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A statistical model of protein families, called profile conditional random fields (CRFs), is proposed. This model may be regarded as an integration of the profile hidden Markov model (HMM) and the Finkelstein-Reva (FR) theory of protein…

Biomolecules · Quantitative Biology 2009-06-01 Akira R. Kinjo

This paper proposes, analyzes, and demonstrates an efficient low-rank solver for the stochastic Stokes-Darcy interface model with a random hydraulic conductivity both in the porous media domain and on the interface. We consider three…

Numerical Analysis · Mathematics 2025-08-08 Yujun Zhu , Yulan Ning , Zhipeng Yang , Xiaoming He , Ju Ming

We consider minimization of composite functions of the form $f(g(x))+h(x)$, where $f$ and $h$ are convex functions (which can be nonsmooth) and $g$ is a smooth vector mapping. In addition, we assume that $g$ is the average of finite number…

Optimization and Control · Mathematics 2021-05-17 Junyu Zhang , Lin Xiao

In many branches of engineering, Banach contraction mapping theorem is employed to establish the convergence of certain deterministic algorithms. Randomized versions of these algorithms have been developed that have proved useful in…

Probability · Mathematics 2023-09-25 Abhishek Gupta , Rahul Jain , Peter Glynn

Markov chain analysis is a key technique in formal verification. A practical obstacle is that all probabilities in Markov models need to be known. However, system quantities such as failure rates or packet loss ratios, etc. are often not --…

Logic in Computer Science · Computer Science 2023-11-08 Sebastian Junges , Erika Ábrahám , Christian Hensel , Nils Jansen , Joost-Pieter Katoen , Tim Quatmann , Matthias Volk

We study a class of multi-stage stochastic programs, which incorporate modeling features from Markov decision processes (MDPs). This class includes structured MDPs with continuous action and state spaces. We extend policy graphs to include…

Machine Learning · Computer Science 2026-04-09 David P. Morton , Oscar Dowson , Bernardo K. Pagnoncelli

We introduce a general procedure for directly ascertaining how many independent stochastic sources exist in a complex system modeled through a set of coupled Langevin equations of arbitrary dimension. The procedure is based on the…

Data Analysis, Statistics and Probability · Physics 2013-06-03 V. V. Vasconcelos , F. Raischel , M. Haase , J. Peinke , M. Wächter , P. G. Lind , D. Kleinhans

The probability current is a vital quantity in the Fokker-Planck description of stochastic processes. It characterizes non-equilibrium stationary states and appears in linear response calculations. We recover and review the probability…

Statistical Mechanics · Physics 2025-08-15 Valentin Wilhelm , Matthias Krüger , Matthias Fuchs , Florian Vogel

Machine learning techniques not only offer efficient tools for modelling dynamical systems from data, but can also be employed as frontline investigative instruments for the underlying physics. Nontrivial information about the original…

Data Analysis, Statistics and Probability · Physics 2021-02-24 Francesco Borra , Marco Baldovin

This paper investigates the gradient flow structure, well-posedness, and asymptotic behavior of the Fokker-Planck equation defined on locally uniformly finite graphs, which is highly non-trivial compared with the finite case. We first…

Probability · Mathematics 2025-11-13 Cong Wang

In this paper a class of higher order finite element methods for the discretization of surface Stokes equations is studied. These methods are based on an unfitted finite element approach in which standard Taylor-Hood spaces on an underlying…

Numerical Analysis · Mathematics 2019-09-19 Thomas Jankuhn , Arnold Reusken

We introduce a flexible framework for modeling dependent feature allocations. Our approach addresses limitations in traditional nonparametric methods by directly modeling the logit-probability surface of the feature paintbox, enabling the…

Methodology · Statistics 2025-12-22 Bernardo Flores , Yang Ni , Yanxun Xu , Peter Müller

Efficient and accurate integration of stochastic (partial) differential equations with multiplicative noise can be obtained through a split-step scheme, which separates the integration of the deterministic part from that of the stochastic…

Statistical Mechanics · Physics 2009-11-10 Ivan Dornic , Hugues Chate , M. A. Munoz

Nanostructured surfaces usually exhibit complicated morphologies that cannot be described in terms of Euclidean geometry. Simultaneously, they do not constitute fully random noise fields to be characterized by simple stochastics and…

Mesoscale and Nanoscale Physics · Physics 2022-02-03 A. Arapis , V. Constantoudis , D. Kontziampasis , A. Milionis , C. W. E. Lam , A. Tripathy , D. Poulikakos , E. Gogolides

Markov parameters play a key role in system identification. There exists many algorithms where these parameters are estimated using least-squares in a first, pre-processing, step, including subspace identification and multi-step…

Systems and Control · Electrical Eng. & Systems 2024-05-08 Jiabao He , Cristian R. Rojas , Håkan Hjalmarsson

Surface-based data is commonly observed in diverse practical applications spanning various fields. In this paper, we introduce a novel nonparametric method to discover the underlying signals from data distributed on complex surface-based…

Methodology · Statistics 2024-03-12 Zhiling Gu , Shan Yu , Guannan Wang , Ming-Jun Lai , Li Wang

The last decade has seen the success of stochastic parameterizations in short-term, medium-range and seasonal forecasts: operational weather centers now routinely use stochastic parameterization schemes to better represent model inadequacy…

Pre-asymptotic transport of a scalar quantity passively advected by a velocity field formed by a large-scale component superimposed to a small-scale fluctuation is investigated both analytically and by means of numerical simulations.…

Chaotic Dynamics · Physics 2007-05-23 A. Mazzino , S. Musacchio , A. Vulpiani

In this paper, we define random quasi-periodic paths for random dynamical systems and quasi-periodic measures for Markovian semigroups. We give a sufficient condition for the existence and uniqueness of random quasi-periodic paths and…

Probability · Mathematics 2021-03-19 Chunrong Feng , Baoyou Qu , Huaizhong Zhao

We examine the relation between a stochastic version of the rough path integral with the symmetric-Stratonovich integral in the sense of regularization. Under mild regularity conditions in the sense of Malliavin calculus, we establish…

Probability · Mathematics 2023-09-18 Alberto Ohashi , Francesco Russo
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