On local time for Markov chains

Local Alignment of Markov Chains

We consider local alignments without gaps of two independent Markov chains from a finite alphabet, and we derive sufficient conditions for the number of essentially different local alignments with a score exceeding a high threshold to be asymptotically Poisson distributed. From the Poisson approximation a Gumbel approximation of the maximal local alignment score is obtained. The results extend ...

Continuos Time Markov Chains

Continuous Time Markov Chains

Discrete-time Markov chains are useful in simulation, since updating algorithms are easier to construct in discrete steps. They can also be useful as crude models of physical, biological, and social processes. However, in the physical and biological worlds time runs continuously, and so discrete-time mathematical models are not always appropriate. This is especially true in population biology –...

Continuous-time Markov Chains

Taylor Expansion for the Entropy Rate of Hidden Markov Chains

We study the entropy rate of a hidden Markov process, defined by observing the output of a symmetric channel whose input is a first order Markov process. Although this definition is very simple, obtaining the exact amount of entropy rate in calculation is an open problem. We introduce some probability matrices based on Markov chain's and channel's parameters. Then, we try to obtain an estimate ...