package spatPomp

We describe a computational framework for modeling and statistical inference on high-dimensional stochastic dynamic systems. Our primary motivation is the investigation of metapopulation dynamics arising from a collection of spatially distributed, interacting biological populations. To make progress on this goal, we embed it in a more general problem: inference for a collection of interacting partially observed nonlinear non-Gaussian stochastic processes. Each process in the collection is called a unit; in the case of spatiotemporal models, the units correspond to distinct spatial locations. The dynamic state for each unit may be discrete or continuous, scalar or vector valued. In metapopulation applications, the state can represent a structured population or the abundances of a collection of species at a single location. We consider models where the collection of states has a Markov property. A sequence of noisy measurements is made on each unit, resulting in a collection of time series. A model of this form is called a spatiotemporal partially observed Markov process (SpatPOMP). The R package spatPomp provides an environment for implementing SpatPOMP models, analyzing data using existing methods, and developing new inference approaches. Our presentation of spatPomp reviews various methodologies in a unifying notational framework. We demonstrate the package on a simple Gaussian system and on a nontrivial epidemiological model for measles transmission within and between cities. We show how to construct user-specified SpatPOMP models within spatPomp.

stat.ME↗

arXiv2024

Inference on spatiotemporal dynamics for networks of biological populations

Mathematical models in ecology and epidemiology must be consistent with observed data in order to generate reliable knowledge and evidence-based policy. Metapopulation systems, which consist of a network of connected sub-populations, pose technical challenges in statistical inference due to nonlinear, stochastic interactions. Numerical difficulties encountered in conducting inference can obstruct the core scientific questions concerning the link between the mathematical models and the data. Recently, an algorithm has been developed which enables effective likelihood-based inference for the high-dimensional partially observed stochastic dynamic models arising in metapopulation systems. The COVID-19 pandemic provides a situation where mathematical models and their policy implications were widely visible, and we use the new inferential technology to revisit an influential metapopulation model used to inform basic epidemiological understanding early in the pandemic. Our methods support self-critical data analysis, enabling us to identify and address model limitations, and leading to a new model with substantially improved statistical fit and parameter identifiability. Our results suggest that the lockdown initiated on January 23, 2020 in China was more effective than previously thought. We proceed to recommend statistical analysis standards for future metapopulation system modeling.

stat.AP↗

arXiv2023

Iterated Block Particle Filter for High-dimensional Parameter Learning: Beating the Curse of Dimensionality

Parameter learning for high-dimensional, partially observed, and nonlinear stochastic processes is a methodological challenge. Spatiotemporal disease transmission systems provide examples of such processes giving rise to open inference problems. We propose the iterated block particle filter (IBPF) algorithm for learning high-dimensional parameters over graphical state space models with general state spaces, measures, transition densities and graph structure. Theoretical performance guarantees are obtained on beating the curse of dimensionality (COD), algorithm convergence, and likelihood maximization. Experiments on a highly nonlinear and non-Gaussian spatiotemporal model for measles transmission reveal that the iterated ensemble Kalman filter algorithm (Li et al. (2020)) is ineffective and the iterated filtering algorithm (Ionides et al. (2015)) suffers from the COD, while our IBPF algorithm beats COD consistently across various experiments with different metrics.

stat.ML↗

arXiv2022

An iterated block particle filter for inference on coupled dynamic systems with shared and unit-specific parameters

We consider inference for a collection of partially observed, stochastic, interacting, nonlinear dynamic processes. Each process is identified with a label called its unit, and our primary motivation arises in biological metapopulation systems where a unit corresponds to a spatially distinct sub-population. Metapopulation systems are characterized by strong dependence through time within a single unit and relatively weak interactions between units, and these properties make block particle filters an effective tool for simulation-based likelihood evaluation. Iterated filtering algorithms can facilitate likelihood maximization for simulation-based filters. We introduce an iterated block particle filter applicable when parameters are unit-specific or shared between units. We demonstrate this algorithm by performing inference on a coupled epidemiological model describing spatiotemporal measles case report data for twenty towns.

stat.ME↗

arXiv2022

Systemic Infinitesimal Over-dispersion on Graphical Dynamic Models

Stochastic models for collections of interacting populations have crucial roles in scientific fields such as epidemiology and ecology, yet the standard approach to extending an ordinary differential equation model to a Markov chain does not have sufficient flexibility in the mean-variance relationship to match data. To handle that, over-dispersed Markov chains have previously been constructed using gamma white noise on the rates. We develop new approaches using Dirichlet noise to construct collections of independent or dependent noise processes. This permits the modeling of high-frequency variation in transition rates both within and between the populations under study. Our theory is developed in a general framework of time-inhomogeneous Markov processes equipped with a graphical structure, for which ecological and epidemiological models provide motivating examples. We demonstrate our approach on a widely analyzed measles dataset, adding Dirichlet noise to a classical SEIR (Susceptible-Exposed-Infected-Recovered) model. Our methodology shows improved statistical fit measured by log-likelihood and provides new insights into the dynamics of this biological system.

stat.ME↗

arXiv2022

Markov Genealogy Processes

We construct a family of genealogy-valued Markov processes that are induced by a continuous-time Markov population process. We derive exact expressions for the likelihood of a given genealogy conditional on the history of the underlying population process. These lead to a nonlinear filtering equation which can be used to design efficient Monte Carlo inference algorithms. We demonstrate these calculations with several examples. Existing full-information approaches for phylodynamic inference are special cases of the theory.

math.PR↗

arXiv2021

Bagged filters for partially observed interacting systems

Bagging (i.e., bootstrap aggregating) involves combining an ensemble of bootstrap estimators. We consider bagging for inference from noisy or incomplete measurements on a collection of interacting stochastic dynamic systems. Each system is called a unit, and each unit is associated with a spatial location. A motivating example arises in epidemiology, where each unit is a city: the majority of transmission occurs within a city, with smaller yet epidemiologically important interactions arising from disease transmission between cities. Monte Carlo filtering methods used for inference on nonlinear non-Gaussian systems can suffer from a curse of dimensionality as the number of units increases. We introduce bagged filter (BF) methodology which combines an ensemble of Monte Carlo filters, using spatiotemporally localized weights to select successful filters at each unit and time. We obtain conditions under which likelihood evaluation using a BF algorithm can beat a curse of dimensionality, and we demonstrate applicability even when these conditions do not hold. BF can out-perform an ensemble Kalman filter on a coupled population dynamics model describing infectious disease transmission. A block particle filter also performs well on this task, though the bagged filter respects smoothness and conservation laws that a block particle filter can violate.

stat.ME↗