Related papers: Average-case analysis of perfect sorting by revers…
We describe an implementation of a genetic algorithm on partially commutative groups and apply it to the double coset search problem on a subclass of groups. This transforms a combinatorial group theory problem to a problem of combinatorial…
Over the past decade, random forest models have become widely used as a robust method for high-dimensional data regression tasks. In part, the popularity of these models arises from the fact that they require little hyperparameter tuning…
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…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
The NP-complete Permutation Pattern Matching problem asks whether a $k$-permutation $P$ is contained in a $n$-permutation $T$ as a pattern. This is the case if there exists an order-preserving embedding of $P$ into $T$. In this paper, we…
The Permutation Pattern Matching problem, asking whether a pattern permutation $\pi$ is contained in a permutation $\tau$, is known to be NP-complete. In this paper we present two polynomial time algorithms for special cases. The first…
Theorems relating permutations with objects in other fields of mathematics are often stated in terms of avoided patterns. Examples include various classes of Schubert varieties from algebraic geometry (Billey and Abe 2013), commuting…
We study sorting in the evolving data model, introduced by [AKMU11], where the true total order changes while the sorting algorithm is processing the input. More precisely, each comparison operation of the algorithm is followed by a…
In comparative genomics, a transposition is an operation that exchanges two consecutive sequences of genes in a genome. The transposition distance, that is, the minimum number of transpositions needed to transform a genome into another, is,…
We study very simple sorting algorithms based on a probabilistic comparator model. In our model, errors in comparing two elements are due to (1) the energy or effort put in the comparison and (2) the difference between the compared…
The Subset Sum Problem is a fundamental NP-complete problem in cryptography and combinatorial optimization, with many real-world applications. The Random Subset Sum Problem (RSSP) is a more applicable version of subset sum, where numbers…
Poisson restart assumes that a stochastic process is interrupted and starts again at random time moments. A number of studies have demonstrated that this strategy may minimize the expected completion time in some classes of random search…
An occurrence of a classical pattern p in a permutation \pi is a subsequence of \pi whose letters are in the same relative order (of size) as those in p. In an occurrence of a generalized pattern, some letters of that subsequence may be…
Sorting is one of the oldest computing problems and is still very important in the age of big data. Various algorithms and implementation techniques have been proposed. In this study, we focus on comparison based, internal sorting…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
In this paper, we combine the operator splitting methodology for abstract evolution equations with that of stochastic methods for large-scale optimization problems. The combination results in a randomized splitting scheme, which in a given…
Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, etc. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a…
The permutation test is known as the exact test procedure in statistics. However, often it is not exact in practice and only an approximate method since only a small fraction of every possible permutation is generated. Even for a small…
Generalizing stack sorting and $c$-sorting for permutations, we define the permutree sorting algorithm. Given two disjoint subsets $U$ and $D$ of $\{2, \dots, n-1\}$, the $(U,D)$-permutree sorting tries to sort the permutation $\pi \in…
The problem of aligning Erd\"os-R\'enyi random graphs is a noisy, average-case version of the graph isomorphism problem, in which a pair of correlated random graphs is observed through a random permutation of their vertices. We study a…