Related papers: A Fixed-Parameter Algorithm for Minimum Common Str…
We study the problem of partitioning a given simple polygon $P$ into a minimum number of connected polygonal pieces, each of bounded size. We describe a general technique for constructing such partitions that works for several notions of…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
In this study, we address the problem of clustering string data in an unsupervised manner by developing a theory of a mixture model and an EM algorithm for string data based on probability theory on a topological monoid of strings developed…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
Two kinds of approximation algorithms exist for the k-BALANCED PARTITIONING problem: those that are fast but compute unsatisfying approximation ratios, and those that guarantee high quality ratios but are slow. In this paper we prove that…
We study the problem of finding a maximum cardinality minimal separator of a graph. This problem is known to be NP-hard even for bipartite graphs. In this paper, we strengthen this hardness by showing that for planar bipartite graphs, the…
In this paper, we present an efficient algorithm to sample random sparse matrices to be used as check matrices for quantum Low-Density Parity-Check (LDPC) codes. To ease the treatment, we mainly describe our algorithm as a technique to…
We consider the minimal k-grouping problem: given a graph G=(V,E) and a constant k, partition G into subgraphs of diameter no greater than k, such that the union of any two subgraphs has diameter greater than k. We give a silent…
The NP-hard general factor problem asks, given a graph and for each vertex a list of integers, whether the graph has a spanning subgraph where each vertex has a degree that belongs to its assigned list. The problem remains NP-hard even if…
In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
There has been surprisingly little work on algorithms for sorting strings on distributed-memory parallel machines. We develop efficient algorithms for this problem based on the multi-way merging principle. These algorithms inspect only…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
We study the optimization version of the set partition problem (where the difference between the partition sums are minimized), which has numerous applications in decision theory literature. While the set partitioning problem is NP-hard and…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…