Related papers: Unranking permutations in transposition order and …
Given a set $\Pi$ of permutation patterns of length at most $k$, we present an algorithm for building $S_{\le n}(\Pi)$, the set of permutations of length at most $n$ avoiding the patterns in $\Pi$, in time $O(|S_{\le n - 1}(\Pi)| \cdot k +…
In [4] we describe a variation of the classical permutation decoding algorithm that can be applied to any binary affine-invariant code; in particular, it can be applied to first-order Reed-Muller codes successfully. In this paper we study…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
This paper addresses the general problem of modelling and learning rank data with ties. We propose a probabilistic generative model, that models the process as permutations over partitions. This results in super-exponential combinatorial…
The method for analyzing algorithmic runtime complexity using decision trees is discussed using the sorting algorithm. This method is then extended to optimal algorithms which may find all cliques of size q in network N, or simply the first…
Let $s$ be West's deterministic stack-sorting map. A well-known result (West) is that any length $n$ permutation can be sorted with $n-1$ iterations of $s.$ In 2020, Defant introduced the notion of highly-sorted permutations -- permutations…
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 describe a seriation algorithm for ranking a set of items given pairwise comparisons between these items. Intuitively, the algorithm assigns similar rankings to items that compare similarly with all others. It does so by constructing a…
Sorting a Permutation by Transpositions (SPbT) is an important problem in Bioinformtics. In this paper, we improve the running time of the best known approximation algorithm for SPbT. We use the permutation tree data structure of Feng and…
We consider the set of permutations that are sorted after two passes through a pop stack. We characterize these permutations in terms of forbidden patterns (classical and barred) and enumerate them according to the ascent statistic. Then we…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
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…
In a quaternion order of class number one, an element can be factored in multiple ways depending on the order of the factorization of its reduced norm. The fact that multiplication is not commutative causes an element to induce a…
Given a signed permutation on $n$ elements, we need to sort it with the fewest reversals. This is a fundamental algorithmic problem motivated by applications in comparative genomics, as it allows to accurately model rearrangements in small…
In 1937, biologists Sturtevant and Tan posed a computational question: transform a chromosome represented by a permutation of genes, into a second permutation, using a minimum-length sequence of reversals, each inverting the order of a…
We present an iterative algorithm, called the symmetric tensor eigen-rank-one iterative decomposition (STEROID), for decomposing a symmetric tensor into a real linear combination of symmetric rank-1 unit-norm outer factors using only…
We introduce a lifting of West's stack-sorting map $s$ to partition diagrams, which are combinatorial objects indexing bases of partition algebras. Our lifting $\mathscr{S}$ of $s$ is such that $\mathscr{S}$ behaves in the same way as $s$…
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…
We introduce forest straight-line programs (FSLPs) as a compressed representation of unranked ordered node-labelled trees. FSLPs are based on the operations of forest algebra and generalize tree straight-line programs. We compare the…