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Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have…

Molecular Networks · Quantitative Biology 2016-10-19 Brian K. Chu , Margaret J. Tse , Royce R. Sato , Elizabeth L. Read

Motivated by disease progression-related studies, we propose an estimation method for fitting general non-homogeneous multi-state Markov models. The proposal can handle many types of multi-state processes, with several states and various…

Methodology · Statistics 2024-07-22 Alessia Eletti , Giampiero Marra , Rosalba Radice

Time series modeling is a well-established problem, which often requires that methods (1) expressively represent complicated dependencies, (2) forecast long horizons, and (3) efficiently train over long sequences. State-space models (SSMs)…

Machine Learning · Computer Science 2023-03-17 Michael Zhang , Khaled K. Saab , Michael Poli , Tri Dao , Karan Goel , Christopher Ré

State-space models (SSMs) have garnered attention for effectively processing long data sequences, reducing the need to segment time series into shorter intervals for model training and inference. Traditionally, SSMs capture only the…

Machine Learning · Computer Science 2024-07-26 Xuan-The Tran , Linh Le , Quoc Toan Nguyen , Thomas Do , Chin-Teng Lin

Many state of the art methods for the thermodynamic and kinetic characterization of large and complex biomolecular systems by simulation rely on ensemble approaches, where data from large numbers of relatively short trajectories are…

Data Analysis, Statistics and Probability · Physics 2017-04-05 Feliks Nüske , Hao Wu , Jan-Hendrik Prinz , Christoph Wehmeyer , Cecilia Clementi , Frank Noé

Modern time series data often display complex nonlinear dependencies along with irregular regime-switching behaviors. These features present technical challenges in modeling, inference, and in offering insightful understanding into the…

Machine Learning · Computer Science 2025-01-13 Xiuqin Xu , Hanqiu Peng , Ying Chen

Identifiability is central to the interpretability of deep latent variable models, ensuring parameterisations are uniquely determined by the data-generating distribution. However, it remains underexplored for deep regime-switching time…

Machine Learning · Statistics 2026-01-08 Carles Balsells-Rodas , Toshiko Matsui , Pedro A. M. Mediano , Yixin Wang , Yingzhen Li

Switching state-space models (SSSM) are a very popular class of time series models that have found many applications in statistics, econometrics and advanced signal processing. Bayesian inference for these models typically relies on Markov…

Computation · Statistics 2010-11-11 Nick Whiteley , Christophe Andrieu , Arnaud Doucet

In the post-deep learning era, the Transformer architecture has demonstrated its powerful performance across pre-trained big models and various downstream tasks. However, the enormous computational demands of this architecture have deterred…

This paper proposes a stochastic model using the concept of Markov chains for the inter-state transitions of the millisecond order quasi-stable phase synchronized patterns or synchrostates, found in multi-channel Electroencephalogram (EEG)…

Neurons and Cognition · Quantitative Biology 2014-10-21 Wasifa Jamal , Saptarshi Das , Ioana-Anastasia Oprescu , Koushik Maharatna

Markov switching models (MSMs) are probabilistic models that employ multiple sets of parameters to describe different dynamic regimes that a time series may exhibit at different periods of time. The switching mechanism between regimes is…

Machine Learning · Statistics 2019-09-13 Silvia Chiappa

State Space Models (SSMs) have emerged as a promising alternative to the popular transformer-based models and have been increasingly gaining attention. Compared to transformers, SSMs excel at tasks with sequential data or longer contexts,…

Machine Learning · Computer Science 2025-03-17 Xingtai Lv , Youbang Sun , Kaiyan Zhang , Shang Qu , Xuekai Zhu , Yuchen Fan , Yi Wu , Ermo Hua , Xinwei Long , Ning Ding , Bowen Zhou

Switching ARMA models greatly enhance the standard linear models to the extent that different ARMA model is allowed in a different regime, and the regime switching is typically assumed a Markov chain on the finite states of potential…

Statistics Theory · Mathematics 2007-06-13 Gopal K. Basak , Zhan-Qian Lu

State space models (SSMs) have recently emerged as a powerful framework for long sequence processing, outperforming traditional methods on diverse benchmarks. Fundamentally, SSMs can generalize both recurrent and convolutional networks and…

Signal Processing · Electrical Eng. & Systems 2025-12-24 Xiaoyu Zhang , Mingtao Hu , Sen Lu , Soohyeon Kim , Eric Yeu-Jer Lee , Yuyang Liu , Wei D. Lu

The field of deep-learning-based ECG analysis has been largely dominated by convolutional architectures. This work explores the prospects of applying the recently introduced structured state space models (SSMs) as a particularly promising…

Machine Learning · Computer Science 2022-11-15 Temesgen Mehari , Nils Strodthoff

State Space Models (SSM) is a MATLAB 7.0 software toolbox for doing time series analysis by state space methods. The software features fully interactive construction and combination of models, with support for univariate and multivariate…

Computation · Statistics 2007-06-26 Jyh-Ying Peng , John A. D. Aston

This paper considers estimating the parameters in a regime-switching stochastic differential equation(SDE) driven by Normal Inverse Gaussian(NIG) noise. The model under consideration incorporates a continuous-time finite state Markov chain…

Computation · Statistics 2024-12-10 Yuzhong Cheng , Hiroki Masuda

State space models (SSMs) are a flexible approach to modeling complex time series. However, inference in SSMs is often computationally prohibitive for long time series. Stochastic gradient MCMC (SGMCMC) is a popular method for scalable…

Machine Learning · Statistics 2019-07-11 Christopher Aicher , Yi-An Ma , Nicholas J. Foti , Emily B. Fox

This paper considers maximum likelihood (ML) estimation in a large class of models with hidden Markov regimes. We investigate consistency of the ML estimator and local asymptotic normality for the models under general conditions which allow…

Statistics Theory · Mathematics 2021-12-07 Demian Pouzo , Zacharias Psaradakis , Martin Sola

We develop efficient simulation techniques for Bayesian inference on switching GARCH models. Our contribution to existing literature is manifold. First, we discuss different multi-move sampling techniques for Markov Switching (MS) state…

Statistics Theory · Mathematics 2012-12-24 Monica Billio , Roberto Casarin , Anthony Osuntuyi