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Integral circulant graphs are proposed as models for quantum spin networks that permit a quantum phenomenon called perfect state transfer. Specifically, it is important to know how far information can potentially be transferred between nodes of the quantum networks modelled by integral circulant graphs and this task is related to calculating the maximal diameter of a graph. The integral circulant graph $ICG_n (D)$ has the vertex set $Z_n = \{0, 1, 2, \ldots, n - 1\}$ and vertices $a$ and $b$ are adjacent if $\gcd(a-b,n)\in D$, where $D \subseteq \{d : d \mid n,\ 1\leq d 1,\ 1\leq i\leq k \}|$, depending on whether $n\not\in 4N+2$ or not, respectively. Furthermore, we show that, for a given order $n$, a divisor set $D$ with $|D|\leq k$ can always be found such that this bound is attained. Finally, we calculate the maximal diameter in the class of integral circulant graphs of a given order $n$ and cardinality of the divisor set $t\leq k$ and characterize all extremal graphs. We actually show that the maximal diameter can have the values $2t$, $2t+1$, $r(n)$ and $r(n)+1$ depending on the values of $t$ and $n$. This way we further improve the upper bound of Saxena, Severini and Shparlinski and we also characterize all graphs whose diameters are equal to $2|D|+1$, thus generalizing a result in that paper., Comment: 29 pages, 1 figure

Developments in Genome-Wide Association Studies have led to the increasing notion that future healthcare techniques will be personalized to the patient, by relying on genetic tests to determine the risk of developing a disease. To this end, the detection of gene interactions that cause complex diseases constitutes an important application. Similarly to many applications in this field, extensive data sets containing genetic information for a series of patients are used (such as Single-Nucleotide Polymorphisms), leading to high computational complexity and memory utilization, thus constituting a major challenge when targeting high-performance execution in modern computing systems. To close this gap, this work proposes several novel approaches for the detection of three-way gene interactions in modern CPUs and GPUs, making use of different optimizations to fully exploit the target architectures. Crucial insights from the Cache-Aware Roofline Model are used to ensure the suitability of the applications to the computing devices. An extensive study of the architectural features of 13 CPU and GPU devices from all main vendors is also presented, allowing to understand the features relevant to obtain high-performance in this bioinformatics domain. To the best of our knowledge, this study is the first to perform such evaluation for epistasis detection. The proposed approaches are able to surpass the performance of state-of-the-art works in the tested platforms, achieving an average speedup of 3.9$\times$ (7.3$\times$ on CPUs and 2.8$\times$ on GPUs) and maximum speedup of 10.6$\times$ on Intel UHD P630 GPU., Comment: To appear in 36th IEEE International Parallel & Distributed Processing Symposium (IPDPS 2022)

The Steiner $k$-eccentricity of a vertex $v$ of a graph $G$ is the maximum Steiner distance over all $k$-subsets of $V (G)$ which contain $v$. A linear time algorithm for calculating the Steiner $k$-eccentricity of a vertex on block graphs is presented. For general graphs, an $O(n^{\nu(G)+1}(n(G) + m(G) + k))$ algorithm is designed, where $\nu(G)$ is the cyclomatic number of $G$. A linear algorithm for computing the Steiner $3$-eccentricities of all vertices of a tree is also presented which improves the quadratic algorithm from [Discrete Appl.\ Math.\ 304 (2021) 181--195].

The Steiner $k$-eccentricity of a vertex $v$ of a graph $G$ is the maximum Steiner distance over all $k$-subsets of $V (G)$ which contain $v$. In this note, we design a linear algorithm for computing the Steiner $3$-eccentricities and the connective Steiner $3$-eccentricity index on a tree and thus improving a quadratic algorithm presented in [G. Yu, X. Li, \emph{Connective Steiner 3-eccentricity index and network similarity measure}, Appl. Math. Comput. 386 (2020), 125446.], Comment: Merged into another paper

In this note we resolve three conjectures from [M. Dehmer, S. Pickl, Y. Shi, G. Yu, \emph{New inequalities for network distance measures by using graph spectra}, Discrete Appl. Math. 252 (2019), 17--27] on the comparison of distance measures based on the graph spectra, by constructing families of counterexamples and using computer search., Comment: 4, pages, 2 figures

The transmission of a vertex $v$ of a graph $G$ is the sum of distances from $v$ to all the other vertices in $G$. The Wiener complexity of $G$ is the number of different transmissions of its vertices. Similarly, the eccentric complexity of $G$ is defined as the number of different eccentricities of its vertices. In this paper these two complexities are compared. The complexities are first studied on Cartesian product graphs. Transmission indivisible graphs and arithmetic transmission graphs are introduced to demonstrate sharpness of upper and lower bounds on the Wiener complexity, respectively. It is shown that for almost all graphs the Wiener complexity is not smaller than the eccentric complexity. This property is proved for trees, the equality holding precisely for center-regular trees. Several families of graphs in which the complexities are equal are constructed. Using the Cartesian product, it is proved that the eccentric complexity can be arbitrarily larger than the Wiener complexity. Additional infinite families of graphs with this property are constructed by amalgamating universally diametrical graphs with center-regular trees.

Modern heterogeneous computing architectures, which couple multi-core CPUs with discrete many-core GPUs (or other specialized hardware accelerators), enable unprecedented peak performance and energy efficiency levels. Unfortunately, though, developing applications that can take full advantage of the potential of heterogeneous systems is a notoriously hard task. This work takes a step towards reducing the complexity of programming heterogeneous systems by introducing the abstraction of Heterogeneous Transactional Memory (HeTM). HeTM provides programmers with the illusion of a single memory region, shared among the CPUs and the (discrete) GPU(s) of a heterogeneous system, with support for atomic transactions. Besides introducing the abstract semantics and programming model of HeTM, we present the design and evaluation of a concrete implementation of the proposed abstraction, which we named Speculative HeTM (SHeTM). SHeTM makes use of a novel design that leverages on speculative techniques and aims at hiding the inherently large communication latency between CPUs and discrete GPUs and at minimizing inter-device synchronization overhead. SHeTM is based on a modular and extensible design that allows for easily integrating alternative TM implementations on the CPU's and GPU's sides, which allows the flexibility to adopt, on either side, the TM implementation (e.g., in hardware or software) that best fits the applications' workload and the architectural characteristics of the processing unit. We demonstrate the efficiency of the SHeTM via an extensive quantitative study based both on synthetic benchmarks and on a porting of a popular object caching system., Comment: The current work was accepted in the 28th International Conference on Parallel Architectures and Compilation Techniques (PACT'19)

Given a graph $G$, we associate a path matrix $P$ whose $(i, j)$ entry represents the maximum number of vertex disjoint paths between the vertices $i$ and $j$, with zeros on the main diagonal. In this note, we resolve four conjectures from [M. M. Shikare, P. P. Malavadkar, S. C. Patekar, I. Gutman, \emph{On Path Eigenvalues and Path Energy of Graphs}, MATCH Commun. Math. Comput. Chem. {\bf 79} (2018), 387--398.] on the path energy of graphs and finally present efficient $O(|E| |V|^3)$ algorithm for computing the path matrix used for verifying computational results., Comment: 8 pages

In this paper we disprove three conjectures from [M. Dehmer, F. Emmert-Streib, Y. Shi, Interrelations of graph distance measures based on topological indices, PLoS ONE 9 (2014) e94985] on graph distance measures based on topological indices by providing explicit classes of trees that do not satisfy proposed inequalities. The constructions are based on the families of trees that have the same Wiener index, graph energy or Randic index - but different degree sequences., Comment: 9 pages, 2 figures

In this note, we discuss the method explained in the recent paper [P. Manuel, I. Rajasingh, B. Rajan, R. Sundara Rajan, A New Approach To Compute Wiener Index, Journal of Computational and Theoretical Nanoscience 10, (2013) 1515-1521.] for computing the Wiener index of special chemical graphs. The method is actually already well-known and equivalent to the 'cut method' introduced in 1995 by Klavzar, Gutman and Mohar, and used in multiple papers for computing various distance based graph invariants., Comment: 5 pages

We consider a special case of the ordinary NP-hard two-machine flow shop problem with the objective of determining simultaneously a minimal common due date and the minimal number of tardy jobs. In [S. S. Panwalkar, C. Koulamas, An O(n^2) algorithm for the variable common due date, minimal tardy jobs bicriteria two-machine flow shop problem with ordered machines, European Journal of Operational Research 221 (2012), 7-13.], the authors presented quadratic algorithm for the problem when each job has its smaller processing time on the first machine. In this note, we improve the running time of the algorithm to O(n log n) by efficient implementation using recently introduced modified binary tree data structure., Comment: 6 pages, 1 algorithm

The harmonic index of a graph $G$ is defined as the sum of weights $\frac{2}{deg(v) + deg(u)}$ of all edges $uv$ of $E (G)$, where $deg (v)$ denotes the degree of a vertex $v$ in $V (G)$. In this note we generalize results of [L. Zhong, The harmonic index on graphs, Appl. Math. Lett. 25 (2012), 561--566] and establish some upper and lower bounds on the harmonic index of $G$., Comment: 5 pages

Let $G$ be a simple graph with $n$ vertices and let $\mu_1 \geqslant \mu_2 \geqslant...\geqslant \mu_{n - 1} \geqslant \mu_n = 0$ be the eigenvalues of its Laplacian matrix. The Laplacian Estrada index of a graph $G$ is defined as $LEE (G) = \sum\limits_{i = 1}^n e^{\mu_i}$. Using the recent connection between Estrada index of a line graph and Laplacian Estrada index, we prove that the path $P_n$ has minimal, while the star $S_n$ has maximal $LEE$ among trees on $n$ vertices. In addition, we find the unique tree with the second maximal Laplacian Estrada index., Comment: 8 pages, 1 figure

The intersection graph of a collection of trapezoids with corner points lying on two parallel lines is called a trapezoid graph. These graphs and their generalizations were applied in various fields, including modeling channel routing problems in VLSI design and identifying the optimal chain of non-overlapping fragments in bioinformatics. Using modified binary indexed tree data structure, we design an algorithm for calculating the vertex connectivity of trapezoid graph $G$ with time complexity $O (n \log n)$, where $n$ is the number of trapezoids. Furthermore, we establish sufficient and necessary condition for a trapezoid graph $G$ to be bipartite and characterize trees that can be represented as trapezoid graphs., Comment: 12 pages, 2 figures

The eccentricity of a vertex is the maximum distance from it to another vertex and the average eccentricity $ecc (G)$ of a graph $G$ is the mean value of eccentricities of all vertices of $G$. The average eccentricity is deeply connected with a topological descriptor called the eccentric connectivity index, defined as a sum of products of vertex degrees and eccentricities. In this paper we analyze extremal properties of the average eccentricity, introducing two graph transformations that increase or decrease $ecc (G)$. Furthermore, we resolve four conjectures, obtained by the system AutoGraphiX, about the average eccentricity and other graph parameters (the clique number, the Randi\' c index and the independence number), refute one AutoGraphiX conjecture about the average eccentricity and the minimum vertex degree and correct one AutoGraphiX conjecture about the domination number., Comment: 15 pages, 3 figures

In theoretical chemistry, distance-based molecular structure descriptors are used for modeling physical, pharmacologic, biological and other properties of chemical compounds. We introduce a generalized Wiener polarity index $W_k (G)$ as the number of unordered pairs of vertices ${u, v}$ of $G$ such that the shortest distance $d (u, v)$ between $u$ and $v$ is $k$ (this is actually the $k$-th coefficient in the Wiener polynomial). For $k = 3$, we get standard Wiener polarity index. Furthermore, we generalize the terminal Wiener index $TW_k (G)$ as the sum of distances between all pairs of vertices of degree $k$. For $k = 1$, we get standard terminal Wiener index. In this paper we describe a linear time algorithm for computing these indices for trees and partial cubes, and characterize extremal trees maximizing the generalized Wiener polarity index and generalized terminal Wiener index among all trees of given order $n$., Comment: 3pages, 4 figures

The intersection graph of a collection of trapezoids with corner points lying on two parallel lines is called a trapezoid graph. Using binary indexed tree data structure, we improve algorithms for calculating the size and the number of minimum vertex covers (or independent sets), as well as the total number of vertex covers, and reduce the time complexity from $O (n^2)$ to $O (n \log n)$, where $n$ is the number of trapezoids. Furthermore, we present the family of counterexamples for recently proposed algorithm with time complexity $O (n^2)$ for calculating the maximum cardinality matching in trapezoid graphs., Comment: 9 pages, 1 figure, 4 algorithms

Let $G$ be a simple undirected $n$-vertex graph with the characteristic polynomial of its Laplacian matrix $L(G)$, $\det (\lambda I - L (G))=\sum_{k = 0}^n (-1)^k c_k \lambda^{n - k}$. It is well known that for trees the Laplacian coefficient $c_{n-2}$ is equal to the Wiener index of $G$. Using a result of Zhou and Gutman on the relation between the Laplacian coefficients and the matching numbers in subdivided bipartite graphs, we characterize first the trees with given diameter and then the connected graphs with given radius which simultaneously minimize all Laplacian coefficients. This approach generalizes recent results of Liu and Pan [MATCH Commun. Math. Comput. Chem. 60 (2008), 85--94] and Wang and Guo [MATCH Commun. Math. Comput. Chem. 60 (2008), 609--622] who characterized $n$-vertex trees with fixed diameter $d$ which minimize the Wiener index. In conclusion, we illustrate on examples with Wiener and modified hyper-Wiener index that the opposite problem of simultaneously maximizing all Laplacian coefficients has no solution., Comment: 10 pages, 5 figures

The Hosoya index $Z (G)$ of a graph $G$ is defined as the total number of edge independent sets of $G$. In this paper, we extend the research of [J. Ou, On extremal unicyclic molecular graphs with maximal Hosoya index, \textit{Discrete Appl. Math.} 157 (2009) 391--397.] and [Y. Ye, X. Pan, H. Liu, Ordering unicyclic graphs with respect to Hosoya indices and Merrifield-Simmons indices, \textit{MATCH Commun. Math. Comput. Chem.} 59 (2008) 191--202.] and order the largest $n-1$ unicyclic graphs with respect to the Hosoya index., Comment: 10 pages, 4 figures

Circulant graphs are an important class of interconnection networks in parallel and distributed computing. Integral circulant graphs play an important role in modeling quantum spin networks supporting the perfect state transfer as well. The integral circulant graph $\ICG_n (D)$ has the vertex set $Z_n = \{0, 1, 2, ..., n - 1\}$ and vertices $a$ and $b$ are adjacent if $\gcd(a-b,n)\in D$, where $D \subseteq \{d : d \mid n,\ 1\leq d

Let $G=(V,E)$ be a simple graph with $n = |V|$ vertices and $m = |E|$ edges. The first and second Zagreb indices are among the oldest and the most famous topological indices, defined as $M_1 = \sum_{i \in V} d_i^2$ and $M_2 = \sum_{(i, j) \in E} d_i d_j$, where $d_i$ denote the degree of vertex $i$. Recently proposed conjecture $M_1 / n \leqslant M_2 / m$ has been proven to hold for trees, unicyclic graphs and chemical graphs, while counterexamples were found for both connected and disconnected graphs. Our goal is twofold, both in favor of a conjecture and against it. Firstly, we show that the expressions $M_1/n$ and $M_2/m$ have the same lower and upper bounds, which attain equality for and only for regular graphs. We also establish sharp lower bound for variable first and second Zagreb indices. Secondly, we show that for any fixed number $k\geqslant 2$, there exists a connected graph with $k$ cycles for which $M_1/n>M_2/m$ holds, effectively showing that the conjecture cannot hold unless there exists some kind of limitation on the number of cycles or the maximum vertex degree in a graph. In particular, we show that the conjecture holds for subdivision graphs., Comment: 7 pages, 1 figure

The concept of gcd-graphs is introduced by Klotz and Sander, which arises as a generalization of unitary Cayley graphs. The gcd-graph $X_n (d_1,...,d_k)$ has vertices $0,1,...,n-1$, and two vertices $x$ and $y$ are adjacent iff $\gcd(x-y,n)\in D = \{d_1,d_2,...,d_k\}$. These graphs are exactly the same as circulant graphs with integral eigenvalues characterized by So. In this paper we deal with the clique number of integral circulant graphs and investigate the conjecture proposed in \cite{klotz07} that clique number divides the number of vertices in the graph $X_n (D)$. We completely solve the problem of finding clique number for integral circulant graphs with exactly one and two divisors. For $k \geqslant 3$, we construct a family of counterexamples and disprove the conjecture in this case., Comment: 6 pages, 1 figure

Design of monomeric unit, by using sequences of map operations, and the growing process in the building of a double-shell multi torus with all-pentagonal faces, is presented. It is shown that the monomer and some small intermediates, as hydrogenated species, have a moderate stability, between adamantane and C60 fullerene, as calculated at the PM3 level of theory. The topology of these high genera structures is described in terms of Omega polynomial as a function of the net parameters. Closed formulas for this polynomial and examples are presented., Comment: 8 pages, 5 figure

Let $G$ be a simple undirected $n$-vertex graph with the characteristic polynomial of its Laplacian matrix $L(G)$, $\det (\lambda I - L (G))=\sum_{k = 0}^n (-1)^k c_k \lambda^{n - k}$. Laplacian--like energy of a graph is newly proposed graph invariant, defined as the sum of square roots of Laplacian eigenvalues. For bipartite graphs, the Laplacian--like energy coincides with the recently defined incidence energy $IE (G)$ of a graph. In [D. Stevanovi\' c, \textit{Laplacian--like energy of trees}, MATCH Commun. Math. Comput. Chem. 61 (2009), 407--417.] the author introduced a partial ordering of graphs based on Laplacian coefficients. We point out that original proof was incorrect and illustrate the error on the example using Laplacian Estrada index. Furthermore, we found the inverse of Jacobian matrix with elements representing derivatives of symmetric polynomials of order $n$, and provide a corrected elementary proof of the fact: Let $G$ and $H$ be two $n$-vertex graphs; if for Laplacian coefficients holds $c_k (G) \leqslant c_k (H)$ for $k = 1, 2, ..., n - 1$, then $LEL (G) \leqslant LEL (H)$. In addition, we generalize this theorem and provide a necessary condition for functions that satisfy partial ordering based on Laplacian coefficients., Comment: 10 pages

The eccentric connectivity index $\xi^c$ is a novel distance--based molecular structure descriptor that was recently used for mathematical modeling of biological activities of diverse nature. It is defined as $\xi^c (G) = \sum_{v \in V (G)} deg (v) \cdot \epsilon (v)$\,, where $deg (v)$ and $\epsilon (v)$ denote the vertex degree and eccentricity of $v$\,, respectively. We survey some mathematical properties of this index and furthermore support the use of eccentric connectivity index as topological structure descriptor. We present the extremal trees and unicyclic graphs with maximum and minimum eccentric connectivity index subject to the certain graph constraints. Sharp lower and asymptotic upper bound for all graphs are given and various connections with other important graph invariants are established. In addition, we present explicit formulae for the values of eccentric connectivity index for several families of composite graphs and designed a linear algorithm for calculating the eccentric connectivity index of trees. Some open problems and related indices for further study are also listed., Comment: 25 pages, 5 figures

For a connected graph, the distance spectral radius is the largest eigenvalue of its distance matrix, and the distance energy is defined as the sum of the absolute values of the eigenvalues of its distance matrix. We establish lower and upper bounds for the distance spectral radius of graphs and bipartite graphs, lower bounds for the distance energy of graphs, and characterize the extremal graphs. We also discuss upper bounds for the distance energy., Comment: 20 pages