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Star formation is a multi-scale problem, and only global simulations that account for the connection from the molecular cloud scale gas flow to the accreting protostar can reflect the observed complexity of protostellar systems.…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Markov decision processes are a ubiquitous formalism for modelling systems with non-deterministic and probabilistic behavior. Verification of these models is subject to the famous state space explosion problem. We alleviate this problem by…
We present metrics for measuring the similarity of states in a finite Markov decision process (MDP). The formulation of our metrics is based on the notion of bisimulation for MDPs, with an aim towards solving discounted infinite horizon…
We present a new algorithm for discovering patterns in time series and other sequential data. We exhibit a reliable procedure for building the minimal set of hidden, Markovian states that is statistically capable of producing the behavior…
Markov Chain Monte Carlo (MCMC) algorithms are often used for approximate inference inside learning, but their slow mixing can be difficult to diagnose and the approximations can seriously degrade learning. To alleviate these issues, we…
A valuable step in the modeling of multiscale dynamical systems in fields such as computational chemistry, biology, materials science and more, is the representative sampling of the phase space over long timescales of interest; this task is…
We address the problem of approximating the posterior probability distribution of the fixed parameters of a state-space dynamical system using a sequential Monte Carlo method. The proposed approach relies on a nested structure that employs…
Spectral clustering techniques are valuable tools in signal processing and machine learning for partitioning complex data sets. The effectiveness of spectral clustering stems from constructing a non-linear embedding based on creating a…
To analyze high-dimensional systems, many fields in science and engineering rely on high-level descriptions, sometimes called "macrostates," "coarse-grainings," or "effective theories". Examples of such descriptions include the…
The quasi-steady-state approximation (or stochastic averaging principle) is a useful tool in the study of multiscale stochastic systems, giving a practical method by which to reduce the number of degrees of freedom in a model. The method is…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
This work presents an efficient algorithm for generating statistically representative microstructures of particulate composites in periodic representative volume elements. The Swelling and Random Migration (SRM) algorithm combines…
State space models (SSM) have been widely applied for the analysis and visualization of large sequential datasets. Sequential Monte Carlo (SMC) is a very popular particle-based method to sample latent states from intractable posteriors.…
State aggregation is a popular model reduction method rooted in optimal control. It reduces the complexity of engineering systems by mapping the system's states into a small number of meta-states. The choice of aggregation map often depends…
Pseudo-marginal Metropolis-Hastings (pmMH) is a versatile algorithm for sampling from target distributions which are not easy to evaluate point-wise. However, pmMH requires good proposal distributions to sample efficiently from the target,…
It is a challenge to obtain an accurate model of the state-to-state dynamics of a complex biological system from molecular dynamics (MD) simulations. In recent years, Markov State Models have gained immense popularity for computing…
In this paper, we study the problem of determining a minimum state probabilistic finite state machine capable of generating statistically identical symbol sequences to samples provided. This problem is qualitatively similar to the classical…
Analysis of Markov Decision Processes (MDP) is often hindered by state space explosion. Abstraction is a well-established technique in model checking to mitigate this issue. This paper presents a novel lazy abstraction method for MDP…
Genetic fitness optimization using small populations or small population updates across generations generally suffers from randomly diverging evolutions. We propose a notion of highly probable fitness optimization through feasible…