Subgraph densities in a surface

Given a fixed graph H that embeds in a surface $\Sigma$ , what is the maximum number of copies of H in an n-vertex graph G that embeds in $\Sigma$ ? We show that the answer is $\Theta(n^{f(H)})$ , where f(H) is a graph invariant called the ‘flap-number’ of H, which is independent of $\Sigma$ . This simultaneously answers two open problems posed by Eppstein ((1993) J. Graph Theory17(3) 409–416.). The same proof also answers the question for minor-closed classes. That is, if H is a $K_{3,t}$ minor-free graph, then the maximum number of copies of H in an n-vertex $K_{3,t}$ minor-free graph G is $\Theta(n^{f'(H)})$ , where f′(H) is a graph invariant closely related to the flap-number of H. Finally, when H is a complete graph we give more precise answers.

Exact stability for Turán’s Theorem

Turán's Theorem says that an extremal Kr+1-free graph is r-partite. The Stability Theorem of Erdős and Simonovits shows that if a Kr+1-free graph with n vertices has close to the maximal tr(n) edges, then it is close to being r-partite. In this paper we determine exactly the Kr+1-free graphs with at least m edges that are farthest from being r-partite, for any m≥tr(n)−δrn2. This extends work by Erdős, Győri and Simonovits, and proves a conjecture of Balogh, Clemen, Lavrov, Lidický and Pfender.

Domination and Independent Domination in Hexagonal Systems

A vertex subset D of G is a dominating set if every vertex in V(G)∖D is adjacent to a vertex in D. A dominating set D is independent if G[D], the subgraph of G induced by D, contains no edge. The domination number γ(G) of a graph G is the minimum cardinality of a dominating set of G, and the independent domination number i(G) of G is the minimum cardinality of an independent dominating set of G. A classical work related to the relationship between γ(G) and i(G) of a graph G was established in 1978 by Allan and Laskar. They proved that every K1,3-free graph G satisfies γ(G)=i(H). Hexagonal systems (2 connected planar graphs whose interior faces are all hexagons) have been extensively studied as they are used to present bezenoid hydrocarbon structures which play an important role in organic chemistry. The domination numbers of hexagonal systems have been studied continuously since 2018 when Hutchinson et al. posted conjectures, generated from a computer program called Conjecturing, related to the domination numbers of hexagonal systems. Very recently in 2021, Bermudo et al. answered all of these conjectures. In this paper, we extend these studies by considering the relationship between the domination number and the independent domination number of hexagonal systems. Although every hexagonal system H with at least two hexagons contains K1,3 as an induced subgraph, we find many classes of hexagonal systems whose domination number is equal to an independent domination number. However, we establish the existence of a hexagonal system H such that γ(H)<i(H) with the prescribed number of hexagons.

KAGE: Fast alignment-free graph-based genotyping of SNPs and short indels

One of the core applications of high-throughput sequencing is the characterization of individual genetic variation. Traditionally, variants have been inferred by comparing sequenced reads to a reference genome. There has recently been an emergence of genotyping methods, which instead infer variants of an individual based on variation present in population-scale repositories like the 1000 Genomes Project. However, commonly used methods for genotyping are slow since they still require mapping of reads to a reference genome. Also, since traditional reference genomes do not include genetic variation, traditional genotypers suffer from reference bias and poor accuracy in variation-rich regions where reads cannot accurately be mapped.We here present KAGE, a genotyper for SNPs and short indels that is inspired by recent developments within graph-based genome representations and alignment-free genotyping. We propose two novel ideas to improve both the speed and accuracy: we (1) use known genotypes from thousands of individuals in a Bayesian model to predict genotypes, and (2) propose a computationally efficient method for leveraging correlation between variants.We show through experiments on experimental data that KAGE is both faster and more accurate than other alignment-free genotypers. KAGE is able to genotype a new sample (15x coverage) in less than half an hour on a consumer laptop, more than 10 times faster than the fastest existing methods, making it ideal in clinical settings or when large numbers of individuals are to be genotyped at low computational cost.

Paths of Length Three are $K_{r+1}$-Turán-Good

The generalized Turán problem ex$(n,T,F)$ is to determine the maximal number of copies of a graph $T$ that can exist in an $F$-free graph on $n$ vertices. Recently, Gerbner and Palmer noted that the solution to the generalized Turán problem is often the original Turán graph. They gave the name "$F$-Turán-good" to graphs $T$ for which, for large enough $n$, the solution to the generalized Turán problem is realized by a Turán graph. They prove that the path graph on two edges, $P_2$, is $K_{r+1}$-Turán-good for all $r \ge 3$, but they conjecture that the same result should hold for all $P_\ell$. In this paper, using arguments based in flag algebras, we prove that the path on three edges, $P_3$, is also $K_{r+1}$-Turán-good for all $r \ge 3$.

Generalized Planar Turán Numbers

In a generalized Turán problem, we are given graphs $H$ and $F$ and seek to maximize the number of copies of $H$ in an $n$-vertex graph not containing $F$ as a subgraph. We consider generalized Turán problems where the host graph is planar. In particular, we obtain the order of magnitude of the maximum number of copies of a fixed tree in a planar graph containing no even cycle of length at most $2\ell$, for all $\ell$, $\ell \geqslant 1$. We also determine the order of magnitude of the maximum number of cycles of a given length in a planar $C_4$-free graph. An exact result is given for the maximum number of $5$-cycles in a $C_4$-free planar graph. Multiple conjectures are also introduced.

Structural Synthesis of Articulated Manipulators with Non-Fractionated or Fractionated Kinematic Chains without Isomorphism

As the kinematic structure of an articulated manipulator affects the characteristics of its motion, rigidity, vibration, and force transmissibility, finding the most suitable kinematic structure for the desired task is important in the conceptual design phase. This paper proposes a systematic method for generating non-isomorphic graphs of articulated manipulators that consist of a fixed base, an end-effector, and a two-degree-of-freedom (DOF) intermediate kinematic chain connecting the two. Based on the analysis of the structural characteristics of articulated manipulators, the conditions that must be satisfied for manipulators to have a desired DOF is identified. Then, isomorphism-free graph generation methods are proposed based on the concepts of the symmetry of a graph, and the number of graphs generated are determined. As a result, 969 graphs of articulated manipulators that have two-DOF non-fractionated intermediate kinematic chains and 33,438 graphs with two-DOF fractionated intermediate kinematic chains are generated, including practical articulated manipulators widely used in industry.

Structural Properties of Connected Domination Critical Graphs

A graph G is said to be k-γc-critical if the connected domination number γc(G) is equal to k and γc(G+uv)<k for any pair of non-adjacent vertices u and v of G. Let ζ be the number of cut vertices of G and let ζ0 be the maximum number of cut vertices that can be contained in one block. For an integer ℓ≥0, a graph G is ℓ-factor critical if G−S has a perfect matching for any subset S of vertices of size ℓ. It was proved by Ananchuen in 2007 for k=3, Kaemawichanurat and Ananchuen in 2010 for k=4 and by Kaemawichanurat and Ananchuen in 2020 for k≥5 that every k-γc-critical graph has at most k−2 cut vertices and the graphs with maximum number of cut vertices were characterized. In 2020, Kaemawichanurat and Ananchuen proved further that, for k≥4, every k-γc-critical graphs satisfies the inequality ζ0(G)≤mink+23,ζ. In this paper, we characterize all k-γc-critical graphs having k−3 cut vertices. Further, we establish realizability that, for given k≥4, 2≤ζ≤k−2 and 2≤ζ0≤mink+23,ζ, there exists a k-γc-critical graph with ζ cut vertices having a block which contains ζ0 cut vertices. Finally, we proved that every k-γc-critical graph of odd order with minimum degree two is 1-factor critical if and only if 1≤k≤2. Further, we proved that every k-γc-critical K1,3-free graph of even order with minimum degree three is 2-factor critical if and only if 1≤k≤2.

Two Results on Ramsey-Turán Theory

Let $f(n)$ be a positive function and $H$ a graph. Denote by $\textbf{RT}(n,H,f(n))$ the maximum number of edges of an $H$-free graph on $n$ vertices with independence number less than $f(n)$. It is shown that $\textbf{RT}(n,K_4+mK_1,o(\sqrt{n\log n}))=o(n^2)$ for any fixed integer $m\geqslant 1$ and $\textbf{RT}(n,C_{2m+1},f(n))=O(f^2(n))$ for any fixed integer $m\geqslant 2$ as $n\to\infty$.

Random Cyclic Triangle-Free Graphs of Prime Order

Cyclic triangle-free process (CTFP) is the cyclic analog of the triangle-free process. It begins with an empty graph of order n and generates a cyclic graph of order n by iteratively adding parameters, chosen uniformly at random, subject to the constraint that no triangle is formed in the cyclic graph obtained, until no more parameters can be added. The structure of a cyclic triangle-free graph of the prime order is different from that of composite integer order. Cyclic graphs of prime order have better properties than those of composite number order, which enables generating cyclic triangle-free graphs more efficiently. In this paper, a novel approach to generating cyclic triangle-free graphs of prime order is proposed. Based on the cyclic graphs of prime order, obtained by the CTFP and its variant, many new lower bounds on R 3 , t are computed, including R 3,34 ≥ 230 , R 3,35 ≥ 242 , R 3,36 ≥ 252 , R 3,37 ≥ 264 , R 3,38 ≥ 272 . Our experimental results demonstrate that all those related best known lower bounds, except the bound on R 3,34 , are improved by 5 or more.