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In the previous paper of this series [D. P. Varn, G. S. Canright, and J. P. Crutchfield, Physical Review B, submitted] we detailed a procedure--epsilon-machine spectral reconstruction--to discover and analyze patterns and disorder in…
Factorial hidden Markov models (FHMMs) are powerful tools of modeling sequential data. Learning FHMMs yields a challenging simultaneous model selection issue, i.e., selecting the number of multiple Markov chains and the dimensionality of…
Hidden Markov models (HMMs) are widely applied in studies where a discrete-valued process of interest is observed indirectly. They have for example been used to model behaviour from human and animal tracking data, disease status from…
This research focuses on solving time-dependent partial differential equations (PDEs), in particular the time-dependent Schr\"odinger equation, using matrix product states (MPS). We propose an extension of Hermite Distributed Approximating…
This paper presents a mathematical framework for causal nonlinear prediction in settings where observations are generated from an underlying hidden Markov model (HMM). Both the problem formulation and the proposed solution are motivated by…
It is of some interest to understand how statistically based mechanisms for signal processing might be integrated with biologically motivated mechanisms such as neural networks. This paper explores a novel hybrid approach for classifying…
This paper introduces the hhsmm R package, which involves functions for initializing, fitting, and predication of hidden hybrid Markov/semi-Markov models. These models are flexible models with both Markovian and semi-Markovian states, which…
Recently, hidden Markov models (HMMs) have achieved promising results for offline handwritten Chinese text recognition. However, due to the large vocabulary of Chinese characters with each modeled by a uniform and fixed number of hidden…
A fundamental prediction of the cold dark matter (CDM) model of structure formation is the existence of a vast population of dark matter haloes extending to subsolar masses. By contrast, other dark matter models, such as a warm thermal…
We introduce a Cascaded Diffusion Model (Cas-DM) that improves a Denoising Diffusion Probabilistic Model (DDPM) by effectively incorporating additional metric functions in training. Metric functions such as the LPIPS loss have been proven…
We consider finite state space stationary hidden Markov models (HMMs) in the situation where the number of hidden states is unknown. We provide a frequentist asymptotic evaluation of Bayesian analysis methods. Our main result gives…
Standard practice in Hidden Markov Model (HMM) selection favors the candidate with the highest full-sequence likelihood, although this is equivalent to making a decision based on a single realization. We introduce a \emph{fragment-based}…
Hidden Markov Models are widely used in classical computer science to model stochastic processes with a wide range of applications. This paper concerns the quantum analogues of these machines --- so-called Hidden Quantum Markov Models…
The nature of stacking faults - whether intrinsic or extrinsic - plays a pivotal role in defect-mediated processes in crystalline materials. Yet, current electron microscopy techniques for their reliable analysis remain limited to either…
An intrinsic problem of classifiers based on machine learning (ML) methods is that their learning time grows as the size and complexity of the training dataset increases. For this reason, it is important to have efficient computational…
The formalism of state estimation and hidden Markov models (HMMs) can simplify and clarify the discussion of stochastic thermodynamics in the presence of feedback and measurement errors. After reviewing the basic formalism, we use it to…
Information seeking process is an important topic in information seeking behavior research. Both qualitative and empirical methods have been adopted in analyzing information seeking processes, with major focus on uncovering the latent…
The hidden Markov model (HMM) has been a workhorse of single molecule data analysis and is now commonly used as a standalone tool in time series analysis or in conjunction with other analyses methods such as tracking. Here we provide a…
We present a polyphonic MIDI score-following algorithm capable of following performances with arbitrary repeats and skips, based on a probabilistic model of musical performances. It is attractive in practical applications of score following…
We model and study the patterns created through the interaction of collectively moving self-propelled particles (SPPs) and elastically tethered obstacles. Simulations of an individual-based model reveal at least three distinct large-scale…