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We introduce the minimal maximally predictive models ({\epsilon}-machines) of processes generated by certain hidden semi-Markov models. Their causal states are either hybrid discrete-continuous or continuous random variables and…
Consider a finite set $A$ and an integer $n \geq 1$. This paper studies the concept of complete simulation in the context of semigroups of transformations of $A^n$, also known as finite state-homogeneous automata networks. For $m \geq n$, a…
For Finite State Machines (FSMs) a rich testing theory has been developed to discover aspects of their behavior and ensure their correct functioning. Although this theory is widely used, e.g., to check conformance of protocol…
We present the stochastic thermodynamics analysis of an open quantum system weakly coupled to multiple reservoirs and driven by a rapidly oscillating external field. The analysis is built on a modified stochastic master equation in the…
Latent force models (LFM) are principled approaches to incorporating solutions to differential equations within non-parametric inference methods. Unfortunately, the development and application of LFMs can be inhibited by their computational…
We present a variational approach for quantum simulators to realize finite temperature Gibbs states by preparing thermofield double (TFD) states. Our protocol is motivated by the quantum approximate optimization algorithm (QAOA) and…
Imprecise continuous-time Markov chains are a robust type of continuous-time Markov chains that allow for partially specified time-dependent parameters. Computing inferences for them requires the solution of a non-linear differential…
The existence of generalized steady states (GSSs) in nonlinear mechanical systems under moderate temporally aperiodic forcing has only been shown recently. Here we derive systematic expansions for such GSSs and construct a numerical…
This paper presents the implementation of a self-replicating finite-state machine (FSM) and a self-replicating Turing Machine (TM) using bio-inspired mechanisms. Building on previous work that introduced self-replicating structures capable…
The problem of estimating entropy production from incomplete information in stochastic thermodynamics is essential for theory and experiments. Whereas a considerable amount of work has been done on this topic, arguably, most of it is…
We consider the problem of performing parameter and state inference in a state-space model (SSM) parametrized by a static parameter $\theta$. A popular idea to address this problem consists of incorporating $\theta$ in the state of the…
Analyses of serially-sampled data often begin with the assumption that the observations represent discrete samples from a latent continuous-time stochastic process. The continuous-time Markov chain (CTMC) is one such generative model whose…
The promise of chemical computation lies in controlling systems incompatible with traditional electronic micro-controllers, with applications in synthetic biology and nano-scale manufacturing. Computation is typically embedded in…
This paper presents the PUF finite state machine (PUF-FSM) that is served as a practical {\it controlled} strong PUF. Previous controlled PUF designs have the difficulties of stabilizing the noisy PUF responses where the error correction…
The Gaussian process state-space model (GPSSM) has attracted extensive attention for modeling complex nonlinear dynamical systems. However, the existing GPSSM employs separate Gaussian processes (GPs) for each latent state dimension,…
We present an efficient exact algorithm for estimating state sequences from outputs (or observations) in imprecise hidden Markov models (iHMM), where both the uncertainty linking one state to the next, and that linking a state to its…
A central task in many applications is reasoning about processes that change in a continuous time. The mathematical framework of Continuous Time Markov Processes provides the basic foundations for modeling such systems. Recently, Nodelman…
Probabilistic model checking for systems with large or unbounded state space is a challenging computational problem in formal modelling and its applications. Numerical algorithms require an explicit representation of the state space, while…
Markov state models (MSMs)---or discrete-time master equation models---are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative…
We develop a thermodynamic theory for machine learning (ML) systems. Similar to physical thermodynamic systems which are characterized by energy and entropy, ML systems possess these characteristics as well. This comparison inspire us to…