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We propose a numerical technique for parameter inference in Markov models of biological processes. Based on time-series data of a process we estimate the kinetic rate constants by maximizing the likelihood of the data. The computation of…

Quantitative Methods · Quantitative Biology 2011-02-15 Aleksandr Andreychenko , Linar Mikeev , David Spieler , Verena Wolf

Adaptive Markov chain Monte Carlo (MCMC) algorithms, which automatically tune their parameters based on past samples, have proved extremely useful in practice. The self-tuning mechanism makes them `non-Markovian', which means that their…

Probability · Mathematics 2024-08-28 Pietari Laitinen , Matti Vihola

A key challenge in science and engineering is to design experiments to learn about some unknown quantity of interest. Classical experimental design optimally allocates the experimental budget to maximize a notion of utility (e.g., reduction…

Machine Learning · Computer Science 2022-11-10 Mojmír Mutný , Tadeusz Janik , Andreas Krause

A decision maker records measurements of a finite-state Markov chain corrupted by noise. The goal is to decide when the Markov chain hits a specific target state. The decision maker can choose from a finite set of sampling intervals to pick…

Optimization and Control · Mathematics 2012-08-17 Vikram Krishnamurthy

Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition…

Logic in Computer Science · Computer Science 2018-06-14 Sebastian Arming , Ezio Bartocci , Krishnendu Chatterjee , Joost-Pieter Katoen , Ana Sokolova

The two-parameter Macdonald polynomials are a central object of algebraic combinatorics and representation theory. We give a Markov chain on partitions of k with eigenfunctions the coefficients of the Macdonald polynomials when expanded in…

Probability · Mathematics 2010-07-28 Persi Diaconis , Arun Ram

Design and control of autonomous systems that operate in uncertain or adversarial environments can be facilitated by formal modelling and analysis. Probabilistic model checking is a technique to automatically verify, for a given temporal…

Logic in Computer Science · Computer Science 2021-11-23 Marta Kwiatkowska , Gethin Norman , David Parker

Hidden Markov Chains (HMCs) are commonly used mathematical models of probabilistic systems. They are employed in various fields such as speech recognition, signal processing, and biological sequence analysis. We consider the problem of…

Data Structures and Algorithms · Computer Science 2016-05-10 Stefan Kiefer , A. Prasad Sistla

Spectral methods have proven to be a highly effective tool in understanding the intrinsic geometry of a high-dimensional data set $\left\{x_i \right\}_{i=1}^{n} \subset \mathbb{R}^d$. The key ingredient is the construction of a Markov chain…

Discrete Mathematics · Computer Science 2014-11-07 Stefan Steinerberger

In this paper we study various properties of finite stochastic systems or hidden Markov chains as they are alternatively called. We discuss their construction following different approaches and we also derive recursive filtering formulas…

Probability · Mathematics 2014-07-15 Peter Spreij

The formal verification of large probabilistic models is important and challenging. Exploiting the concurrency that is often present is one way to address this problem. Here we study a restricted class of asynchronous distributed…

Distributed, Parallel, and Cluster Computing · Computer Science 2014-08-06 Sumit Kumar Jha , Madhavan Mukund , Ratul Saha , P S Thiagarajan

Markov Chain Monte Carlo (MCMC) method is a widely used algorithm design scheme with many applications. To make efficient use of this method, the key step is to prove that the Markov chain is rapid mixing. Canonical paths is one of the two…

Data Structures and Algorithms · Computer Science 2015-10-15 Lingxiao Huang , Pinyan Lu , Chihao Zhang

Motivated by techniques developed in recent progress on lower bounds for sublinear time algorithms (Behnezhad, Roghani and Rubinstein, STOC 2023, FOCS 2023, and STOC 2024) we introduce and study a new class of randomized algorithmic…

Data Structures and Algorithms · Computer Science 2026-03-19 Amir Azarmehr , Soheil Behnezhad , Alma Ghafari , Madhu Sudan

Probabilistic model checking computes probabilities and expected values related to designated behaviours of interest in Markov models. As a formal verification approach, it is applied to critical systems; thus we trust that probabilistic…

Logic in Computer Science · Computer Science 2021-10-19 Arnd Hartmanns

We introduce the problem of formally verifying properties of Markov processes where the parameters are given by the output of machine learning models. For a broad class of machine learning models, including linear models, tree-based models,…

Machine Learning · Computer Science 2025-05-13 Muhammad Maaz , Timothy C. Y. Chan

Quantitative properties of stochastic systems are usually specified in logics that allow one to compare the measure of executions satisfying certain temporal properties with thresholds. The model checking problem for stochastic systems with…

Logic in Computer Science · Computer Science 2010-05-11 Axel Legay , Benoit Delahaye

This paper analyzes a (1, $\lambda$)-Evolution Strategy, a randomized comparison-based adaptive search algorithm, optimizing a linear function with a linear constraint. The algorithm uses resampling to handle the constraint. Two cases are…

Optimization and Control · Mathematics 2015-10-16 Alexandre Chotard , Anne Auger , Nikolaus Hansen

Constructing an accurate system model for formal model verification can be both resource demanding and time-consuming. To alleviate this shortcoming, algorithms have been proposed for automatically learning system models based on observed…

Machine Learning · Computer Science 2012-12-18 Hua Mao , Yingke Chen , Manfred Jaeger , Thomas D. Nielsen , Kim G. Larsen , Brian Nielsen

The subject of this paper is to study conformance checking for timed models, that is, process models that consider both the sequence of events in a process as well as the timestamps at which each event is recorded. Time-aware process mining…

Formal Languages and Automata Theory · Computer Science 2022-07-06 Thomas Chatain , Neha Rino

Today, cheap numerical hardware offers huge amounts of parallel computing power, much of which is used for the task of fitting neural networks to data. Adoption of this hardware to accelerate statistical Markov chain Monte Carlo (MCMC)…

Computation · Statistics 2024-11-08 Pavel Sountsov , Colin Carroll , Matthew D. Hoffman