Related papers: Inference of higher order substitution dynamics by…
Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…
Rule-based modelling allows to represent molecular interactions in a compact and natural way. The underlying molecular dynamics, by the laws of stochastic chemical kinetics, behaves as a continuous-time Markov chain. However, this Markov…
A lumping of a Markov chain is a coordinate-wise projection of the chain. We characterise the entropy rate preservation of a lumping of an aperiodic and irreducible Markov chain on a finite state space by the random growth rate of the…
In this paper, we explore a general Aggregated Gradient Langevin Dynamics framework (AGLD) for the Markov Chain Monte Carlo (MCMC) sampling. We investigate the nonasymptotic convergence of AGLD with a unified analysis for different data…
Complex systems made of interacting elements are commonly abstracted as networks, in which nodes are associated with dynamic state variables, whose evolution is driven by interactions mediated by the edges. Markov processes have been the…
We introduce LAMP: the Linear Additive Markov Process. Transitions in LAMP may be influenced by states visited in the distant history of the process, but unlike higher-order Markov processes, LAMP retains an efficient parametrization. LAMP…
A class of Monte Carlo algorithms which incorporate absorbing Markov chains is presented. In a particular limit, the lowest-order of these algorithms reduces to the $n$-fold way algorithm. These algorithms are applied to study the escape…
We construct different classes of lumpings for a family of Markov chain products which reflect the structure of a given finite poset. We use essentially combinatorial methods. We prove that, for such a product, every lumping can be obtained…
Detecting broken time-reversibility at micro- and nanoscale is often difficult when experiments offer limited state resolution. We introduce a lumping method that builds an effective semi-Markov model able to reproduce exactly the full…
A function on the state space of a Markov chain is a "lumping" if observing only the function values gives a Markov chain. We give very general conditions for lumpings of a large class of algebraically-defined Markov chains, which include…
Langevin algorithms are popular Markov chain Monte Carlo methods that are often used to solve high-dimensional large-scale sampling problems in machine learning. The most classical Langevin Monte Carlo algorithm is based on the overdamped…
The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same…
We propose a new Markov chain Monte Carlo method in which trial configurations are generated by evolving a state, sampled from a prior distribution, using a Markov transition matrix. We present two prototypical algorithms and derive their…
Kingman derived the Ewens sampling formula for random partitions describing the genetic variation in a neutral mutation model defined by a Poisson process of mutations along lines of descent governed by a simple coalescent process, and…
The embedding problem of Markov transition matrices into continuous-time Markov semigroups is a classic problem that regained a lot of impetus and activities in recent years. We consider it here for the following generalisation of the…
Markov Chain Monte Carlo (MCMC) algorithms are often used for approximate inference inside learning, but their slow mixing can be difficult to diagnose and the approximations can seriously degrade learning. To alleviate these issues, we…
Continuous-time Markov chains on non-negative integers can be used for modeling biological systems, population dynamics, and queueing models. Qualitative behaviors of birth-and-death models, typical examples of such one-dimensional…
We describe a class of growth algorithms for finding low energy states of heteropolymers. These polymers form toy models for proteins, and the hope is that similar methods will ultimately be useful for finding native states of real proteins…
We study the class structure of finite-alphabet Markov chains with arbitrary memory length. To capture the structural constraints induced by prohibited transitions, we introduce the skeleton of a higher-order transition kernel, defined as a…
We present a first-order aggregation model on the space of complex matrices which can be derived from the Lohe tensor model on the space of tensors with the same rank and size. We call such matrix-valued aggregation model as "the…