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Alignment algorithms usually rely on simplified models of gaps for computational efficiency. Based on an isomorphism between alignments and physical helix-coil models, we show in statistical mechanics that alignments with realistic laws for…

Genomics · Quantitative Biology 2015-06-26 E. Yeramian , E. Debonneuil

Recent advances in statistical inference have significantly expanded the toolbox of probabilistic modeling. Historically, probabilistic modeling has been constrained to (i) very restricted model classes where exact or approximate…

Machine Learning · Computer Science 2019-10-03 Andrés R. Masegosa , Rafael Cabañas , Helge Langseth , Thomas D. Nielsen , Antonio Salmerón

Markov automata combine non-determinism, probabilistic branching, and exponentially distributed delays. This compositional variant of continuous-time Markov decision processes is used in reliability engineering, performance evaluation and…

Logic in Computer Science · Computer Science 2017-05-11 Tim Quatmann , Sebastian Junges , Joost-Pieter Katoen

Randomized algorithms provide solutions to two ubiquitous problems: (1) the distributed calculation of a principal component analysis or singular value decomposition of a highly rectangular matrix, and (2) the distributed calculation of a…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-04-09 Huamin Li , Yuval Kluger , Mark Tygert

Dominating Set is a well-known combinatorial optimization problem which finds application in computational biology or mobile communication. Because of its $\mathrm{NP}$-hardness, one often turns to heuristics for good solutions. Many such…

Data Structures and Algorithms · Computer Science 2026-01-21 Hendrik Higl

Heuristic search is a powerful approach that has successfully been applied to a broad class of planning problems, including classical planning, multi-objective planning, and probabilistic planning modelled as a stochastic shortest path…

Artificial Intelligence · Computer Science 2024-10-29 Dillon Chen , Felipe Trevizan , Sylvie Thiébaux

Performance analysis of all kinds of randomised search heuristics is a rapidly growing and developing field. Run time and solution quality are two popular measures of the performance of these algorithms. The focus of this paper is on the…

Neural and Evolutionary Computing · Computer Science 2019-11-11 Jun He , Thomas Jansen , Christine Zarges

Probabilistic forecasts in the form of probability distributions over future events have become popular in several fields including meteorology, hydrology, economics, and demography. In typical applications, many alternative statistical…

Computation · Statistics 2018-07-31 Alexander Jordan , Fabian Krüger , Sebastian Lerch

The analysis of formal models that include quantitative aspects such as timing or probabilistic choices is performed by quantitative verification tools. Broad and mature tool support is available for computing basic properties such as…

We introduce a framework for uncertainty estimation that both describes and extends many existing methods. We consider typical hyperparameters involved in classical training as random variables and marginalise them out to capture various…

Machine Learning · Computer Science 2021-07-07 Francesco Farina , Lawrence Phillips , Nicola J Richmond

Markov random fields area popular model for high-dimensional probability distributions. Over the years, many mathematical, statistical and algorithmic problems on them have been studied. Until recently, the only known algorithms for…

Machine Learning · Computer Science 2017-06-01 Linus Hamilton , Frederic Koehler , Ankur Moitra

Speculative optimisation relies on the estimation of the probabilities that certain properties of the control flow are fulfilled. Concrete or estimated branch probabilities can be used for searching and constructing advantageous speculative…

Programming Languages · Computer Science 2013-07-18 Alessandra Di Pierro , Herbert Wiklicky

Meta-heuristics are powerful tools for solving optimization problems whose structural properties are unknown or cannot be exploited algorithmically. We propose such a meta-heuristic for a large class of optimization problems over discrete…

Discrete Mathematics · Computer Science 2021-06-22 Moritz Mühlenthaler , Alexander Raß , Manuel Schmitt , Rolf Wanka

Recursive stochastic algorithms have gained significant attention in the recent past due to data driven applications. Examples include stochastic gradient descent for solving large-scale optimization problems and empirical dynamic…

Machine Learning · Computer Science 2020-07-27 Abhishek Gupta , Hao Chen , Jianzong Pi , Gaurav Tendolkar

It is well known that options can make planning more efficient, among their many benefits. Thus far, algorithms for autonomously discovering a set of useful options were heuristic. Naturally, a principled way of finding a set of useful…

Machine Learning · Computer Science 2018-02-01 Roy Fox , Michal Moshkovitz , Naftali Tishby

Markov decision processes model systems subject to nondeterministic and probabilistic uncertainty. A plethora of verification techniques addresses variations of reachability properties, such as: Is there a scheduler resolving the…

Logic in Computer Science · Computer Science 2025-05-26 Lina Gerlach , Tobias Winkler , Erika Ábrahám , Borzoo Bonakdarpour , Sebastian Junges

Hidden Markov models (HMMs) and partially observable Markov decision processes (POMDPs) form a useful tool for modeling dynamical systems. They are particularly useful for representing environments such as road networks and office…

Artificial Intelligence · Computer Science 2013-01-30 Hagit Shatkay

Randomized algorithms for very large matrix problems have received a great deal of attention in recent years. Much of this work was motivated by problems in large-scale data analysis, and this work was performed by individuals from many…

Data Structures and Algorithms · Computer Science 2011-11-16 Michael W. Mahoney

It is becoming increasingly apparent that probabilistic approaches can overcome conservatism and computational complexity of the classical worst-case deterministic framework and may lead to designs that are actually safer. In this paper we…

Applications · Statistics 2008-11-01 Xinjia Chen , Kemin Zhou , Jorge L. Aravena

This paper presents a fully distributed resource discovery and reservation system. Verification of such a system is important to ensure the execution of distributed applications on a set of resources in appropriate conditions. A semi-formal…

Distributed, Parallel, and Cluster Computing · Computer Science 2016-08-03 Camille Coti