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Two Latin squares of order $n$ are $r$-orthogonal if, when superimposed, there are exactly $r$ distinct ordered pairs. The spectrum of all values of $r$ for Latin squares of order $n$ is known. A Latin square $A$ of order $n$ is $r$-self-orthogonal if $A$ and its transpose are $r$-orthogonal. The spectrum of all values of $r$ is known for all orders $n\ne 14$. We develop randomized algorithms for computing pairs of $r$-orthogonal Latin squares of order $n$ and algorithms for computing $r$-self-orthogonal Latin squares of order $n$.

Permutation arrays under the Chebyshev metric have been considered for error correction in noisy channels. Let $P(n,d)$ denote the maximum size of any array of permutations on $n$ symbols with pairwise Chebyshev distance $d$. We give new techniques and improved upper and lower bounds on $P(n,d)$, including a precise formula for $P(n,2)$.

In this paper, we start with a variation of the star cover problem called the Two-Squirrel problem. Given a set $P$ of $2n$ points in the plane, and two sites $c_1$ and $c_2$, compute two $n$-stars $S_1$ and $S_2$ centered at $c_1$ and $c_2$ respectively such that the maximum weight of $S_1$ and $S_2$ is minimized. This problem is strongly NP-hard by a reduction from Equal-size Set-Partition with Rationals. Then we consider two variations of the Two-Squirrel problem, namely the Two-MST and Two-TSP problem, which are both NP-hard. The NP-hardness for the latter is obvious while the former needs a non-trivial reduction from Equal-size Set-Partition with Rationals. In terms of approximation algorithms, for Two-MST and Two-TSP we give factor 3.6402 and $4+\varepsilon$ approximations respectively. Finally, we also show some interesting polynomial-time solvable cases for Two-MST., Comment: 17 pages, 7 figures

Permutation arrays under the Kendall-$\tau$ metric have been considered for error-correcting codes. Given $n$ and $d\in [1..\binom{n}{2}]$, the task is to find a large permutation array of permutations on $n$ symbols with pairwise Kendall-$\tau$ distance at least $d$. Let $P(n,d)$ denote the maximum size of any permutation array of permutations on $n$ symbols with pairwise Kendall-$\tau$ distance $d$. New algorithms and several theorems are presented, giving improved lower bounds for $P(n,d)$. Also, $(n,m,d)$-arrays are defined, which are permutation arrays on n symbols with Kendall-$\tau$ distance d, with the restriction that symbols {1...(n-m)} appear in increasing order. Let $P(n,m,d)$ denote the maximum size of any $(n,m,d)$-array. For example, (n,m,d)-arrays are useful for recursively computing lower bounds for $P(n,d)$. Lower and upper bounds are given for $P(n.m,d)$.

The term melodic template or skeleton refers to a basic melody which is subject to variation during a music performance. In many oral music tradition, these templates are implicitly passed throughout generations without ever being formalized in a score. In this work, we introduce a new geometric optimization problem, the spanning tube problem, to approximate a melodic template for a set of labeled performance transcriptions corresponding to an specific style in oral music traditions. Given a set of $n$ piecewise linear functions, we solve the problem of finding a continuous function, $f^*$, and a minimum value, $\varepsilon^*$, such that, the vertical segment of length $2\varepsilon^*$ centered at $(x,f^*(x))$ intersects at least $p$ functions ($p\leq n$). The method explored here also provide a novel tool for quantitatively assess the amount of melodic variation which occurs across performances.

We study the problem of optimally inspecting an underground (underwater) gallery with k agents. We consider a gallery with a single opening and with a tree topology rooted at the opening. Due to the small diameter of the pipes (caves), the agents are small robots with limited autonomy and there is a supply station at the gallery's opening. Therefore, they are initially placed at the root and periodically need to return to the supply station. Our goal is to design off-line strategies to efficiently cover the tree with $k$ small robots. We consider two objective functions: the covering time (maximum collective time) and the covering distance (total traveled distance). The maximum collective time is the maximum time spent by a robot needs to finish its assigned task (assuming that all the robots start at the same time); the total traveled distance is the sum of the lengths of all the covering walks. Since the problems are intractable for big trees, we propose approximation algorithms. Both efficiency and accuracy of the suboptimal solutions are empirically showed for random trees through intensive numerical experiments.

A given order type in the plane can be represented by a point set. However, it might be difficult to recognize the orientations of some point triples. Recently, Aichholzer \etal \cite{abh19} introduced exit graphs for visualizing order types in the plane. We present a new class of geometric graphs, called {\em OT-graphs}, using abstract order types and their axioms described in the well-known book by Knuth \cite{k92}. Each OT-graph corresponds to a unique order type. We develop efficient algorithms for recognizing OT-graphs and computing a minimal OT-graph for a given order type in the plane. We provide experimental results on all order types of up to nine points in the plane including a comparative analysis of exit graphs and OT-graphs.

We consider rational functions of the form $V(x)/U(x)$, where both $V(x)$ and $U(x)$ are polynomials over the finite field $\mathbb{F}_q$. Polynomials that permute the elements of a field, called {\it permutation polynomials ($PPs$)}, have been the subject of research for decades. Let ${\mathcal P}^1(\mathbb{F}_q)$ denote $\mathbb{Z}_q \cup \{\infty\}$. If the rational function, $V(x)/U(x)$, permutes the elements of ${\mathcal P}^1(\mathbb{F}_q)$, it is called a {\em permutation rational function (PRf)}. Let $N_d(q)$ denote the number of PPs of degree $d$ over $\mathbb{F}_q$, and let $N_{v,u}(q)$ denote the number of PRfs with a numerator of degree $v$ and a denominator of degree $u$. It follows that $N_{d,0}(q) = N_d(q)$, so PRFs are a generalization of PPs. The number of monic degree 3 PRfs is known [11]. We develop efficient computational techniques for $N_{v,u}(q)$, and use them to show $N_{4,3}(q) = (q+1)q^2(q-1)^2/3$, for all prime powers $q \le 307$, $N_{5,4}(q) > (q+1)q^3(q-1)^2/2$, for all prime powers $q \le 97$, and $N_{4,4}(p) = (p+1)p^2(p-1)^3/3$, for all primes $p \le 47$. We conjecture that these formulas are, in fact, true for all prime powers $q$. Let $M(n,D)$ denote the maximum number of permutations on $n$ symbols with pairwise Hamming distance $D$. Computing improved lower bounds for $M(n,D)$ is the subject of much current research with applications in error correcting codes. Using PRfs, we obtain significantly improved lower bounds on $M(q,q-d)$ and $M(q+1,q-d)$, for $d \in \{5,7,9\}$.

Let $P$ be a set $n$ points in a $d$-dimensional space. Tverberg's theorem says that, if $n$ is at least $(k-1)(d+1)+1$, then $P$ can be partitioned into $k$ sets whose convex hulls intersect. Partitions with this property are called {\em Tverberg partitions}. A partition has tolerance $t$ if the partition remains a Tverberg partition after removal of any set of $t$ points from $P$. Tolerant Tverberg partitions exist in any dimension provided that $n$ is sufficiently large. Let $N(d,k,t)$ be the smallest value of $n$ such that tolerant Tverberg partitions exist for any set of $n$ points in $\mathbb{R}^d$. Only few exact values of $N(d,k,t)$ are known. In this paper we establish a new tight bound for $N(2,2,2)$. We also prove many new lower bounds on $N(2,k,t)$ for $k\ge 2$ and $t\ge 1$., Comment: 10 figures

We present a new technique for computing permutation polynomials based on equivalence relations. The equivalence relations are defined by expanded normalization operations and new functions that map permutation polynomials (PPs) to other PPs. Our expanded normalization applies to almost all PPs, including when the characteristic of the finite field divides the degree of the polynomial. The equivalence relations make it possible to reduce the size of the space, when doing an exhaustive search. As a result, we have been able to compute almost all permutation polynomials of degree $d$ at most 10 over $GF(q)$, where $q$ is at most 97. We have also been able to compute nPPs of degrees 11 and 12 in a few cases. The techniques apply to arbitrary $q$ and $d$. In addition, the equivalence relations allow the set all PPs for a given degree and a given field $GF(q)$ to be succinctly described by their representative nPPs. We give several tables at the end of the paper listing the representative nPPs (\ie the equivalence classes) for several values of $q$ and $d$. We also give several new lower bounds for $M(n,D)$, the maximum number of permutations on $n$ symbols with pairwise Hamming distance $D$, mostly derived from our results on PPs.

Huemer et al. (Discrete Mathematics, 2019) proved that for any two point sets $R$ and $B$ with $|R|=|B|$, the perfect matching that matches points of $R$ with points of $B$, and maximizes the total \emph{squared} Euclidean distance of the matched pairs, verifies that all the disks induced by the matching have a common point. Each pair of matched points $p\in R$ and $q\in B$ induces the disk of smallest diameter that covers $p$ and $q$. Following this research line, in this paper we consider the perfect matching that maximizes the total Euclidean distance. First, we prove that this new matching for $R$ and $B$ does not always ensure the common intersection property of the disks. Second, we extend the study of this new matching for sets of $2n$ uncolored points in the plane, where a matching is just a partition of the points into $n$ pairs. As the main result, we prove that in this case all disks of the matching do have a common point. This implies a big improvement on a conjecture of Andy Fingerhut in 1995, about a maximum matching of $2n$ points in the plane.

A classical recursive construction for mutually orthogonal latin squares (MOLS) is shown to hold more generally for a class of permutation codes of length $n$ and minimum distance $n-1$. When such codes of length $p+1$ are included as ingredients, we obtain a general lower bound $M(n,n-1) \ge n^{1.079}$ for large $n$, gaining a small improvement on the guarantee given from MOLS.

Given a set of $n$ points $P$ in the plane, each colored with one of the $t$ given colors, a color-spanning set $S\subset P$ is a subset of $t$ points with distinct colors. The minimum diameter color-spanning set (MDCS) is a color-spanning set whose diameter is minimum (among all color-spanning sets of $P$). Somehow symmetrically, the largest closest pair color-spanning set (LCPCS) is a color-spanning set whose closest pair is the largest (among all color-spanning sets of $P$). Both MDCS and LCPCS have been shown to be NP-complete, but whether they are fixed-parameter tractable (FPT) when $t$ is a parameter is still open. Motivated by this question, we consider the FPT tractability of some matching problems under this color-spanning model, where $t=2k$ is the parameter. The problems are summarized as follows: (1) MinSum Matching Color-Spanning Set, namely, computing a matching of $2k$ points with distinct colors such that their total edge length is minimized; (2) MaxMin Matching Color-Spanning Set, namely, computing a matching of $2k$ points with distinct colors such that the minimum edge length is maximized; (3) MinMax Matching Color-Spanning Set, namely, computing a matching of $2k$ points with distinct colors such that the maximum edge length is minimized; and (4) $k$-Multicolored Independent Matching, namely, computing a matching of $2k$ vertices in a graph such that the vertices of the edges in the matching do not share common edges in the graph. We show that the first three problems are polynomially solvable (hence in FPT), while problem (4) is W[1]-hard., Comment: 12 pages, 2 figures, earlier version appeared in FAW'17

Let $M(n,d)$ be the maximum size of a permutation array on $n$ symbols with pairwise Hamming distance at least $d$. Some permutation arrays can be constructed using blocks of certain type [2] called product blocks in this paper. We study the problem of designing $(q,k)$-product blocks with a fixed block size $k$.

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 $n$ symbols with pairwise Hamming distance $d$ is a necessary component of constructing error correcting permutation codes, which have been proposed for power-line communications. Our technique, {\em partition and extension}, is universally applicable to constructing such sets for all $n$ and all $d$, $d

A permutation array $A$ is a set of permutations on a finite set $\Omega$, say of size $n$. Given distinct permutations $\pi, \sigma\in \Omega$, we let $hd(\pi, \sigma) = |\{ x\in \Omega: \pi(x) \ne \sigma(x) \}|$, called the Hamming distance between $\pi$ and $\sigma$. Now let $hd(A) =$ min$\{ hd(\pi, \sigma): \pi, \sigma \in A \}$. For positive integers $n$ and $d$ with $d\le n$, we let $M(n,d)$ be the maximum number of permutations in any array $A$ satisfying $hd(A) \geq d$. There is an extensive literature on the function $M(n,d)$, motivated in part by suggested applications to error correcting codes for message transmission over power lines. A basic fact is that if a permutation group $G$ is sharply $k$-transitive on a set of size $n\geq k$, then $M(n,n-k+1) = |G|$. Motivated by this we consider the permutation groups $AGL(1,q)$ and $PGL(2,q)$ acting sharply $2$-transitively on $GF(q)$ and sharply $3$-transitively on $GF(q)\cup \{\infty\}$ respectively. Applying a contraction operation to these groups, we obtain the following new lower bounds for prime powers $q$ satisfying $q\equiv 1$ (mod $3$). 1. $M(q-1,q-3)\geq (q^{2} - 1)/2$ for $q$ odd, $q\geq 7$, 2. $M(q-1,q-3)\geq (q-1)(q+2)/3$ for $q$ even, $q\geq 8$, 3. $M(q,q-3)\geq Kq^{2}\log q$ for some constant $K$ if $q$ is odd, $q\geq 13$. These results resolve a case left open in a previous paper \cite{BLS}, where it was shown that $M(q-1, q-3) \geq q^{2} - q$ and $M(q,q-3) \geq q^{3} - q$ for all prime powers $q$ such that $q\not \equiv 1$ (mod $3$). We also obtain lower bounds for $M(n,d)$ for a finite number of exceptional pairs $n,d$, by applying this contraction operation to the sharply $4$ and $5$-transitive Mathieu groups.

The {\em double-cut-and-join} (DCJ) operation, introduced by Yancopoulos \emph{et al.}, allows minimum edit distance to be computed by modeling all possible classical rearrangement operations, such as inversions, fusions, fissions, translocations, and transpositions, in linear-time between two genomes. However, there is lack of visualization tool that can effectively present DCJ operations that will help biologists to use DCJ operation. In this paper, a new visualization program is introduced, DCJVis, to create a diagram of each DCJ operation necessary to transform between the genomes of two distinct organisms by describing a possible sequence of genome graphs based on the selected gene adjacency on the source genome for the DCJ operation. Our program is the first visualization tool for DCJ operations using circular layout. Specifically, the genomes of \textit{Saccharomyces cerevisiae} and \textit{Candida albicans} are used to demonstrate the functionality of this program and provide an example of the type of problem this program can solve for biologists.

Let $S$ be a finite set of geometric objects partitioned into classes or \emph{colors}. A subset $S'\subseteq S$ is said to be \emph{balanced} if $S'$ contains the same amount of elements of $S$ from each of the colors. We study several problems on partitioning $3$-colored sets of points and lines in the plane into two balanced subsets: (a) We prove that for every 3-colored arrangement of lines there exists a segment that intersects exactly one line of each color, and that when there are $2m$ lines of each color, there is a segment intercepting $m$ lines of each color. (b) Given $n$ red points, $n$ blue points and $n$ green points on any closed Jordan curve $\gamma$, we show that for every integer $k$ with $0 \leq k \leq n$ there is a pair of disjoint intervals on $\gamma$ whose union contains exactly $k$ points of each color. (c) Given a set $S$ of $n$ red points, $n$ blue points and $n$ green points in the integer lattice satisfying certain constraints, there exist two rays with common apex, one vertical and one horizontal, whose union splits the plane into two regions, each one containing a balanced subset of $S$., Comment: This paper was published in Discrete Applied Mathematics, 181:21--32, 2015

We study an optimization problem that arises in the design of covering strategies for multi-robot systems. Consider a team of $n$ cooperating robots traveling along predetermined closed and disjoint trajectories. Each robot needs to periodically communicate information to nearby robots. At places where two trajectories are within range of each other, a communication link is established, allowing two robots to exchange information, provided they are "synchronized", i.e., they visit the link at the same time. In this setting a communication graph is defined and a system of robots is called \emph{synchronized} if every pair of neighbors is synchronized. If one or more robots leave the system, then some trajectories are left unattended. To handle such cases in a synchronized system, when a live robot arrives to a communication link and detects the absence of the neighbor, it shifts to the neighboring trajectory to assume the unattended task. If enough robots leave, it may occur that a live robot enters a state of \emph{starvation}, failing to permanently meet other robots during flight. To measure the tolerance of the system under this phenomenon we define the \emph{$k$-resilience} as the minimum number of robots whose removal may cause $k$ surviving robots to enter a state of starvation. We show that the problem of computing the $k$-resilience is NP-hard if $k$ is part of the input, even if the communication graph is a tree. We propose algorithms to compute the $k$-resilience for constant values of $k$ in general communication graphs and show more efficient algorithms for systems whose communication graph is a tree.

Node overlap removal is a necessary step in many scenarios including laying out a graph, or visualizing a tag cloud. Our contribution is a new overlap removal algorithm that iteratively builds a Minimum Spanning Tree on a Delaunay triangulation of the node centers and removes the node overlaps by "growing" the tree. The algorithm is simple to implement yet produces high quality layouts. According to our experiments it runs several times faster than the current state-of-the-art methods.

Let M(n, d) be the maximum size of a permutation array on n symbols with pairwise Hamming distance at least d. We use various combinatorial, algebraic, and computational methods to improve lower bounds for M(n, d). We compute the Hamming distances of affine semilinear groups and projective semilinear groups, and unions of cosets of AGL(1,q) and PGL(2,q) with Frobenius maps to obtain new, improved lower bounds for M(n,d). We give new randomized algorithms. We give better lower bounds for M(n,d) also using new theorems concerning the contraction operation. For example, we prove a quadratic lower bound for M(n,n-2) for all n=2 (mod 3) such that n+1 is a prime power.

Given a set of $k$-colored points in the plane, we consider the problem of finding $k$ trees such that each tree connects all points of one color class, no two trees cross, and the total edge length of the trees is minimized. For $k=1$, this is the well-known Euclidean Steiner tree problem. For general $k$, a $k\rho$-approximation algorithm is known, where $\rho \le 1.21$ is the Steiner ratio. We present a PTAS for $k=2$, a $(5/3+\varepsilon)$-approximation algorithm for $k=3$, and two approximation algorithms for general~$k$, with ratios $O(\sqrt n \log k)$ and $k+\varepsilon$.

Consider a finite sequence of permutations of the elements 1,...,n, with the property that each element changes its position by at most 1 from any permutation to the next. We call such a sequence a tangle, and we define a move of element i to be a maximal subsequence of at least two consecutive permutations during which its positions form an arithmetic progression of common difference +1 or -1. We prove that for any initial and final permutations, there is a tangle connecting them in which each element makes at most 5 moves, and another in which the total number of moves is at most 4n. On the other hand, there exist permutations that require at least 3 moves for some element, and at least 2n-2 moves in total. If we further require that every pair of elements exchange positions at most once, then any two permutations can be connected by a tangle with at most O(log n) moves per element, but we do not know whether this can be reduced to O(1) per element, or to O(n) in total. A key tool is the introduction of certain restricted classes of tangle that perform pattern-avoiding permutations.

A permutation may be represented by a collection of paths in the plane. We consider a natural class of such representations, which we call tangles, in which the paths consist of straight segments at 45 degree angles, and the permutation is decomposed into nearest-neighbour transpositions. We address the problem of minimizing the number of crossings together with the number of corners of the paths, focusing on classes of permutations in which both can be minimized simultaneously. We give algorithms for computing such tangles for several classes of permutations.

In 1926, Jarn\'ik introduced the problem of drawing a convex $n$-gon with vertices having integer coordinates. He constructed such a drawing in the grid $[1,c\cdot n^{3/2}]^2$ for some constant $c>0$, and showed that this grid size is optimal up to a constant factor. We consider the analogous problem for drawing the double circle, and prove that it can be done within the same grid size. Moreover, we give an O(n)-time algorithm to construct such a point set.

In this paper we study problems of drawing graphs in the plane using edge length constraints and angle optimization. Specifically we consider the problem of maximizing the minimum angle, the MMA problem. We solve the MMA problem using a spring-embedding approach where two forces are applied to the vertices of the graph: a force optimizing edge lengths and a force optimizing angles. We solve analytically the problem of computing an optimal displacement of a graph vertex optimizing the angles between edges incident to it if the degree of the vertex is at most three. We also apply a numerical approach for computing the forces applied to vertices of higher degree. We implemented our algorithm in Java and present drawings of some graphs.

Edge bundling reduces the visual clutter in a drawing of a graph by uniting the edges into bundles. We propose a method of edge bundling drawing each edge of a bundle separately as in metro-maps and call our method ordered bundles. To produce aesthetically looking edge routes it minimizes a cost function on the edges. The cost function depends on the ink, required to draw the edges, the edge lengths, widths and separations. The cost also penalizes for too many edges passing through narrow channels by using the constrained Delaunay triangulation. The method avoids unnecessary edge-node and edge-edge crossings. To draw edges with the minimal number of crossings and separately within the same bundle we develop an efficient algorithm solving a variant of the metro-line crossing minimization problem. In general, the method creates clear and smooth edge routes giving an overview of the global graph structure, while still drawing each edge separately and thus enabling local analysis.