Hidden Markov models (HMMs) are popular models to identify a finite number of latent states from sequential data. However, fitting them to large datasets can be computationally demanding because most likelihood maximization techniques require iterating through the entire underlying dataset for every parameter update. We propose a novel optimization algorithm that updates the parameters of an HMM without iterating through the entire dataset. Namely, we combine a partial E step with variance-reduced stochastic optimization within the M step. We prove the algorithm converges under certain regularity conditions. We test our algorithm empirically using a simulation study as well as a case study of kinematic data collected using suction-cup attached biologgers from eight northern resident killer whales (Orcinus orca) off the western coast of Canada. In both, our algorithm converges in fewer epochs, with less computation time, and to regions of higher likelihood compared to standard numerical optimization techniques. Our algorithm allows practitioners to fit complicated HMMs to large time-series datasets more efficiently than existing baselines. Supplemental materials are available online.

Simulated Tempering (ST) is an MCMC algorithm for complex target distributions that operates on a path between the target and a more amenable reference distribution. Crucially, if the reference enables iid sampling, ST is regenerative and can be parallelized across independent tours. However, the difficulty of tuning ST has hindered its widespread adoption. In this work, we develop a simple nonreversible ST (NRST) algorithm, a general theoretical analysis of ST, and an automated tuning procedure for ST. A core contribution that arises from the analysis is a novel performance metric—Tour Effectiveness (TE)—that controls the asymptotic variance of estimates from ST for bounded test functions. We use the TE to show that NRST dominates its reversible counterpart. We then develop an automated tuning procedure for NRST algorithms that targets the TE while minimizing computational cost. This procedure enables straightforward integration of NRST into existing probabilistic programming languages. We provide extensive experimental evidence that our tuning scheme improves the performance and robustness of NRST algorithms on a diverse set of probabilistic models. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.

Simulated Tempering (ST) is an MCMC algorithm for complex target distributions that operates on a path between the target and a more amenable reference distribution. Crucially, if the reference enables i.i.d. sampling, ST is regenerative and can be parallelized across independent tours. However, the difficulty of tuning ST has hindered its widespread adoption. In this work, we develop a simple nonreversible ST (NRST) algorithm, a general theoretical analysis of ST, and an automated tuning procedure for ST. A core contribution that arises from the analysis is a novel performance metric—Tour Effectiveness (TE)—that controls the asymptotic variance of estimates from ST for bounded test functions. We use the TE to show that NRST dominates its reversible counterpart. We then develop an automated tuning procedure for NRST algorithms that targets the TE while minimizing computational cost. This procedure enables straightforward integration of NRST into existing probabilistic programming languages. We provide extensive experimental evidence that our tuning scheme improves the performance and robustness of NRST algorithms on a diverse set of probabilistic models.

Simulated Tempering (ST) is an MCMC algorithm for complex target distributions that operates on a path between the target and a more amenable reference distribution. Crucially, if the reference enables iid sampling, ST is regenerative and can be parallelized across independent tours. However, the difficulty of tuning ST has hindered its widespread adoption. In this work, we develop a simple nonreversible ST (NRST) algorithm, a general theoretical analysis of ST, and an automated tuning procedure for ST. A core contribution that arises from the analysis is a novel performance metric—Tour Effectiveness (TE)—that controls the asymptotic variance of estimates from ST for bounded test functions. We use the TE to show that NRST dominates its reversible counterpart. We then develop an automated tuning procedure for NRST algorithms that targets the TE while minimizing computational cost. This procedure enables straightforward integration of NRST into existing probabilistic programming languages. We provide extensive experimental evidence that our tuning scheme improves the performance and robustness of NRST algorithms on a diverse set of probabilistic models. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.

Hidden Markov models (HMMs) are popular models to identify a finite number of latent states from sequential data. However, fitting them to large datasets can be computationally demanding because most likelihood maximization techniques require iterating through the entire underlying dataset for every parameter update. We propose a novel optimization algorithm that updates the parameters of an HMM without iterating through the entire dataset. Namely, we combine a partial E step with variance-reduced stochastic optimization within the M step. We prove the algorithm converges under certain regularity conditions. We test our algorithm empirically using a simulation study as well as a case study of kinematic data collected using suction-cup attached biologgers from eight northern resident killer whales (Orcinus orca) off the western coast of Canada. In both, our algorithm converges in fewer epochs, with less computation time, and to regions of higher likelihood compared to standard numerical optimization techniques. Our algorithm allows practitioners to fit complicated HMMs to large time-series datasets more efficiently than existing baselines. Supplemental materials are available online.

Bayesian inference for Continuous-Time Markov chains (CTMCs) on countably infinite spaces is notoriously difficult because evaluating the likelihood exactly is intractable. One way to address this challenge is to first build a nonnegative and unbiased estimate of the likelihood—involving the matrix exponential of finite truncations of the true rate matrix—and then to use the estimates in a pseudo-marginal inference method. In this work, we show that we can dramatically increase the efficiency of this approach by avoiding the computation of exact matrix exponentials. In particular, we develop a general methodology for constructing an unbiased, nonnegative estimate of the likelihood using doubly-monotone matrix exponential approximations. We further develop a novel approximation in this family—the skeletoid—as well as theory regarding its approximation error and how that relates to the variance of the estimates used in pseudo-marginal inference. Experimental results show that our approach yields more efficient posterior inference for a wide variety of CTMCs. Supplementary materials for this article are available online.

Bayesian inference for Continuous-Time Markov Chains (CTMCs) on countably infinite spaces is notoriously difficult because evaluating the likelihood exactly is intractable. One way to address this challenge is to first build a non-negative and unbiased estimate of the likelihood—involving the matrix exponential of finite truncations of the true rate matrix—and then to use the estimates in a pseudo-marginal inference method. In this work, we show that we can dramatically increase the efficiency of this approach by avoiding the computation of exact matrix exponentials. In particular, we develop a general methodology for constructing an unbiased, non-negative estimate of the likelihood using doubly-monotone matrix exponential approximations. We further develop a novel approximation in this family—the skeletoid—as well as theory regarding its approximation error and how that relates to the variance of the estimates used in pseudo-marginal inference. Experimental results show that our approach yields more efficient posterior inference for a wide variety of CTMCs.

Bayesian inference for Continuous-Time Markov chains (CTMCs) on countably infinite spaces is notoriously difficult because evaluating the likelihood exactly is intractable. One way to address this challenge is to first build a nonnegative and unbiased estimate of the likelihood—involving the matrix exponential of finite truncations of the true rate matrix—and then to use the estimates in a pseudo-marginal inference method. In this work, we show that we can dramatically increase the efficiency of this approach by avoiding the computation of exact matrix exponentials. In particular, we develop a general methodology for constructing an unbiased, nonnegative estimate of the likelihood using doubly-monotone matrix exponential approximations. We further develop a novel approximation in this family—the skeletoid—as well as theory regarding its approximation error and how that relates to the variance of the estimates used in pseudo-marginal inference. Experimental results show that our approach yields more efficient posterior inference for a wide variety of CTMCs. Supplementary materials for this article are available online.

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