Search

We identify a sufficient condition, treewidth-pliability, that gives a polynomial-time algorithm for an arbitrarily good approximation of the optimal value in a large class of Max-2-CSPs parameterised by the class of allowed constraint graphs (with arbitrary constraints on an unbounded alphabet). Our result applies more generally to the maximum homomorphism problem between two rational-valued structures. The condition unifies the two main approaches for designing a polynomial-time approximation scheme. One is Baker's layering technique, which applies to sparse graphs such as planar or excluded-minor graphs. The other is based on Szemerédi's regularity lemma and applies to dense graphs. We extend the applicability of both techniques to new classes of Max-CSPs. However, we prove that the condition cannot be used to find solutions (as opposed to approximating the optimal value) in general. Treewidth-pliability turns out to be a robust notion that can be defined in several equivalent ways, including characterisations via size, treedepth, or the Hadwiger number. We show connections to the notions of fractional-treewidth-fragility from structural graph theory, hyperfiniteness from the area of property testing, and regularity partitions from the theory of dense graph limits. These may be of independent interest. In particular, we show that a monotone class of graphs is hyperfinite if and only if it is fractionally-treewidth-fragile and has bounded degree. [ABSTRACT FROM AUTHOR]

A graph is O k -free if it does not contain k pairwise vertex-disjoint and non-adjacent cycles. We prove that "sparse" (here, not containing large complete bipartite graphs as subgraphs) O k -free graphs have treewidth (even, feedback vertex set number) at most logarithmic in the number of vertices. This is optimal, as there is an infinite family of O 2 -free graphs without K 2 , 3 as a subgraph and whose treewidth is (at least) logarithmic. Using our result, we show that Maximum Independent Set and 3-Coloring in O k -free graphs can be solved in quasi-polynomial time. Other consequences include that most of the central NP-complete problems (such as Maximum Independent Set , Minimum Vertex Cover , Minimum Dominating Set , Minimum Coloring) can be solved in polynomial time in sparse O k -free graphs, and that deciding the O k -freeness of sparse graphs is polynomial time solvable. [ABSTRACT FROM AUTHOR]

We consider the Shortest Odd Path problem, where given an undirected graph G , a weight function on its edges, and two vertices s and t in G , the aim is to find an (s , t) -path with odd length and, among all such paths, of minimum weight. For the case when the weight function is conservative, i.e., when every cycle has non-negative total weight, the complexity of the Shortest Odd Path problem had been open for 20 years, and was recently shown to be NP -hard. We give a polynomial-time algorithm for the special case when the weight function is conservative and the set E − of negative-weight edges forms a single tree. Our algorithm exploits the strong connection between Shortest Odd Path and the problem of finding two internally vertex-disjoint paths between two terminals in an undirected edge-weighted graph. It also relies on solving an intermediary problem variant called Shortest Parity-Constrained Odd Path where for certain edges we have parity constraints on their position along the path. Also, we exhibit two FPT algorithms for solving Shortest Odd Path. The first FPT algorithm is parameterized by | E − | , the number of negative edges, or more generally, by the maximum size of a matching in the subgraph of G spanned by E − , when the weight function is conservative. Our second FPT algorithm is parameterized by the treewidth of G , and the algorithm does not rely on conservativeness. • The problem with conservative weights and negative edges forming a tree is in P. • FPT algorithm with parameter the number of negative edges (conservativeness assumed). • FPT algorithm with parameter treewidth. [ABSTRACT FROM AUTHOR]

We present a parameterized dichotomy for the k - Sparsest Cut problem in weighted and unweighted versions. In particular, we show that the weighted k - Sparsest Cut problem is NP-hard for every k ≥ 3 even on graphs with bounded vertex cover number. Also, the unweighted k - Sparsest Cut problem is W[1]-hard when parameterized by the three combined parameters tree-depth, feedback vertex set number, and k. On the positive side, we show that the unweighted k - Sparsest Cut problem is FPT when parameterized by the vertex cover number and k , and when k is fixed, it is FPT with respect to the treewidth. Moreover, we show that the generalized version κ - Small-Set Expansion problem is FPT when parameterized by κ and the maximum degree of the graph, though it is W[1]-hard for each of these parameters separately. [ABSTRACT FROM AUTHOR]

Let t be a positive real number. A graph is called t-tough if the removal of any vertex set S that disconnects the graph leaves at most |S|/t components. The toughness of a graph is the largest t for which the graph is t-tough. We prove that toughness is fixed-parameter tractable parameterized with the treewidth. More precisely, we give an algorithm to compute the toughness of a graph G with running time O (| V (G) | 3 · tw (G) 2 tw (G)) where tw (G) is the treewidth. If the treewidth is bounded by a constant, then this is a polynomial algorithm. [ABSTRACT FROM AUTHOR]

The tree‐independence number tree‐α, first defined and studied by Dallard, Milanič, and Štorgel, is a variant of treewidth tailored to solving the maximum independent set problem. Over a series of papers, Abrishami et al. developed the so‐called central bag method to study induced obstructions to bounded treewidth. Among others, they showed that, in a certain superclass C of (even hole, diamond, pyramid)‐free graphs, treewidth is bounded by a function of the clique number. In this paper, we relax the bounded clique number assumption, and show that C has bounded tree‐α. Via existing results, this yields a polynomial‐time algorithm for the Maximum Weight Independent Set problem in this class. Our result also corroborates, for this class of graphs, a conjecture of Dallard, Milanič, and Štorgel that in a hereditary graph class, tree‐α is bounded if and only if the treewidth is bounded by a function of the clique number. [ABSTRACT FROM AUTHOR]

In 2019, Dvořák asked whether every connected graph G $G$ has a tree decomposition (T,B) $(T,{\rm{ {\mathcal B} }})$ so that T $T$ is a subgraph of G $G$ and the width of (T,B) $(T,{\rm{ {\mathcal B} }})$ is bounded by a function of the treewidth of G $G$. We prove that this is false, even when G $G$ has treewidth 2 and T $T$ is allowed to be a minor of G $G$. [ABSTRACT FROM AUTHOR]

The Feedback Vertex Set problem is undoubtedly one of the most well-studied problems in Parameterized Complexity. In this problem, given an undirected graph G and a non-negative integer k, the objective is to test whether there exists a subset S ⊆ V (G) of size at most k such that G - S is a forest. After a long line of improvement, recently, Li and Nederlof [TALG, 2022] designed a randomized algorithm for the problem running in time O ⋆ (2. 7 k) ∗ . In the Parameterized Complexity literature, several problems around Feedback Vertex Set have been studied. Some of these include Independent Feedback Vertex Set (where the set S should be an independent set in G), Almost Forest Deletion and Pseudoforest Deletion. In Pseudoforest Deletion, each connected component in G - S has at most one cycle in it. However, in Almost Forest Deletion, the input is a graph G and non-negative integers k , ℓ ∈ N , and the objective is to test whether there exists a vertex subset S of size at most k, such that G - S is ℓ edges away from a forest. In this paper, using the methodology of Li and Nederlof [TALG, 2022], we obtain the current fastest algorithms for all these problems. In particular we obtain the following randomized algorithms. Independent Feedback Vertex Set can be solved in time O ⋆ (2. 7 k) . Pseudo Forest Deletion can be solved in time O ⋆ (2. 85 k) . Almost Forest Deletion can be solved in time O ⋆ (min { 2. 85 k · 8. 54 ℓ , 2. 7 k · 36. 61 ℓ , 3 k · 1. 78 ℓ }) . [ABSTRACT FROM AUTHOR]

In this paper, we study the Harmless Set problem from a parameterized complexity perspective. Given a graph G = (V , E) , a threshold function t : V → N and an integer k, we study Harmless Set, where the goal is to find a subset of vertices S ⊆ V of size at least k such that every vertex v ∈ V has fewer than t(v) neighbours in S. On the positive side, we obtain fixed-parameter algorithms for the problem when parameterized by the neighbourhood diversity, the twin-cover number and the vertex integrity of the input graph. We complement two of these results from the negative side. On dense graphs, we show that the problem is W[1]-hard parameterized by cluster vertex deletion number—a natural generalization of the twin-cover number. We show that the problem is W[1]-hard parameterized by a wide range of fairly restrictive structural parameters such as the feedback vertex set number, pathwidth, and treedepth—a natural generalization of the vertex integrity. We thereby resolve one open question stated by Bazgan and Chopin (Discrete Optim 14(C):170–182, 2014) concerning the complexity of Harmless Set parameterized by the treewidth of the input graph. We also show that Harmless Set for a special case where each vertex has the threshold set to half of its degree (the so-called Majority Harmless Set problem) is W[1]-hard when parameterized by the treewidth of the input graph. Given a graph G and an irredundant c-expression of G, we prove that Harmless Set can be solved in XP-time when parameterized by clique-width. [ABSTRACT FROM AUTHOR]

We show that many graphs with bounded treewidth can be described as subgraphs of the strong product of a graph with smaller treewidth and a bounded-size complete graph. To this end, define the underlying treewidth of a graph class $\mathcal{G}$ to be the minimum non-negative integer $c$ such that, for some function $f$ , for every graph $G \in \mathcal{G}$ there is a graph $H$ with $\textrm{tw}(H) \leqslant c$ such that $G$ is isomorphic to a subgraph of $H \boxtimes K_{f(\textrm{tw}(G))}$. We introduce disjointed coverings of graphs and show they determine the underlying treewidth of any graph class. Using this result, we prove that the class of planar graphs has underlying treewidth $3$ ; the class of $K_{s,t}$ -minor-free graphs has underlying treewidth $s$ (for $t \geqslant \max \{s,3\}$); and the class of $K_t$ -minor-free graphs has underlying treewidth $t-2$. In general, we prove that a monotone class has bounded underlying treewidth if and only if it excludes some fixed topological minor. We also study the underlying treewidth of graph classes defined by an excluded subgraph or excluded induced subgraph. We show that the class of graphs with no $H$ subgraph has bounded underlying treewidth if and only if every component of $H$ is a subdivided star, and that the class of graphs with no induced $H$ subgraph has bounded underlying treewidth if and only if every component of $H$ is a star. [ABSTRACT FROM AUTHOR]

Let G be a graph with treewidth k. In the paper, it is proved that if k ≤ 3 and maximum degree Δ ≥ 5, or k = 4 and Δ ≥ 9, or Δ ≥ 4k - 3 and k ≥ 5, then the linear arboricity la(G) of G is ⌈Δ/2 ⌉. [ABSTRACT FROM AUTHOR]

What are the unavoidable induced subgraphs of graphs with large treewidth? It is well‐known that the answer must include a complete graph, a complete bipartite graph, all subdivisions of a wall and line graphs of all subdivisions of a wall (we refer to these graphs as the "basic treewidth obstructions"). So it is natural to ask whether graphs excluding the basic treewidth obstructions as induced subgraphs have bounded treewidth. Sintiari and Trotignon answered this question in the negative. Their counterexamples, the so‐called "layered wheels," contain wheels, where a wheel consists of a hole (i.e., an induced cycle of length at least four) along with a vertex with at least three neighbors in the hole. This leads one to ask whether graphs excluding wheels and the basic treewidth obstructions as induced subgraphs have bounded treewidth. This also turns out to be false due to Davies' recent example of graphs with large treewidth, no wheels and no basic treewidth obstructions as induced subgraphs. However, in Davies' example there exist holes and vertices (outside of the hole) with two neighbors in them. Here we prove that a hole with a vertex with at least two neighbors in it is inevitable in graphs with large treewidth and no basic obstruction. Our main result is that graphs in which every vertex has at most one neighbor in every hole (that does not contain it) and with the basic treewidth obstructions excluded as induced subgraphs have bounded treewidth. [ABSTRACT FROM AUTHOR]

Given two integers ℓ and p as well as ℓ graph classes H1, . . ., Hℓ, the problems GraphPart(H1, . . ., Hℓ, p), VertPart(H1, . . ., Hℓ), and EdgePart(H1, . . ., Hℓ) ask, given graph G as input, whether V (G), V (G), E(G) respectively can be partitioned into ℓ sets S1, . . ., Sℓ such that, for each i between 1 and ℓ, G[Si] ∈ Hi, G[Si] ∈ Hi, (V (G), Si) ∈ Hi respectively. Moreover in GraphPart(H1, . . ., Hℓ, p), we request that the number of edges with endpoints in different sets of the partition is bounded by p. We show that if there exist dynamic programming treedecomposition-based algorithms for recognizing the graph classes Hi, for each i, then we can constructively create a dynamic programming tree-decomposition-based algorithms for GraphPart(H1, . . ., Hℓ, p), VertPart(H1, . . ., Hℓ), and EdgePart(H1, . . ., Hℓ). We apply this approach to known problems. For well-studied problems, like VERTEX COVER and GRAPH q-COLORING, we obtain running times that are comparable to those of the best known problemspecific algorithms. For an exotic problem from bioinformatics, called DISPLAYGRAPH, this approach improves the known algorithm parameterized by treewidth. [ABSTRACT FROM AUTHOR]

The goal of this work is to give precise bounds on the counting complexity of a family of generalized coloring problems (list homomorphisms) on bounded-treewidth graphs. Given graphs G, H, and lists L (v) ⊆ V(H) for every v∈ V(G), a f:V(G)→ V(H) that preserves the edges (i.e., uv∈ E(G) implies f(u)f(v)∈ E(H)) and respects the lists (i.e., f(v)∈ L(v)). Standard techniques show that if G is given with a tree decomposition of width t, then the number of list homomorphisms can be counted in time |V(H)|t⋅ n(1). Our main result is determining, for every fixed graph H, how much the base |V(H)| in the running time can be improved. For a connected graph H, we define irr(H) in the following way: if H has a loop or is nonbipartite, then irr(H) is the maximum size of a set S⊆ V(H) where any two vertices have different neighborhoods; if H is bipartite, then irr(H) is the maximum size of such a set that is fully in one of the bipartition classes. For disconnected H, we define irr(H) as the maximum of irr(C) over every connected component C of H. It follows from earlier results that if irr(H)=1, then the problem of counting list homomorphisms to H is polynomial-time solvable, and otherwise it is #P-hard. We show that, for every fixed graph H, the number of list homomorphisms from (G,L) to H — can be counted in time \(\operatorname{irr}(H)^t\cdot n^{\mathcal {O}(1)}\) if a tree decomposition of G having width at most t is given in the input, and, — given that \(\operatorname{irr}(H)\ge 2\) , cannot be counted in time \((\operatorname{irr}(H)-\varepsilon)^t\cdot n^{\mathcal {O}(1)}\) for any \(\varepsilon \gt 0\) , even if a tree decomposition of G having width at most t is given in the input, unless the Counting Strong Exponential-Time Hypothesis (#SETH) fails. Thereby, we give a precise and complete complexity classification featuring matching upper and lower bounds for all target graphs with or without loops. [ABSTRACT FROM AUTHOR]

We show that every graph with pathwidth strictly less than a that contains no path on 2 b vertices as a subgraph has treedepth at most 10ab. The bound is best possible up to a constant factor. [ABSTRACT FROM AUTHOR]

We generalize a problem of finding maximum-scoring segment sets, previously studied by Csűrös (IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004, 1, 139–150), from sequences to graphs. Namely, given a vertex-weighted graph G and a non-negative startup penalty c, we can find a set of vertex-disjoint paths in G with maximum total score when each path’s score is its vertices’ total weight minus c. We call this new problem maximum-scoring path sets (MSPS). We present an algorithm that has a linear-time complexity for graphs with a constant treewidth. Generalization from sequences to graphs allows the algorithm to be used on pangenome graphs representing several related genomes and can be seen as a common abstraction for several biological problems on pangenomes, including searching for CpG islands, ChIP-seq data analysis, analysis of region enrichment for functional elements, or simple chaining problems.

A map is a partition of the sphere into interior-disjoint regions homeomorphic to closed disks. Some regions are labeled as nations, while the remaining ones are labeled as holes. A map in which at most k nations touch at the same point is a k-map, while it is hole-free if it contains no holes. A graph is a map graph if there is a bijection between its vertices and the nations of a map, such that two nations touch if and only the corresponding vertices are connected by an edge. We present a fixed-parameter tractable algorithm for recognizing map graphs parameterized by treewidth. Its time complexity is linear in the size of the graph. It reports a certificate in the form of a so-called witness, if the input is a yes-instance. Our algorithmic framework is general enough to test, for any k, if the input graph admits a k-map or a hole-free k-map. [ABSTRACT FROM AUTHOR]

The circumference of a graph G with at least one cycle is the length of a longest cycle in G. A classic result of Birmel\'e [J. Graph Theory, 43 (2003), pp. 24--25] states that the treewidth of G is at most its circumference minus 1. In case G is 2-connected, this upper bound also holds for the pathwidth of G; in fact, even the treedepth of G is upper bounded by its circumference (Bria\'nski et al. [Treedepth vs circumference, Combinatorica, 43 (2023), pp. 659--664]). In this paper, we study whether similar bounds hold when replacing the circumference of G by its cocircumference, defined as the largest size of a bond in G, an inclusionwise minimal set of edges F such that G F has more components than G. In matroidal terms, the cocircumference of G is the circumference of the bond matroid of G. Our first result is the following "dual" version of Birmel'e's theorem: The treewidth of a graph G is at most its cocircumference. Our second and main result is an upper bound of 3k 2 on the pathwidth of a 2-connected graph G with cocircumference k. Contrary to circumference, no such bound holds for the treedepth of G. Our two upper bounds are best possible up to a constant factor. [ABSTRACT FROM AUTHOR]

A circle graph is an intersection graph of a set of chords of a circle. We describe the unavoidable induced subgraphs of circle graphs with large treewidth. This includes examples that are far from the "usual suspects." Our results imply that treewidth and Hadwiger number are linearly tied on the class of circle graphs and that the unavoidable induced subgraphs of a vertex-minor-closed class with large treewidth are the usual suspects if and only if the class has bounded rank-width. Using the same tools, we also study the treewidth of graphs G that have a circular drawing whose crossing graph is well-behaved in some way. In this setting, we show that if the crossing graph is Kt-minor-free, then G has treewidth at most 12t 23 and has no K2,4t-topological minor. On the other hand, we show that there are graphs with arbitrarily large Hadwiger number that have circular drawings whose crossing graphs are 2-degenerate. [ABSTRACT FROM AUTHOR]

Given two n-vertex graphs G1 and G2 of bounded treewidth, is there an n-vertex graph G of bounded treewidth having subgraphs isomorphic to G1 and G2? Our main result is a negative answer to this question, in a strong sense: we show that the answer is no even if G1 is a binary tree and G2 is a ternary tree. We also provide an extensive study of cases where such "gluing"" is possible. In particular, we prove that if G1 has treewidth k and G2 has pathwidth \l, then there is an n-vertex graph of treewidth at most k + 3\l + 1 containing both G1 and G2 as subgraphs. [ABSTRACT FROM AUTHOR]

This paper is motivated by the following question: what are the unavoidable induced subgraphs of graphs with large treewidth? Aboulker et al. made a conjecture which answers this question in graphs of bounded maximum degree, asserting that for all k and Δ, every graph with maximum degree at most Δ and sufficiently large treewidth contains either a subdivision of the (k × k) -wall or the line graph of a subdivision of the (k × k) -wall as an induced subgraph. We prove two theorems supporting this conjecture, as follows. 1. For t ≥ 2 , a t-theta is a graph consisting of two nonadjacent vertices and three internally vertex-disjoint paths between them, each of length at least t. A t-pyramid is a graph consisting of a vertex v , a triangle B disjoint from v and three paths starting at v and vertex-disjoint otherwise, each joining v to a vertex of B , and each of length at least t. We prove that for all k , t and Δ, every graph with maximum degree at most Δ and sufficiently large treewidth contains either a t -theta, or a t -pyramid, or the line graph of a subdivision of the (k × k) -wall as an induced subgraph. This affirmatively answers a question of Pilipczuk et al. asking whether every graph of bounded maximum degree and sufficiently large treewidth contains either a theta or a triangle as an induced subgraph (where a theta means a t -theta for some t ≥ 2). 2. A subcubic subdivided caterpillar is a tree of maximum degree at most three whose all vertices of degree three lie on a path. We prove that for every Δ and subcubic subdivided caterpillar T , every graph with maximum degree at most Δ and sufficiently large treewidth contains either a subdivision of T or the line graph of a subdivision of T as an induced subgraph. [ABSTRACT FROM AUTHOR]

We say a class C of graphs is clean if for every positive integer t there exists a positive integer w (t) such that every graph in C with treewidth more than w (t) contains an induced subgraph isomorphic to one of the following: the complete graph K t , the complete bipartite graph K t , t , a subdivision of the (t × t) -wall or the line graph of a subdivision of the (t × t) -wall. In this paper, we adapt a method due to Lozin and Razgon (building on earlier ideas of Weißauer) to prove that the class of all H-free graphs (that is, graphs with no induced subgraph isomorphic to a fixed graph H) is clean if and only if H is a forest whose components are subdivided stars. Their method is readily applied to yield the above characterization. However, our main result is much stronger: for every forest H as above, we show that forbidding certain connected graphs containing H as an induced subgraph (rather than H itself) is enough to obtain a clean class of graphs. Along the proof of the latter strengthening, we build on a result of Davies and produce, for every positive integer η , a complete description of unavoidable connected induced subgraphs of a connected graph G containing η vertices from a suitably large given set of vertices in G. This is of independent interest, and will be used in subsequent papers in this series. [ABSTRACT FROM AUTHOR]

Let V be an n -dimensional vector space over a finite field F q , where q is a prime power. Define the generalized q -Kneser graph K q (n , k , t) to be the graph whose vertices are the k -dimensional subspaces of V and two vertices F 1 and F 2 are adjacent if dim (F 1 ∩ F 2) < t. Then K q (n , k , 1) is the well-known q -Kneser graph. In this paper, we determine the treewidth of K q (n , k , t) for n ≥ 2 t (k − t + 1) + k + 1 and t ≥ 1 exactly. Especially, for any possible n , k and q we also determine the treewidth of K q (n , k , k − 1) , which is the complement of the Grassmann graph G q (n , k). [ABSTRACT FROM AUTHOR]

The fundamental Sparsest Cut problem takes as input a graph G together with edge capacities and demands and seeks a cut that minimizes the ratio between the capacities and demands across the cuts. For n-vertex graphs G of treewidth k, Chlamtáč, Krauthgamer, and Raghavendra (APPROX'10) presented an algorithm that yields a factor- \(2^{2^k}\) approximation in time \(2^{O(k)} \cdot n^{O(1)}\). Later, Gupta, Talwar, and Witmer (STOC'13) showed how to obtain a 2-approximation algorithm with a blown-up runtime of \(n^{O(k)}\). An intriguing open question is whether one can simultaneously achieve the best out of the aforementioned results, that is, a factor-2 approximation in time \(2^{O(k)} \cdot n^{O(1)}\). In this article, we make significant progress towards this goal via the following results: (i) A factor- \(O(k^2)\) approximation that runs in time \(2^{O(k)} \cdot n^{O(1)}\) , directly improving the work of Chlamtáč et al. while keeping the runtime single-exponential in k. (ii) For any \(\varepsilon \in (0,1]\) , a factor- \(O(1/\varepsilon ^2)\) approximation whose runtime is \(2^{O(k^{1+\varepsilon }/\varepsilon)} \cdot n^{O(1)}\) , implying a constant-factor approximation whose runtime is nearly single-exponential in k and a factor- \(O(\log ^2 k)\) approximation in time \(k^{O(k)} \cdot n^{O(1)}\). Key to these results is a new measure of a tree decomposition that we call combinatorial diameter, which may be of independent interest. [ABSTRACT FROM AUTHOR]

Abstract Although RNA secondary structure prediction is a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, it remains challenging whenever pseudoknots come into play. Since the prediction of pseudoknotted structures by minimizing (realistically modelled) energy is NP-hard, specialized algorithms have been proposed for restricted conformation classes that capture the most frequently observed configurations. To achieve good performance, these methods rely on specific and carefully hand-crafted DP schemes. In contrast, we generalize and fully automatize the design of DP pseudoknot prediction algorithms. For this purpose, we formalize the problem of designing DP algorithms for an (infinite) class of conformations, modeled by (a finite number of) fatgraphs, and automatically build DP schemes minimizing their algorithmic complexity. We propose an algorithm for the problem, based on the tree-decomposition of a well-chosen representative structure, which we simplify and reinterpret as a DP scheme. The algorithm is fixed-parameter tractable for the treewidth tw of the fatgraph, and its output represents a $${\mathcal {O}}(n^{tw+1})$$ O ( n t w + 1 ) algorithm (and even possibly $${\mathcal {O}}(n^{tw})$$ O ( n tw ) in simple energy models) for predicting the MFE folding of an RNA of length n. We demonstrate, for the most common pseudoknot classes, that our automatically generated algorithms achieve the same complexities as reported in the literature for hand-crafted schemes. Our framework supports general energy models, partition function computations, recursive substructures and partial folding, and could pave the way for algebraic dynamic programming beyond the context-free case.

We introduce the graph theoretical parameter of edge-treewidth. This parameter occurs in a natural way as the tree-like analogue of cutwidth or, alternatively, as an edge-analogue of treewidth. We study the combinatorial properties of edge-treewidth. We first observe that edge-treewidth does not enjoy any closeness properties under the known partial ordering relations on graphs. We introduce a variant of the topological minor relation, namely, the weak topological minor relation and we prove that edge-treewidth is monotone with respect to weak topological minors. Based on this new relation we are able to provide universal obstructions for edge-treewidth. The proofs are based on the fact that edge-treewidth of a graph is parametrically equivalent with the maximum over the treewidth and the maximum degree of the blocks of the graph. We also prove that deciding whether the edge-treewidth of a graph is at most k is an NP -complete problem. [ABSTRACT FROM AUTHOR]

A k-page upward book embedding (kUBE) of a directed acyclic graph G is a book embeddings of G on k pages with the additional requirement that the vertices appear in a topological ordering along the spine of the book. The kUBE Testing problem, which asks whether a graph admits a kUBE, was introduced in 1999 by Heath, Pemmaraju, and Trenk (SIAM J Comput 28(4), 1999). In a companion paper, Heath and Pemmaraju (SIAM J Comput 28(5), 1999) proved that the problem is linear-time solvable for k = 1 and NP-complete for k = 6 . Closing this gap has been a central question in algorithmic graph theory since then. In this paper, we make a major contribution towards a definitive answer to the above question by showing that kUBE Testing is NP-complete for k ≥ 3 , even for st-graphs, i.e., acyclic directed graphs with a single source and a single sink. Indeed, our result, together with a recent work of Bekos et al. (Theor Comput Sci 946, 2023) that proves the NP-completeness of 2UBE for planar st-graphs, closes the question about the complexity of the kUBE problem for any k. Motivated by this hardness result, we then focus on the 2UBE Testing for planar st-graphs. On the algorithmic side, we present an O (f (β) · n + n 3) -time algorithm for 2UBE Testing, where β is the branchwidth of the input graph and f is a singly-exponential function on β . Since the treewidth and the branchwidth of a graph are within a constant factor from each other, this result immediately yields an FPT algorithm for st-graphs of bounded treewidth. Furthermore, we describe an O(n)-time algorithm to test whether a plane st-graph whose faces have a special structure admits a 2UBE that additionally preserves the plane embedding of the input st-graph. On the combinatorial side, we present two notable families of plane st-graphs that always admit an embedding-preserving 2 UBE. [ABSTRACT FROM AUTHOR]

Although RNA secondary structure prediction is a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, it remains challenging whenever pseudoknots come into play. Since the prediction of pseudoknotted structures by minimizing (realistically modelled) energy is NP-hard, specialized algorithms have been proposed for restricted conformation classes that capture the most frequently observed configurations. To achieve good performance, these methods rely on specific and carefully hand-crafted DP schemes. In contrast, we generalize and fully automatize the design of DP pseudoknot prediction algorithms. For this purpose, we formalize the problem of designing DP algorithms for an (infinite) class of conformations, modeled by (a finite number of) fatgraphs, and automatically build DP schemes minimizing their algorithmic complexity. We propose an algorithm for the problem, based on the tree-decomposition of a well-chosen representative structure, which we simplify and reinterpret as a DP scheme. The algorithm is fixed-parameter tractable for the treewidth tw of the fatgraph, and its output represents a O (n t w + 1) algorithm (and even possibly O (n tw) in simple energy models) for predicting the MFE folding of an RNA of length n. We demonstrate, for the most common pseudoknot classes, that our automatically generated algorithms achieve the same complexities as reported in the literature for hand-crafted schemes. Our framework supports general energy models, partition function computations, recursive substructures and partial folding, and could pave the way for algebraic dynamic programming beyond the context-free case. [ABSTRACT FROM AUTHOR]

For a graph G = (V , E) , a collection P of vertex-disjoint (simple) paths is called a path cover of G if every vertex v ∈ V is contained in exactly one path of P . The Path Cover problem (PC for short) is to find a minimum cardinality path cover of G. In this paper, we introduce generalizations of PC, where each path is associated with a weight (cost or profit). Our problem, Minimum (Maximum) Weighted Path Cover [MinPC (MaxPC)], is defined as follows: Let U = { 0 , 1 , ⋯ , n - 1 } . Given a graph G = (V , E) and a weight function f : U → R ∪ { + ∞ , - ∞ } that defines a weight for each path based on its length, the objective of MinPC (MaxPC) is to find a path cover P of G such that the total weight of the paths in P is minimized (maximized). Let L be a subset of U, and P L be the set of paths such that each path is of length ℓ ∈ L . We consider Min P L PC with binary cost, i.e., the cost function is f (ℓ) = 1 if ℓ ∈ L ; otherwise, f (ℓ) = 0 . We also consider Max P L PC with f (ℓ) = ℓ + 1 , if ℓ ∈ L ; otherwise, f (ℓ) = 0 . Many well-known graph theoretic problems such as the Hamiltonian Path and the Maximum Matching problems can be modeled using Min P L PC and Max P L PC. In this paper, we first show that deciding whether Min P { 0 , 1 , 2 } PC has a 0-weight solution is NP-complete for planar bipartite graphs of maximum degree three, and consequently, (i) for any constant σ ≥ 1 , there is no polynomial-time approximation algorithm with approximation ratio σ for Min P { 0 , 1 , 2 } PC unless P = NP, and (ii) Max P { 3 , ⋯ , n - 1 } PC is NP-hard for the same graph class. Next, we present a polynomial-time algorithm for Min P { 0 , 1 , ⋯ , k } PC on graphs with bounded treewidth for a fixed k. Lastly, we present a 4-approximation algorithm for Max P { 3 , ⋯ , n - 1 } PC, which becomes a 2.5-approximation algorithm for subcubic graphs. [ABSTRACT FROM AUTHOR]

A linkage in a graph G of size k is a subgraph L of G whose connected components are k paths. The pattern of a linkage of size k is the set of k pairs formed by the endpoints of these paths. A consequence of the Unique Linkage Theorem is the following: there exists a function f: N rightarrow N such that if a plane graph G contains a sequence\scrC of at least f(k) nested cycles and a linkage of size at most k whose pattern vertices lay outside the outer cycle of scrC, then G contains a linkage with the same pattern avoiding the inner cycle of\scrC. In this paper we prove the following variant of this result: Assume that all the cycles in\scrC are "orthogonally" traversed by a linkage P and L is a linkage whose pattern vertices may lay either outside the outer cycle or inside the inner cycle of scrC := [C1,...,Cp, . . ., C2p-1]. We prove that there are two functions g, f: Nrightarrow N, such that if L has size at most k, P has size at least f(k), and | scrC | geq g(k), then there is a linkage with the same pattern as L that is "internally combed" by P, in the sense that L cap Cp subseteq P\cap Cp. This result applies to any graph that is partially embedded on a disk (wherescrC is also embedded). In fact, we prove this result in the most general version where the linkage L is s-scattered: every two vertices of distinct paths are within a distance bigger than s. We deduce several variants of this result in the cases where s = 0 and s > 0. These variants permit the application of the Unique Linkage Theorem on several path routing problems on embedded graphs. [ABSTRACT FROM AUTHOR]

We study homomorphism polynomials, which are polynomials that enumerate all homomorphisms from a pattern graph H to n-vertex graphs. These polynomials have received a lot of attention recently for their crucial role in several new algorithms for counting and detecting graph patterns, and also for obtaining natural polynomial families which are complete for algebraic complexity classes VBP , V P , and VNP . We discover that, in the monotone setting, the formula complexity, the ABP complexity, and the circuit complexity of such polynomial families are exactly characterized by the treedepth, the pathwidth, and the treewidth of the pattern graph respectively. Furthermore, we establish a single, unified framework, using our characterization, to collect several known results that were obtained independently via different methods. For instance, we attain superpolynomial separations between circuits, ABPs, and formulas in the monotone setting, where the polynomial families separating the classes all correspond to well-studied combinatorial problems. Moreover, our proofs rediscover fine-grained separations between these models for constant-degree polynomials. [ABSTRACT FROM AUTHOR]

Let t be a nonnegative integer and G = (V(G),E(G)) be a graph. For v ∈ V(G), let NG(v) = {u ∈ V(G) \ {v} : uv ∈ E(G)}. And for S ⊆ V(G), we define dS(G; v) = |NG(v) ∩ S| for v ∈ S and dS(G; v) = −1 for v ∈ V(G) \ S. A subset S ⊆ V(G) is called a t-sparse set of G if the maximum degree of the induced subgraph G[S] does not exceed t. In particular, a 0-sparse set is precisely an independent set. A vector-weighted graph $ (G,\vec{w},t)$ is a graph G with a vector weight function $ \vec{w}:V(G)\to {\mathbb{R}}^{t+2}$ , where $ \vec{w}(v)=(w(v;-1),w(v;0),\dots,w(v;t))$ for each v ∈ V(G). The weight of a t-sparse set S in $ (G,\vec{w},t)$ is defined as $ \vec{w}(S,G)={\sum }_v w(v;{d}_S(G;v))$. And a t-sparse set S is a maximum weight t-sparse set of $ (G,\vec{w},t)$ if there is no t-sparse set of larger weight in $ (G,\vec{w},t)$. In this paper, we propose the maximum weight t-sparse set problem on vector-weighted graphs, which is to find a maximum weight t-sparse set of $ (G,\vec{w},t)$. We design a dynamic programming algorithm to find a maximum weight t-sparse set of an outerplane graph $ (G,\vec{w},t)$ which takes O((t + 2)4n) time, where n = |V(G)|. Moreover, we give a polynomial-time algorithm for this problem on graphs with bounded treewidth. [ABSTRACT FROM AUTHOR]

The linear arboricity la(G) of a graph G is the minimum number of linear forests that partition the edges of G. Akiyama, Exoo and Harary conjectured that ⌈ Δ 2 ⌉ ≤ l a (G) ≤ ⌈ Δ + 1 2 ⌉ for any graph G with maximum degree Δ , and proved the conjecture holds for forests. This conjecture has been verified for certain graph families with treewidth at most 3. In the paper we improve these former results by validating the conjecture for all graphs with treewidth at most 4. [ABSTRACT FROM AUTHOR]

The clique transversal problem and its variants have garnered significant attention in the last two decades due to their practical applications in communication networks, social-network theory and transceiver placement for cellular telephones. While previous research primarily focused on determining the polynomial-time solvability or NP-hardness/NP-completeness of specific graphs, this paper adopts a parameterized-complexity approach. It thoroughly explores four clique transversal variants: the d-fold transversal problem, the { d } -clique transversal problem, the signed clique transversal problem and the minus clique transversal problem. The paper presents various findings regarding the parameterized complexity of the clique transversal problem and its variants. It establishes the W[2]-completeness and para-NP-completeness of the d-fold transversal problem, the { d } -clique transversal problem, the signed clique transversal problem and the minus clique transversal problem within specific graph classes. Additionally, it introduces fixed-parameter tractable algorithms for planar graphs and graphs with bounded treewidth, offering efficient solutions for these specific instances of the problems. The research further explores the relationship between planar graphs and graphs with bounded treewidth to enhance the time complexity of the d-fold clique transversal problem and the { d } -clique transversal problem. By analyzing the parameterized complexity of the clique transversal problem and its variants, this research contributes to our understanding of the computational limitations and potentially efficient algorithms for solving these problems. [ABSTRACT FROM AUTHOR]

In 1966 Gallai asked whether all longest paths in a connected graph have nonempty intersection. This is not true in general and various counterexamples have been found. In this paper, we study the related question on longest cycles instead of longest paths (to make the question valid, we require 2‐connectivity). The answer for cycles is also negative and not so much attention has been given to it. Classes for which the answer is known to be positive are dually chordal graphs and 3‐trees. Perhaps the main open class for the question of both paths and cycles is the class of chordal graphs. In this paper, we show that all longest cycles intersect in graphs with treewidth at most three. This class of graphs includes several important subclasses of graphs, such as series‐parallel graphs and K5 ${K}_{5}$‐free chordal graphs. [ABSTRACT FROM AUTHOR]