Related papers: Combinatorics of Palindromes
So far, a very large amount of work in Natural Language Processing (NLP) rely on trees as the core mathematical structure to represent linguistic informations (e.g. in Chomsky's work). However, some linguistic phenomena do not cope properly…
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…
We propose a new deep recurrent neural network (RNN) architecture for sequential signal reconstruction. Our network is designed by unfolding the iterations of the proximal gradient method that solves the l1-l1 minimization problem. As such,…
Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…
We consider a problem of enumerating chemical graphs from given constraints concerning their structures, which has an important application to a novel method for the inverse QSAR/QSPR recently proposed. In this paper, the structure of a…
It is known that the size of the largest common subtree (i.e., the maximum agreement subtree) of two independent random binary trees with $n$ given labeled leaves is of order between $n^{0.366}$ and $n^{1/2}$. We improve the lower bound to…
We investigate the descriptional complexity of limited propagating Lindenmayer systems and their deterministic and tabled variants with respect to the number of rules and the number of symbols. We determine the decrease of complexity when…
We construct maximally recoverable codes (corresponding to partial MDS codes) which are based on linearized Reed-Solomon codes. The new codes have a smaller field size requirement compared with known constructions. For certain asymptotic…
Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…
The graph reconstruction problem has been extensively studied under various query models. In this paper, we propose a new query model regarding the number of connected components, which is one of the most basic and fundamental graph…
We present a method for the reconstruction of networks, based on the order of nodes visited by a stochastic branching process. Our algorithm reconstructs a network of minimal size that ensures consistency with the data. Crucially, we show…
Learning to predict solutions to real-valued combinatorial graph problems promises efficient approximations. As demonstrated based on the NP-hard edge clique cover number, recurrent neural networks (RNNs) are particularly suited for this…
We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…
We consider the following graph reconstruction problem: given an unweighted connected graph $G = (V,E)$ with visible vertex set $V$ and an oracle which takes two vertices $u,v \in V$ and returns the shortest path distance between $u$ and…
The register function (or Horton-Strahler number) of a binary tree is a well-known combinatorial parameter. We study a reduction procedure for binary trees which offers a new interpretation for the register function as the maximal number of…
We give new lower bounds for $M(n,d)$, for various positive integers $n$ and $d$ with $n>d$, where $M(n,d)$ is the largest number of permutations on $n$ symbols with pairwise Hamming distance at least $d$. Large sets of permutations on $n$…
In this paper we study detection and reconstruction of planted structures in Erd\H{o}s-R\'enyi random graphs. Motivated by a problem of communication security, we focus on planted structures that consist in a tree graph. For planted line…
We introduce a new model of indeterminacy in graphs: instead of specifying all the edges of the graph, the input contains all triples of vertices that form a connected subgraph. In general, different (labelled) graphs may have the same set…
This paper sets out the results of a range of searches for linear and cyclic graph colourings with specific Ramsey properties. The new graphs comprise mainly 'template graphs' which can be used in a construction described by the current…
A reconstruction problem of words from scattered factors asks for the minimal information, like multisets of scattered factors of a given length or the number of occurrences of scattered factors from a given set, necessary to uniquely…