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Markov state models (MSMs) have become a popular approach for investigating the conformational dynamics of proteins and other biomolecules. MSMs are typically built from numerous molecular dynamics simulations by dividing the sampled…

Biomolecules · Quantitative Biology 2015-06-12 Yuan Yao , Raymond Z. Cui , Gregory R. Bowman , Daniel Silva , Jian Sun , Xuhui Huang

Long Short-Term Memory (LSTM) neural network models have become the cornerstone for sequential data modeling in numerous applications, ranging from natural language processing to time series forecasting. Despite their success, the problem…

Machine Learning · Statistics 2026-05-26 Fahad Mostafa

Inspired by the work of Tsiamis et al. \cite{tsiamis2022learning}, in this paper we study the statistical hardness of learning to stabilize linear time-invariant systems. Hardness is measured by the number of samples required to achieve a…

Systems and Control · Electrical Eng. & Systems 2023-11-21 Xiong Zeng , Zexiang Liu , Zhe Du , Necmiye Ozay , Mario Sznaier

This paper is concerned with statistical methods for the segmental classification of linear sequence data where the task is to segment and classify the data according to an underlying hidden discrete state sequence. Such analysis is…

Methodology · Statistics 2015-05-05 Christopher Yau , Christopher C. Holmes

This paper addresses the problem of planning under uncertainty in large Markov Decision Processes (MDPs). Factored MDPs represent a complex state space using state variables and the transition model using a dynamic Bayesian network. This…

Artificial Intelligence · Computer Science 2011-06-10 C. Guestrin , D. Koller , R. Parr , S. Venkataraman

In this paper, we study the problem of model-checking quantum pushdown systems from a computational complexity point of view. We arrive at the following equally important, interesting new results: We first extend the notions of the {\it…

Logic in Computer Science · Computer Science 2026-05-11 Deren Lin , Tianrong Lin

We consider the policy synthesis problem for continuous-state controlled Markov processes evolving in discrete time, when the specification is given as a B\"uchi condition (visit a set of states infinitely often). We decompose computation…

Systems and Control · Electrical Eng. & Systems 2020-02-17 Rupak Majumdar , Kaushik Mallik , Sadegh Soudjani

Verification of infinite-state Markov chains is still a challenge despite several fruitful numerical or statistical approaches. For decisive Markov chains, there is a simple numerical algorithm that frames the reachability probability as…

Logic in Computer Science · Computer Science 2024-09-30 Benoît Barbot , Patricia Bouyer , Serge Haddad

We investigate the problems of model estimation and reward-free learning in episodic Block MDPs. In these MDPs, the decision maker has access to rich observations or contexts generated from a small number of latent states. We are first…

Machine Learning · Computer Science 2023-02-27 Yassir Jedra , Junghyun Lee , Alexandre Proutière , Se-Young Yun

In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…

Genomics · Quantitative Biology 2007-05-23 Rudi Cilibrasi , Leo van Iersel , Steven Kelk , John Tromp

With the decreasing cost of data collection, the space of variables or features that can be used to characterize a particular predictor of interest continues to grow exponentially. Therefore, identifying the most characterizing features…

Machine Learning · Computer Science 2021-01-26 Sali Rasoul , Sodiq Adewole , Alphonse Akakpo

In this work, we show, for the well-studied problem of learning parity under noise, where a learner tries to learn $x=(x_1,\ldots,x_n) \in \{0,1\}^n$ from a stream of random linear equations over $\mathrm{F}_2$ that are correct with…

Machine Learning · Computer Science 2021-07-07 Sumegha Garg , Pravesh K. Kothari , Pengda Liu , Ran Raz

The minimum realization problem of hidden Markov models (HMM's) is a fundamental question of stationary discrete-time processes with a finite alphabet. It was shown in the literature that tensor decomposition methods give the hidden Markov…

Optimization and Control · Mathematics 2020-08-27 Yoshito Ohta

We discuss the notorious problem of order selection in hidden Markov models, i.e. of selecting an adequate number of states, highlighting typical pitfalls and practical challenges arising when analyzing real data. Extensive simulations are…

Methodology · Statistics 2017-04-18 Jennifer Pohle , Roland Langrock , Floris van Beest , Niels Martin Schmidt

Scenarios, or Message Sequence Charts, offer an intuitive way of describing the desired behaviors of a distributed protocol. In this paper we propose a new way of specifying finite-state protocols using scenarios: we show that it is…

Formal Languages and Automata Theory · Computer Science 2014-03-03 Rajeev Alur , Milo Martin , Mukund Raghothaman , Christos Stergiou , Stavros Tripakis , Abhishek Udupa

Probabilistic programming languages can simplify the development of machine learning techniques, but only if inference is sufficiently scalable. Unfortunately, Bayesian parameter estimation for highly coupled models such as regressions and…

Machine Learning · Statistics 2015-03-10 Yutian Chen , Vikash Mansinghka , Zoubin Ghahramani

The secret protection problem (SPP) seeks to synthesize a minimum-cost policy ensuring that every execution from an initial state to a secret state includes a sufficient number of protected events. Previous work showed that the problem is…

Formal Languages and Automata Theory · Computer Science 2025-09-19 Tomáš Masopust , Jakub Večeřa

Imitation learning considerably simplifies policy synthesis compared to alternative approaches by exploiting access to expert demonstrations. For such imitation policies, errors away from the training samples are particularly critical. Even…

Machine Learning · Computer Science 2024-03-19 Kaustubh Sridhar , Souradeep Dutta , Dinesh Jayaraman , James Weimer , Insup Lee

We propose a new abstract formalism for probabilistic timed systems, Parametric Interval Probabilistic Timed Automata, based on an extension of Parametric Timed Automata and Interval Markov Chains. In this context, we consider the…

Formal Languages and Automata Theory · Computer Science 2019-06-13 Étienne André , Benoît Delahaye , Paulin Fournier

Robust Markov decision processes (RMDPs) extend standard Markov decision processes (MDPs) to account for uncertainty in the transition probabilities. RMDPs have an uncertainty set that defines a set of possible transition functions, each of…

Logic in Computer Science · Computer Science 2026-04-30 Marnix Suilen , Guillermo A. Pérez