Related papers: De Bruijn Sequences with Minimum Discrepancy
Given a string $w$, another string $v$ is said to be a subsequence of $w$ if $v$ can be obtained from $w$ by removing some of its letters; on the other hand, $v$ is called an absent subsequence of $w$ if $v$ is not a subsequence of $w$. The…
The problem is considered of arranging symbols around a cycle, in such a way that distances between different instances of a same symbol be as uniformly distributed as possible. A sequence of moments is defined for cycles, similarly to the…
Completely antipersistent binary time series are sequences in which every time that an $N$-bit string $\mu$ appears, the sequence is continued with a different bit than at the last occurrence of $\mu$. This dynamics is phrased in terms of a…
A de Bruijn sequence of order $k$ over a finite alphabet is a cyclic sequence with the property that it contains every possible $k$-sequence as a substring exactly once. Orthogonal de Bruijn sequences are collections of de Bruijn sequences…
We study codes that can detect the exact number of deletions and insertions in concatenated binary strings. We construct optimal codes for the case of detecting up to $\del$ deletions. We prove the optimality of these codes by deriving a…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
We introduce two notions of discrepancy between binary vectors, which are not metric functions in general but nonetheless capture the mathematical structure of the binary asymmetric channel. In turn, these lead to two new fundamental…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
We investigate the order of the variance of the optimal alignments score of two independent iid binary random words having the same length. The letters are equiprobable, but the scoring function is such that one letter has a larger score…
An $(m,n,R)$-de Bruijn covering array (dBCA) is a doubly periodic $M \times N$ array over an alphabet of size $q$ such that the set of all its $m \times n$ windows form a covering code with radius $R$. An upper bound of the smallest array…
What is the length of the shortest sequence $S$ of reals so that the set of consecutive $n$-words in $S$ form a covering code for permutations on $\{1,2, >..., n\}$ of radius $R$ ? (The distance between two $n$-words is the number of…
In parametric sequence alignment, optimal alignments of two sequences are computed as a function of the penalties for mismatches and spaces, producing many different optimal alignments. Here we give a 3/(2^{7/3}\pi^{2/3})n^{2/3} +O(n^{1/3}…
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…
We give three different computations of the total number of runs of length $i$ in binary $n$-strings, and we discuss the connection of this problem with the compositions of $n$.
The discrepancy of a sequence measures how quickly it approaches a uniform distribution. Given a natural number $d$, any collection of one-dimensional so-called low discrepancy sequences $\left\{S_i:1\le i \le d\right\}$ can be concatenated…
All codes with minimum distance 8 and codimension up to 14 and all codes with minimum distance 10 and codimension up to 18 are classified. Nonexistence of codes with parameters [33,18,8] and [33,14,10] is proved. This leads to 8 new exact…
Distribution matching is the process of invertibly mapping a uniformly distributed input sequence onto sequences that approximate the output of a desired discrete memoryless source. The special case of a binary output alphabet and…
Aperiodic autocorrelation is an important indicator of performance of sequences used in communications, remote sensing, and scientific instrumentation. Knowing a sequence's autocorrelation function, which reports the autocorrelation at…
We devise an analytically simple as well as invertible approximate expression, which describes the relation between the minimum distance of a binary code and the corresponding maximum attainable code-rate. For example, for a rate-(1/4),…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…