Related papers: Simulations, Computations, and Statistics for Long…
Markov chain Monte Carlo (MCMC) simulations are commonly employed for estimating features of a target distribution, particularly for Bayesian inference. A fundamental challenge is determining when these simulations should stop. We consider…
Sequential Monte Carlo (SMC) methods are a class of Monte Carlo methods that are used to obtain random samples of a high dimensional random variable in a sequential fashion. Many problems encountered in applications often involve different…
The purpose of this paper is to study a statistic that is used to compare the similarity between two strings, which is first introduced by Michael Steele in 1982. It was proposed as an alternative to the length of the longest common…
This paper considers the inference of trends in multiple, nonstationary time series. To test whether trends are parallel to each other, we use a parallelism index based on the L2-distances between nonparametric trend estimators and their…
By facilitating the generation of samples from arbitrary probability distributions, Markov Chain Monte Carlo (MCMC) is, arguably, \emph{the} tool for the evaluation of Bayesian inference problems that yield non-standard posterior…
Weighted histograms in Monte Carlo simulations are often used for the estimation of probability density functions. They are obtained as a result of random experiments with random events that have weights. In this paper, the bin contents of…
The problem of the fluctuation of the Longest Common Subsequence (LCS) of two i.i.d. sequences of length $n>0$ has been open for decades. There exist contradicting conjectures on the topic. Chvatal and Sankoff conjectured in 1975 that…
Monte Carlo method is a broad class of computational algorithms that rely on repeated random sampling to obtain numerical results. They are often used in physical and mathematical problems and are most useful when it is difficult or…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…
We investigate the variance of the length of the longest common subsequences of two independent random words of size $n$, where the letters of one word are i.i.d. uniformly drawn from $\{\alpha_1, \alpha_2, \cdots, \alpha_m\}$, while the…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…
Let $A$ and $B$ be two number sequences of length $n$ and $m$, respectively, where $m\le n$. Given a positive number $\delta$, a common almost increasing sequence $s_1\ldots s_k$ is a common subsequence for both $A$ and $B$ such that for…
In the problem of the longest common substring with $k$ mismatches we are given two strings $X, Y$ and must find the maximal length $\ell$ such that there is a length-$\ell$ substring of $X$ and a length-$\ell$ substring of $Y$ that differ…
We present a practical algorithm for the cyclic longest common subsequence (CLCS) problem that runs in O(mn) time, where m and n are the lengths of the two input strings. While this is not necessarily an asymptotic improvement over the…
Many-shot in-context learning (ICL) has emerged as a unique setup to both utilize and test the ability of large language models to handle long context. This paper delves into long-context language model (LCLM) evaluation through many-shot…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
In the realm of Large Language Model (LLM) functionalities, providing reliable information is paramount, yet reports suggest that LLM outputs lack consistency. This inconsistency, often at-tributed to randomness in token sampling,…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
An introduction to the basics of Monte Carlo is given. The topics covered include, sample space, events, probabilities, random variables, mean, variance, covariance, characteristic function, chebyshev inequality, law of large numbers,…