De Bruijn graphs and DNA graphs

In this paper we prove the NP-hardness of various recognition problems for subgraphs of De Bruijn graphs. In particular, the recognition of DNA graphs is shown to be NP-hard; DNA graphs are the vertex induced subgraphs of De Bruijn graphs over a four letter alphabet. As a consequence, two open questions from a recent paper by Blazewicz, Hertz, Kobler & de Werra [Discrete Applied Mathematics 98, 1999] are answered in the negative

On the Hardness and Inapproximability of Recognizing Wheeler Graphs

In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these are used to index structures far more complex than a single string, as was originally done with the FM-index [Ferragina and Manzini, J. ACM 2005]. As such, there has been an increasing effort to better understand under which conditions such an indexing scheme is possible. This has led to the introduction of Wheeler graphs [Gagie et al., Theor. Comput. Sci., 2017]. Gagie et al. showed that de Bruijn graphs, generalized compressed suffix arrays, and several other BWT related structures can be represented as Wheeler graphs, and that Wheeler graphs can be indexed in a way which is space efficient. Hence, being able to recognize whether a given graph is a Wheeler graph, or being able to approximate a given graph by a Wheeler graph, could have numerous applications in indexing. Here we resolve the open question of whether there exists an efficient algorithm for recognizing if a given graph is a Wheeler graph. We present: - The problem of recognizing whether a given graph G=(V,E) is a Wheeler graph is NP-complete for any edge label alphabet of size sigma >= 2, even when G is a DAG. This holds even on a restricted, subset of graphs called d-NFA\u27s for d >= 5. This is in contrast to recent results demonstrating the problem can be solved in polynomial time for d-NFA\u27s where d <= 2. We also show the recognition problem can be solved in linear time for sigma =1; - There exists an 2^{e log sigma + O(n + e)} time exact algorithm where n = |V| and e = |E|. This algorithm relies on graph isomorphism being computable in strictly sub-exponential time; - We define an optimization variant of the problem called Wheeler Graph Violation, abbreviated WGV, where the aim is to remove the minimum number of edges in order to obtain a Wheeler graph. We show WGV is APX-hard, even when G is a DAG, implying there exists a constant C >= 1 for which there is no C-approximation algorithm (unless P = NP). Also, conditioned on the Unique Games Conjecture, for all C >= 1, it is NP-hard to find a C-approximation; - We define the Wheeler Subgraph problem, abbreviated WS, where the aim is to find the largest subgraph which is a Wheeler Graph (the dual of the WGV). In contrast to WGV, we prove that the WS problem is in APX for sigma=O(1); The above findings suggest that most problems under this theme are computationally difficult. However, we identify a class of graphs for which the recognition problem is polynomial time solvable, raising the open question of which parameters determine this problem\u27s difficulty

On the chromatic number of the \u3cem\u3eAO\u3c/em\u3e(2, \u3cem\u3ek \u3c/em\u3e, \u3cem\u3ek\u3c/em\u3e-1) graphs.

The alphabet overlap graph is a modification of the well known de Bruijn graph. De Bruijn graphs have been highly studied and hence many properties of these graphs have been determined. However, very little is known about alphabet overlap graphs. In this work we determine the chromatic number for a special case of these graphs. We define the alphabet overlap graph by G = AO(a, k, t, where a, k and t are positive integers such that 0 ≤ t ≤ k. The vertex set of G is the set of all k-letter sequences over an alphabet of size a. Also there is an edge between vertices u, v if and only if the last t letters in u match the first t letters in v or the first t letters in u match the last t letters in v. We consider the chromatic number for the AO(a, k, t graphs when k \u3e 2, t = k - 1 and a = 2

Simplicial decompositions of graphs: a survey of applications

AbstractWe survey applications of simplicial decompositions (decompositions by separating complete subgraphs) to problems in graph theory. Among the areas of application are excluded minor theorems, extremal graph theorems, chordal and interval graphs, infinite graph theory and algorithmic aspects

Translation invariant extensions of finite volume measures

We investigate the following questions: Given a measure μΛ on configurations on a subset Λ of a lattice L, where a configuration is an element of ΩΛ for some fixed set Ω, does there exist a measure μ on configurations on all of L, invariant under some specified symme- try group of L, such that μΛ is its marginal on configurations on Λ? When the answer is yes, what are the properties, e.g., the entropies, of such measures? Our primary focus is the case in which L = Zd and the symmetries are the translations. For the case in which Λ is an interval in Z we give a simple necessary and sufficient condition, local translation invariance (LTI), for extendibility. For LTI measures we construct extensions having maximal entropy, which we show are Gibbs measures; this construction extends to the case in which L is the Bethe lattice. On Z we also consider extensions supported on periodic configurations, which are analyzed using de Bruijn graphs and which include the extensions with minimal entropy. When Λ ⊂ Z is not an interval, or when Λ ⊂ Zd with d > 1, the LTI condition is necessary but not sufficient for extendibility. For Zd with d > 1, extendibility is in some sense undecidable

On embeddings of CAT(0) cube complexes into products of trees

We prove that the contact graph of a 2-dimensional CAT(0) cube complex ${\bf X}$ of maximum degree $\Delta$ can be coloured with at most $\epsilon(\Delta)=M\Delta^{26}$ colours, for a fixed constant $M$. This implies that ${\bf X}$ (and the associated median graph) isometrically embeds in the Cartesian product of at most $\epsilon(\Delta)$ trees, and that the event structure whose domain is ${\bf X}$ admits a nice labeling with $\epsilon(\Delta)$ labels. On the other hand, we present an example of a 5-dimensional CAT(0) cube complex with uniformly bounded degrees of 0-cubes which cannot be embedded into a Cartesian product of a finite number of trees. This answers in the negative a question raised independently by F. Haglund, G. Niblo, M. Sageev, and the first author of this paper.Comment: Some small corrections; main change is a correction of the computation of the bounds in Theorem 1. Some figures repaire

Chromatic Number of the Alphabet Overlap Graph, \u3cem\u3eG\u3c/em\u3e(2, \u3cem\u3ek \u3c/em\u3e, \u3cem\u3ek\u3c/em\u3e-2).

A graph G(a, k, t) is called an alphabet overlap graph where a, k, and t are positive integers such that 0 ≤ t \u3c k and the vertex set V of G is defined as, V = {v : v = (v1v2...vk); vi ∊ {1, 2, ..., a}, (1 ≤ i ≤ k)}. That is, each vertex, v, is a word of length k over an alphabet of size a. There exists an edge between two vertices u, v if and only if the last t letters in u equal the first t letters in v or the first t letters in u equal the last t letters in v. We determine the chromatic number of G(a, k, t) for all k ≥ 3, t = k − 2, and a = 2; except when k = 7, 8, 9, and 11