Related papers: On the Variance of the Optimal Alignments Score fo…
Considering the optimal alignment of two i.i.d. random sequences of length $n$, we show that when the scoring function is chosen randomly, almost surely the empirical distribution of aligned letter pairs in all optimal alignments converges…
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…
We consider two independent binary i.i.d. random strings $X$ and $Y$ of equal length $n$ and the optimal alignments according to a symmetric scoring functions only. We decompose the space of scoring functions into five components. Two of…
Considering two optimally aligned random sequences, we investigate the effect on the alignment score caused by changing a random letter in one of the two sequences. Using this idea in conjunction with large deviations theory, we show that…
We present a general approach to the problem of determining the asymptotic order of the variance of the optimal score between two independent random sequences defined over an arbitrary finite alphabet. Our general approach is based on…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
Consider finite sequences $X_{[1,n]}=X_1\dots X_n$ and $Y_{[1,n]}=Y_1\dots Y_n$ of length $n$, consisting of i.i.d.\ samples of random letters from a finite alphabet, and let $S$ and $T$ be chosen i.i.d.\ randomly from the unit ball in the…
We present a general approach to the problem of determining tight asymptotic lower bounds for generalized central moments of the optimal alignment score of two independent sequences of i.i.d. random variables. At first, these are obtained…
The problem of determining the correct order of fluctuation of the optimal alignment score of two random strings of length $n$ has been open for several decades. It is known that the biased expected effect of a random letter-change on the…
Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…
It is often stated that human languages, as other biological systems, are shaped by cost-cutting pressures but, to what extent? Attempts to quantify the degree of optimality of languages by means of an optimality score have been scarce and…
We investigate the order of the $r$-th, $1\le r < +\infty$, central moment of the length of the longest common subsequence of two independent random words of size $n$ whose letters are identically distributed and independently drawn from a…
We consider the set of finite random words $\mathcal A^\star$, with independent letters drawn from a finite or infinite totally ordered alphabet according to a general probability distribution. On a specific subset of $\mathcal A^\star$,…
We investigate the behavior of optimal alignment paths for homologous (related) and independent random sequences. An alignment between two finite sequences is optimal if it corresponds to the longest common subsequence (LCS). We prove the…
The distributions of the $m$-th longest runs of multivariate random sequences are considered. For random sequences made up of $k$ kinds of letters, the lengths of the runs are sorted in two ways to give two definitions of run length…
We characterize the optimal reward functions (scoring rules) that incentivize an agent to acquire information and report it truthfully to the principal. The optimal scoring rules let the agent make a simple binary bet in single-dimensional…
We study the space requirements of a sorting algorithm where only items that at the end will be adjacent are kept together. This is equivalent to the following combinatorial problem: Consider a string of fixed length n that starts as a…
Simon's congruence $\sim_k$ is defined as follows: two words are $\sim_k$-equivalent if they have the same set of subsequences of length at most $k$. We propose an algorithm which computes, given two words $s$ and $t$, the largest $k$ for…
Sparse linear discriminant analysis via penalized optimal scoring is a successful tool for classification in high-dimensional settings. While the variable selection consistency of sparse optimal scoring has been established, the…
The task of the binary classification problem is to determine which of two distributions has generated a length-$n$ test sequence. The two distributions are unknown; two training sequences of length $N$, one from each distribution, are…