Related papers: Duplication Distance to the Root for Binary Sequen…
Binary periodic sequences with good autocorrelation property have many applications in many aspects of communication. In past decades many series of such binary sequences have been constructed. In the application of cryptography, such…
In this work, we derive upper bounds on the cardinality of tandem duplication and palindromic deletion correcting codes by deriving the generalized sphere packing bound for these error types. We first prove that an upper bound for tandem…
We give cell-probe bounds for the computation of edit distance, Hamming distance, convolution and longest common subsequence in a stream. In this model, a fixed string of $n$ symbols is given and one $\delta$-bit symbol arrives at a time in…
We study the problems of finding a shortest synchronizing word and its length for a given prefix code. This is done in two different settings: when the code is defined by an arbitrary decoder recognizing its star and when the code is…
Computing the rotation distance between two binary trees with $n$ internal nodes efficiently (in $poly(n)$ time) is a long standing open question in the study of height balancing in tree data structures. In this paper, we initiate the study…
Correlation measure of order $k$ is an important measure of randomness in binary sequences. This measure tries to look for dependence between several shifted version of a sequence. We study the relation between the correlation measure of…
This paper introduces the sequence covering similarity, that we formally define for evaluating the similarity between a symbolic sequence (string) and a set of symbolic sequences (strings). From this covering similarity we derive a…
We consider the problem of distributed binary hypothesis testing of two sequences that are generated by an i.i.d. doubly-binary symmetric source. Each sequence is observed by a different terminal. The two hypotheses correspond to different…
Given two strings $A[1..n]$ and $B[1..m]$, and a set of operations allowed to edit the strings, the edit distance between $A$ and $B$ is the minimum number of operations required to transform $A$ into $B$. Sequentially, a standard Dynamic…
There is a unique path from the root of a tree to any other vertex. Every vertex, except the root, has a parent: the adjoining vertex on this unique path. This is the conventional definition of the parent vertex. For complete binary trees,…
We develop combinatorial methods for computing the rotation distance between binary trees, i.e., equivalently, the flip distance between triangulations of a polygon. As an application, we prove that, for each n, there exist size n trees at…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
Symbol-pair codes are proposed to protect against pair errors in symbol-pair read channels. One of the most important task in symbol-pair coding theory is to determine the minimum pair-distance of symbol-pair codes. In this paper, we…
We consider the classical sequential binary hypothesis testing problem in which there are two hypotheses governed respectively by distributions $P_0$ and $P_1$ and we would like to decide which hypothesis is true using a sequential test. It…
We study various aspects of Dyck words appearing in binary sequences, where $0$ is treated as a left parenthesis and $1$ as a right parenthesis. We show that binary words that are $7/3$-power-free have bounded nesting level, but this no…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
Symbol-pair codes are proposed to combat pair-errors in symbol-pair read channels. The minimum symbol-pair distance is of significance in determining the error-correcting capability of a symbol-pair code. Maximum distance separable (MDS)…
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…
In Soda'06, Chaudhuri, Chen, Mihaescu and Rao study algorithmic properties of the tandem duplication - random loss model of genome rearrangement, well-known in evolutionary biology. In their model, the cost of one step of duplication-loss…
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…