Related papers: Using Markov State Models to Study Self-Assembly
Sampling the phase space of molecular systems -- and, more generally, of complex systems effectively modeled by stochastic differential equations -- is a crucial modeling step in many fields, from protein folding to materials discovery.…
Generative modeling, which learns joint probability distribution from data and generates samples according to it, is an important task in machine learning and artificial intelligence. Inspired by probabilistic interpretation of quantum…
We present the first finite-sample goodness-of-fit test for the mixed membership stochastic block model (MMSBM). Using algebraic statistics theory, we derive a Markov basis that lets a Metropolis-Hastings sampler explore exactly the set of…
Many models in natural and social sciences are comprised of sets of inter-acting entities whose intensity of interaction decreases with distance. This often leads to structures of interest in these models composed of dense packs of…
In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…
Cyber-physical systems (CPSs) are naturally modelled as reactive systems with nondeterministic and probabilistic dynamics. Model-based verification techniques have proved effective in the deployment of safety-critical CPSs. Central for a…
Recent State Space Models (SSMs) such as S4, S5, and Mamba have shown remarkable computational benefits in long-range temporal dependency modeling. However, in many sequence modeling problems, the underlying process is inherently modular…
In today's industrial practice, safety, reliability or availability artifacts such as fault trees, Markov models or FMEAs are mainly created manually by experts, often distinctively decoupled from systems engineering activities. Significant…
We consider exchangeable Markov multi-state survival processes -- temporal processes taking values over a state-space$\mathcal{S}$ with at least one absorbing failure state $\flat \in \mathcal{S}$ that satisfy natural invariance properties…
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained…
We present new algorithms for computing and approximating bisimulation metrics in Markov Decision Processes (MDPs). Bisimulation metrics are an elegant formalism that capture behavioral equivalence between states and provide strong…
We consider penalized estimation in hidden Markov models (HMMs) with multivariate Normal observations. In the moderate-to-large dimensional setting, estimation for HMMs remains challenging in practice, due to several concerns arising from…
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…
Single-molecule force spectroscopy (smFS) is a powerful approach to studying molecular self-organization. However, the coupling of the molecule with the ever-present experimental device introduces artifacts, that complicates the…
Tensor networks, which are originally developed for characterizing complex quantum many-body systems, have recently emerged as a powerful framework for capturing high-dimensional probability distributions with strong physical…
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…
Galaxies host a wide array of internal stellar components, which need to be decomposed accurately in order to understand their formation and evolution. While significant progress has been made with recent integral-field spectroscopic…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
We introduce MOSCITO (MOlecular Dynamics Subspace Clustering with Temporal Observance), a subspace clustering for molecular dynamics data. MOSCITO groups those timesteps of a molecular dynamics trajectory together into clusters in which the…