相关论文: Mismatch Repair Error Implies Chargaff's Second Pa…

We consider two types of discrete-time Markov chains where the state space is a graded poset and the transitions are taken along the covering relations in the poset. The first type of Markov chain goes only in one direction, either up or…

Matching entries of correlated shuffled databases have practical applications ranging from privacy to biology. In this paper, motivated by synchronization errors in the sampling of time-indexed databases, matching of random databases under…

We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…

In the paper, we study a new rate of convergence estimate for homogeneous discrete-time nonlinear Markov chains based on the Markov-Dobrushin condition. This result generalizes the convergence estimates for any positive number of transition…

When the process underlying DNA substitutions varies across evolutionary history, the standard Markov models underlying standard phylogenetic methods are mathematically inconsistent. The most prominent example is the general time reversible…

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…

We consider the problem of learning a policy for a Markov decision process consistent with data captured on the state-actions pairs followed by the policy. We assume that the policy belongs to a class of parameterized policies which are…

The change detection problem is to determine if the Markov network structures of two Markov random fields differ from one another given two sets of samples drawn from the respective underlying distributions. We study the trade-off between…

The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…

We study plane trees as a model for RNA secondary structure, assigning energy to each tree based on the Nearest Neighbor Thermodynamic Model, and defining a corresponding Gibbs distribution on the trees. Through a bijection between plane…

We describe an exact test of the null hypothesis that a Markov chain is nth order versus the alternate hypothesis that it is $(n+1)$-th order. The procedure does not rely on asymptotic properties, but instead builds up the test statistic…

The information reconstruction problem on an infinite tree, is to collect and analyze massive data samples at the $n$th level of the tree to identify whether there is non-vanishing information of the root, as $n$ goes to infinity. This…

This paper analyzes a (1, $\lambda$)-Evolution Strategy, a randomized comparison-based adaptive search algorithm, optimizing a linear function with a linear constraint. The algorithm uses resampling to handle the constraint. Two cases are…

We establish a large deviation principle for the empirical measure process associated with a general class of finite-state mean field interacting particle systems with Lipschitz continuous transition rates that satisfy a certain ergodicity…

Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…

This paper develops a two gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by $ \sigma_{via} $, yields a…

An algorithm is proposed for computing equilibrium averages of Markov chains which suffer from metastability -- the tendency to remain in one or more subsets of state space for long time intervals. The algorithm, called the parallel replica…

The nuclear Chirality-Parity (ChP) violation, a simultaneous breaking of chiral and reflection symmetries in the intrinsic frame, is investigated with a reflection-asymmetric triaxial particle rotor model. A new symmetry for an ideal ChP…

DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent…

A theory of systems with long-range correlations based on the consideration of binary N-step Markov chains is developed. In our model, the conditional probability that the i-th symbol in the chain equals zero (or unity) is a linear function…