Related papers: Sorting Genomes by Prefix Double-Cut-and-Joins
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
The trie-based radix sort algorithm stores pairwise different infinite binary strings in the leaves of a binary tree in a way that the Ulam-Harris coding of each leaf equals a prefix (that is, an initial segment) of the corresponding…
When solving numerical constraints such as nonlinear equations and inequalities, solvers often exploit pruning techniques, which remove redundant value combinations from the domains of variables, at pruning steps. To find the complete…
We investigate unification problems related to the Cipher Block Chaining (CBC) mode of encryption. We first model chaining in terms of a simple, convergent, rewrite system over a signature with two disjoint sorts: list and element. By…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
A new algorithm, Guidesort, for sorting in the uniprocessor variant of the parallel disk model (PDM) of Vitter and Shriver is presented. The algorithm is deterministic and executes a number of (parallel) I/O operations that comes within a…
This paper is an extended abstract of an analysis of term rewriting where the terms in the rewrite rules as well as the term to be rewritten are compressed by a singleton tree grammar (STG). This form of compression is more general than…
Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
We present a new algorithm to explore or count the numerical semigroups of a given genus which uses the unleaved version of the tree of numerical semigroups. In the unleaved tree there are no leaves rather than the ones at depth equal to…
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…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
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…
The canonical tree-decomposition theorem, given by Robertson and Seymour in their seminal graph minors series, turns out to be one of the most important tool in structural and algorithmic graph theory. In this paper, we provide the…
Modern approaches for semantic segmentation usually employ dilated convolutions in the backbone to extract high-resolution feature maps, which brings heavy computation complexity and memory footprint. To replace the time and memory…
We study a class of bilevel integer programs with second-order cone constraints at the upper level and a convex quadratic objective and linear constraints at the lower level. We develop disjunctive cuts to separate bilevel infeasible points…
In this paper we design {\sf FPT}-algorithms for two parameterized problems. The first is \textsc{List Digraph Homomorphism}: given two digraphs $G$ and $H$ and a list of allowed vertices of $H$ for every vertex of $G$, the question is…
As an essential operation in data cleaning, the similarity join has attracted considerable attention from the database community. In this paper, we study string similarity joins with edit-distance constraints, which find similar string…