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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…

Molecular Networks · Quantitative Biology 2018-02-16 Chuan Zhang , Ziyuan Shen , Wei Wei , Jing Zhao , Zaichen Zhang , Xiaohu You

Sequential Monte Carlo (SMC) is a methodology for sampling approximately from a sequence of probability distributions of increasing dimension and estimating their normalizing constants. We propose here an alternative methodology named…

Statistics Theory · Mathematics 2012-11-13 Anthony Brockwell , Pierre Del Moral , Arnaud Doucet

We propose a Markov chain simulation method to generate simple connected random graphs with a specified degree sequence and level of clustering. The networks generated by our algorithm are random in all other respects and can thus serve as…

Discrete Mathematics · Computer Science 2010-02-09 Shweta Bansal , Shashank Khandelwal , Lauren Ancel Meyers

In this work, we want to learn to model the dynamics of similar yet distinct groups of interacting objects. These groups follow some common physical laws that exhibit specificities that are captured through some vectorial description. We…

Machine Learning · Computer Science 2021-07-05 Joao A. Candido Ramos , Lionel Blondé , Stéphane Armand , Alexandros Kalousis

Reconstructing accurate causal models of dynamic systems from time-series of sensor data is a key problem in many real-world scenarios. In this paper, we present an overview based on our experience about practical challenges that the causal…

Robotics · Computer Science 2023-01-11 Luca Castri , Sariah Mghames , Nicola Bellotto

Many complex systems have natural representations as multi-layer networks. While these formulations retain more information than standard single-layer network models, there is not yet a fully developed theory for computing network metrics…

Social and Information Networks · Computer Science 2017-03-17 Daryl R. DeFord , Scott D. Pauls

Inferring control parameters in non-linear dynamical systems is an important task in analysing general dynamical behaviours, particularly in the presence of inherently deterministic chaos. Traditional approaches often rely on…

Chaotic Dynamics · Physics 2025-06-19 L. Lober , M. S. Palmero , F. A. Rodrigues

Nowadays, neural network models achieve state-of-the-art results in many areas as computer vision or speech processing. For sequential data, especially for Natural Language Processing (NLP) tasks, Recurrent Neural Networks (RNNs) and their…

Computation and Language · Computer Science 2021-02-23 Elie Azeraf , Emmanuel Monfrini , Emmanuel Vignon , Wojciech Pieczynski

Machine Learning (ML) interatomic models and potentials have been widely employed in simulations of materials. Long-range interactions often dominate in some ionic systems whose dynamics behavior is significantly influenced. However, the…

Materials Science · Physics 2022-12-01 Hongyu Yu , Liangliang Hong , Shiyou Chen , Xingao Gong , Hongjun Xiang

The widespread use of large language models (LLMs) raises an important question: how do texts evolve when they are repeatedly processed by LLMs? In this paper, we define this iterative inference process as Markovian generation chains, where…

Computation and Language · Computer Science 2026-03-13 Mingmeng Geng , Amr Mohamed , Guokan Shang , Michalis Vazirgiannis , Thierry Poibeau

This work introduces a method for learning low-dimensional models from data of high-dimensional black-box dynamical systems. The novelty is that the learned models are exactly the reduced models that are traditionally constructed with model…

Numerical Analysis · Mathematics 2019-08-30 Benjamin Peherstorfer

Deep Markov models (DMM) are generative models that are scalable and expressive generalization of Markov models for representation, learning, and inference problems. However, the fundamental stochastic stability guarantees of such models…

Machine Learning · Computer Science 2021-11-09 Ján Drgoňa , Sayak Mukherjee , Jiaxin Zhang , Frank Liu , Mahantesh Halappanavar

Continuous-time Markov processes over finite state-spaces are widely used to model dynamical processes in many fields of natural and social science. Here, we introduce an maximum likelihood estimator for constructing such models from data…

Data Analysis, Statistics and Probability · Physics 2015-07-01 Robert T. McGibbon , Vijay S. Pande

Contextual Markov decision processes (CMDPs) describe a class of reinforcement learning problems in which the transition kernels and reward functions can change over time with different MDPs indexed by a context variable. While CMDPs serve…

Machine Learning · Computer Science 2024-02-06 Junze Deng , Yuan Cheng , Shaofeng Zou , Yingbin Liang

Identifying directed interactions between species from time series of their population densities has many uses in ecology. This key statistical task is equivalent to causal time series inference, which connects to the Granger causality (GC)…

Populations and Evolution · Quantitative Biology 2020-11-10 Frederic Barraquand , Coralie Picoche , Matteo Detto , Florian Hartig

Markov Chain Monte Carlo (MCMC) methods have become a cornerstone of many modern scientific analyses by providing a straightforward approach to numerically estimate uncertainties in the parameters of a model using a sequence of random…

Other Statistics · Statistics 2020-03-10 Joshua S. Speagle

Standard supervised learning breaks down under data distribution shift. However, the principle of independent causal mechanisms (ICM, Peters et al. (2017)) can turn this weakness into an opportunity: one can take advantage of distribution…

Machine Learning · Computer Science 2021-02-09 Jens Müller , Robert Schmier , Lynton Ardizzone , Carsten Rother , Ullrich Köthe

Sequential dynamics are a key feature of many modern recommender systems, which seek to capture the `context' of users' activities on the basis of actions they have performed recently. To capture such patterns, two approaches have…

Information Retrieval · Computer Science 2018-08-30 Wang-Cheng Kang , Julian McAuley

Models for open quantum systems, which play important roles in electron transport problems and quantum computing, must take into account the interaction of the quantum system with the surrounding environment. Although such models can be…

Quantum Physics · Physics 2024-07-17 Ke Wang , Xiantao Li

Motivated by multiple applications in social networks, nervous systems, and financial risk analysis, we consider the problem of learning the underlying (directed) influence graph or causal graph of a high-dimensional multivariate…

Machine Learning · Computer Science 2024-06-14 Smita Bagewadi , Avhishek Chatterjee