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Let $S$ be a set of four points chosen independently, uniformly at random from a square. Join every pair of points of $S$ with a straight line segment. Color these edges red if they have positive slope and blue, otherwise. We show that the probability that $S$ defines a pair of crossing edges of the same color is equal to $1/4$. This is connected to a recent result of Aichholzer et al. [GD 2019] who showed that by 2-colouring the edges of a geometric graph and counting monochromatic crossings instead of crossings, the number of crossings can be more than halfed. Our result shows that for the described random drawings, there is a coloring of the edges such that the number of monochromatic crossings is in expectation $\frac{1}{2}-\frac{7}{50}$ of the total number of crossings.

We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees of $T$. On the one hand, we consider the reconstruction of trees from their (multi)decks. We give lower and upper bounds on the minimum (multi)deck size required to uniquely encode a rooted binary tree on $n$ leaves. On the other hand, we consider problems related to deck cardinalities. In particular, we characterize trees with minimum-size as well as maximum-size decks. Finally, we present some exhaustive computations for $k$-universal trees, i.e., rooted binary trees that contain all $k$-leaf rooted binary trees as induced subtrees., Comment: 18 pages, 14 figures

We provide an $\Omega(n\log n) $ lower bound and an $O(n^2)$ upper bound for the smallest size of rooted binary trees (a.k.a. phylogenetic tree shapes), which are universal for rooted binary trees with $n$ leaves, i.e., contain all of them as induced binary subtrees. We explicitly compute the smallest universal trees for $n\leq 11$. We also provide an $\Omega(n^2) $ lower bound and an $O(n^4)$ upper bound for the smallest size of tanglegrams, which are universal for size $n$ tanglegrams, i.e., which contain all of them as induced subtanglegrams. Some of our results generalize to rooted $d$-ary trees and to $d$-ary tanglegrams., Comment: 18 pages, 14 figures

A tanglegram $\cal T$ consists of two rooted binary trees with the same number of leaves, and a perfect matching between the two leaf sets. In a layout, the tanglegrams is drawn with the leaves on two parallel lines, the trees on either side of the strip created by these lines are drawn as plane trees, and the perfect matching is drawn in straight line segments inside the strip. The tanglegram crossing number ${\rm cr}({\cal T})$ of $\cal T$ is the smallest number of crossings of pairs of matching edges, over all possible layouts of $\cal T$. The size of the tanglegram is the number of matching edges, say $n$. An earlier paper showed that the maximum of the tanglegram crossing number of size $n$ tanglegrams is $<\frac{1}{2}\binom{n}{2}$; but is at least $\frac{1}{2}\binom{n}{2}-\frac{n^{3/2}-n}{2}$ for infinitely many $n$. Now we make better bounds: the maximum crossing number of a size $n$ tanglegram is at most $ \frac{1}{2}\binom{n}{2}-\frac{n}{4}$, but for infinitely many $n$, at least $\frac{1}{2}\binom{n}{2}-\frac{n\log_2 n}{4}$. The problem shows analogy with the Unbalancing Lights Problem of Gale and Berlekamp.

P. Erd\H{o}s, J. Pach, R. Pollack, and Z. Tuza [J. Combin. Theory, B 47 (1989), 279--285] made conjectures for the maximum diameter of connected graphs without a complete subgraph $K_{k+1}$, which have order $n$ and minimum degree $\delta$. Settling a weaker version of a problem, by strengthening the $K_{k+1}$-free condition to $k$-colorable, we solve the problem for $k=3$ and $k=4$ using a unified linear programming duality approach. The case $k=4$ is a substantial simplification of the result of \'E. Czabarka, P. Dankelmann, and L. A. Sz\'ekely [Europ. J. Comb., 30 (2009), 1082--1089]., Comment: 8 pages. arXiv admin note: text overlap with arXiv:2009.02611

Erd\H{o}s, Pach, Pollack and Tuza [J. Combin. Theory, B 47, (1989), 279-285] conjectured that the diameter of a $K_{2r}$-free connected graph of order $n$ and minimum degree $\delta\geq 2$ is at most $\frac{2(r-1)(3r+2)}{(2r^2-1)}\cdot \frac{n}{\delta} + O(1)$ for every $r\ge 2$, if $\delta$ is a multiple of $(r-1)(3r+2)$. For every $r>1$ and $\delta\ge 2(r-1)$, we create $K_{2r}$-free graphs with minimum degree $\delta$ and diameter $\frac{(6r-5)n}{(2r-1)\delta+2r-3}+O(1)$, which are counterexamples to the conjecture for every $r>1$ and $\delta>2(r-1)(3r+2)(2r-3)$. The rest of the paper proves positive results under a stronger hypothesis, $k$-colorability, instead of being $K_{k+1}$-free. We show that the diameter of connected $k$-colorable graphs with minimum degree $\geq \delta$ and order $n$ is at most $\left(3-\frac{1}{k-1}\right)\frac{n}{\delta}+O(1)$, while for $k=3$, it is at most $\frac{57n}{23\delta}+O\left(1\right)$.

Contrary to the expectation arising from the tanglegram Kuratowski theorem of \'E. Czabarka, L.A. Sz\'ekely and S. Wagner [SIAM J. Discrete Math. 31(3): 1732--1750, (2017)], we construct an infinite antichain of planar tanglegrams with respect to the induced subtanglegram partial order. R.E. Tarjan, R. Laver, D.A. Spielman and M. B\'ona, and possibly others, showed that the partially ordered set of finite permutations ordered by deletion of entries contains an infinite antichain, i.e. there exists an infinite collection of permutations, such that none of them contains another as a pattern. Our construction adds a twist to the construction of Spielman and B\'ona [Electr. J. Comb, Vol. 7. N2.]

The Wiener index of a connected graph is the sum of the distances between all unordered pairs of vertices. We provide formulae for the minimum Wiener index of simple triangulations and quadrangulations with connectivity at least $c$, and provide the extremal structures, which attain those values. Our main tool is setting upper bounds for the maximum degree in highly connected triangulations and quadrangulations.

Let $ G $ be a connected graph. If $\bar{\sigma}(v)$ denotes the arithmetic mean of the distances from $v$ to all other vertices of $G$, then the proximity, $\pi(G)$, of $G$ is defined as the smallest value of $\bar{\sigma}(v)$ over all vertices $v$ of $G$. We give upper bounds for the proximity of simple triangulations and quadrangulations of given order and connectivity. We also construct simple triangulations and quadrangulations of given order and connectivity that match the upper bounds asymptotically and are likely optimal., Comment: arXiv admin note: text overlap with arXiv:1905.06753

We find the asymptotic behavior of the Steiner k-diameter of the $n$-cube if $k$ is large. Our main contribution is the lower bound, which utilizes the probabilistic method.

Let $G$ be a a connected graph. The Wiener index of a connected graph is the sum of the distances between all unordered pairs of vertices. We provide asymptotic formulae for the maximum Wiener index of simple triangulations and quadrangulations with given connectivity, as the order increases, and make conjectures for the extremal triangulations and quadrangulations based on computational evidence. If $\overline{\sigma}(v)$ denotes the arithmetic mean of the distances from $v$ to all other vertices of $G$, then the remoteness of $G$ is defined as the largest value of $\overline{\sigma}(v)$ over all vertices $v$ of $G$. We give sharp upper bounds on the remoteness of simple triangulations and quadrangulations of given order and connectivity.

For positive integers $n$ and $e$, let $\kappa(n,e)$ be the minimum crossing number (the standard planar crossing number) taken over all graphs with $n$ vertices and at least $e$ edges. Pach, Spencer and T\'oth [Discrete and Computational Geometry 24 623--644, (2000)] showed that $\kappa(n,e) n^2/e^3$ tends to a positive constant (called midrange crossing constant) as $n\to \infty$ and $n \ll e \ll n^2$, proving a conjecture of Erd\H{o}s and Guy. In this note, we extend their proof to show that the midrange crossing constant exists for graph classes that satisfy a certain set of graph properties. As a corollary, we show that the the midrange crossing constant exists for the family of bipartite graphs. All these results have their analogues for rectilinear crossing numbers.

It was conjectured by Koh and Tay [Graphs Combin. 18(4) (2002), 745--756] that for $n\geq 5$ every simple graph of order $n$ and size at least $\binom{n}{2}-n+5$ has an orientation of diameter two. We prove this conjecture and hence determine for every $n\geq 5$ the minimum value of $m$ such that every graph of order $n$ and size $m$ has an orientation of diameter two.

The crossing number ${\mbox {cr}}(G)$ of a graph $G=(V,E)$ is the smallest number of edge crossings over all drawings of $G$ in the plane. For any $k\ge 1$, the $k$-planar crossing number of $G$, ${\mbox {cr}}_k(G)$, is defined as the minimum of ${\mbox {cr}}(G_1)+{\mbox {cr}}(G_2)+\ldots+{\mbox {cr}}(G_{k})$ over all graphs $G_1, G_2,\ldots, G_{k}$ with $\cup_{i=1}^{k}G_i=G$. Pach et al. [\emph{Computational Geometry: Theory and Applications} {\bf 68} 2--6, (2018)] showed that for every $k\ge 1$, we have ${\mbox {cr}}_k(G)\le \left(\frac{2}{k^2}-\frac1{k^3}\right){\mbox {cr}}(G)$ and that this bound does not remain true if we replace the constant $\frac{2}{k^2}-\frac1{k^3}$ by any number smaller than $\frac1{k^2}$. We improve the upper bound to $\frac{1}{k^2}(1+o(1))$ as $k\rightarrow \infty$. For the class of bipartite graphs, we show that the best constant is exactly $\frac{1}{k^2}$ for every $k$. The results extend to the rectilinear variant of the $k$-planar crossing number., Comment: 13 pages, 1 figure, 1 table

For $n \in \mathbb{N}$ let $\delta_n$ be the smallest value such that every graph of order $n$ and minimum degree at least $\delta_n$ admits an orientation of diameter two. We show that $\delta_n=\frac{n}{2} + \Theta(\ln n)$.

Imitating a recently introduced invariant of trees, we initiate the study of the inducibility of $d$-ary trees (rooted trees whose vertex outdegrees are bounded from above by $d\geq 2$) with a given number of leaves. We determine the exact inducibility for stars and binary caterpillars. For $T$ in the family of strictly $d$-ary trees (every vertex has $0$ or $d$ children), we prove that the difference between the maximum density of a $d$-ary tree $D$ in $T$ and the inducibility of $D$ is of order $\mathcal{O}(|T|^{-1/2})$ compared to the general case where it is shown that the difference is $\mathcal{O}(|T|^{-1})$ which, in particular, responds positively to an existing conjecture on the inducibility in binary trees. We also discover that the inducibility of a binary tree in $d$-ary trees is independent of $d$. Furthermore, we establish a general lower bound on the inducibility and also provide a bound for some special trees. Moreover, we find that the maximum inducibility is attained for binary caterpillars for every $d$.

We give an explicit extension of Spencer's result on the biplanar crossing number of the Erdos-Renyi random graph $G(n,p)$. In particular, we show that the k-planar crossing number of $G(n,p)$ is almost surely $\Omega((n^2p)^2)$. Along the same lines, we prove that for any fixed $k$, the $k$-planar crossing number of various models of random $d$-regular graphs is $\Omega ((dn)^2)$ for $d > c_0$ for some constant $c_0=c_0(k)$.

Tanglegrams are special graphs that consist of a pair of rooted binary trees with the same number of leaves, and a perfect matching between the two leaf-sets. These objects are of use in phylogenetics and are represented with straightline drawings where the leaves of the two plane binary trees are on two parallel lines and only the matching edges can cross. The tangle crossing number of a tanglegram is the minimum crossing number over all such drawings and is related to biologically relevant quantities, such as the number of times a parasite switched hosts. Our main results for tanglegrams which parallel known theorems for crossing numbers are as follows. The removal of a single matching edge in a tanglegram with $n$ leaves decreases the tangle crossing number by at most $n-3$, and this is sharp. Additionally, if $\gamma(n)$ is the maximum tangle crossing number of a tanglegram with $n$ leaves, we prove $\frac{1}{2}\binom{n}{2}(1-o(1))\le\gamma(n)<\frac{1}{2}\binom{n}{2}$. Further, we provide an algorithm for computing non-trivial lower bounds on the tangle crossing number in $O(n^4)$ time. This lower bound may be tight, even for tanglegrams with tangle crossing number $\Theta(n^2)$., Comment: 13 pages, 6 figures

The graphical realization of a given degree sequence and given partition adjacency matrix simultaneously is a relevant problem in data driven modeling of networks. Here we formulate common generalizations of this problem and the Exact Matching Problem, and solve them with an algebraic Monte-Carlo algorithm that runs in polynomial time if the number of partition classes is bounded.

A tanglegram consists of two rooted binary plane trees with the same number of leaves and a perfect matching between the two leaf sets. Tanglegrams are drawn with the leaves on two parallel lines, the trees on either side of the strip created by these lines, and the perfect matching inside the strip. If this can be done without any edges crossing, a tanglegram is called planar. We show that every non-planar tanglegram contains one of two non-planar 4-leaf tanglegrams as induced subtanglegram, which parallels Kuratowski's Theorem.

We determine the maximum distance between any two of the center, centroid, and subtree core among trees with a given order. Corresponding results are obtained for trees with given maximum degree and also for trees with given diameter. The problem of the maximum distance between the centroid and the subtree core among trees with given order and diameter becomes difficult. It can be solved in terms of the problem of minimizing the number of root-containing subtrees in a rooted tree of given order and height. While the latter problem remains unsolved, we provide a partial characterization of the extremal structure.

The crossing number $cr(G)$ of a graph $G=(V,E)$ is the smallest number of edge crossings over all drawings of $G$ in the plane. For any $k\ge 1$, the $k$-planar crossing number of $G$, $cr_k(G)$, is defined as the minimum of $cr(G_0)+cr(G_1)+\ldots+cr(G_{k-1})$ over all graphs $G_0, G_1,\ldots, G_{k-1}$ with $\cup_{i=0}^{k-1}G_i=G$. It is shown that for every $k\ge 1$, we have $cr_k(G)\le \left(\frac{2}{k^2}-\frac1{k^3}\right)cr(G)$. This bound does not remain true if we replace the constant $\frac{2}{k^2}-\frac1{k^3}$ by any number smaller than $\frac1{k^2}$. Some of the results extend to the rectilinear variants of the $k$-planar crossing number.

In analogy to other concepts of a similar nature, we define the inducibility of a rooted binary tree. Given a fixed rooted binary tree $B$ with $k$ leaves, we let $\gamma(B,T)$ be the proportion of all subsets of $k$ leaves in $T$ that induce a tree isomorphic to $B$. The inducibility of $B$ is $\limsup_{|T| \to \infty} \gamma(B,T)$. We determine the inducibility in some special cases, show that every binary tree has positive inducibility and prove that caterpillars are the only binary trees with inducibility $1$. We also formulate some open problems and conjectures on the inducibility. Finally, we present an application to crossing numbers of random tanglegrams.

We show that a tree of order $n$ has at most $O(5^{n/4})$ nonisomorphic subtrees, and that this bound is best possible. We also prove an analogous result for the number of nonisomorphic rooted subtrees of a rooted tree.

The aim of this paper is to provide an affirmative answer to a recent question by Bubeck and Linial on the local profile of trees. For a tree $T$, let $p^{(k)}_1(T)$ be the proportion of paths among all $k$-vertex subtrees (induced connected subgraphs) of $T$, and let $p^{(k)}_2(T)$ be the proportion of stars. Our main theorem states: if $p^{(k)}_1(T_n) \to 0$ for a sequence of trees $T_1,T_2,\ldots$ whose size tends to infinity, then $p^{(k)}_2(T_n) \to 1$. Both are also shown to be equivalent to the statement that the number of $k$-vertex subtrees grows superlinearly and the statement that the $(k-1)$th degree moment grows superlinearly.

Joint degree vectors give the number of edges between vertices of degree $i$ and degree $j$ for $1\le i\le j\le n-1$ in an $n$-vertex graph. We find lower and upper bounds for the maximum number of nonzero elements in a joint degree vector as a function of $n$. This provides an upper bound on the number of estimable parameters in the exponential random graph model with bidegree-distribution as its sufficient statistics.

The eccentricity of a vertex, $ecc_T(v) = \max_{u\in T} d_T(v,u)$, was one of the first, distance-based, tree invariants studied. The total eccentricity of a tree, $Ecc(T)$, is the sum of eccentricities of its vertices. We determine extremal values and characterize extremal tree structures for the ratios $Ecc(T)/ecc_T(u)$, $Ecc(T)/ecc_T(v)$, $ecc_T(u)/ecc_T(v)$, and $ecc_T(u)/ecc_T(w)$ where $u,w$ are leaves of $T$ and $v$ is in the center of $T$. In addition, we determine the tree structures that minimize and maximize total eccentricity among trees with a given degree sequence.

There is much recent interest in excluded subposets. Given a fixed poset $P$, how many subsets of $[n]$ can found without a copy of $P$ realized by the subset relation? The hardest and most intensely investigated problem of this kind is when $P$ is a diamond, i.e. the power set of a 2 element set. In this paper, we show infinitely many asymptotically tight constructions using random set families defined from posets based on Abelian groups. They are provided by the convergence of Markov chains on groups. Such constructions suggest that the diamond problem is hard.

In 1996, Guigo et al. [Mol. Phylogenet. Evol., 6 (1996), 189-203] posed the following problem: for a given species tree and a number of gene trees, what is the minimum number of duplication episodes, where several genes could have undergone duplication together to generate the observed situation. (Gene order is neglected, but duplication of genes could have happened only on certain segments that duplicated). We study two versions of this problem, one of which was algorithmically solved not long ago by Bansal and Eulenstein [Bioinformatics, 24(13), (2008), 132-138]. We provide min-max theorems for both versions that generalize Gallai's archetypal min-max theorem on intervals, allowing simplified proofs to the correctness of the algorithms (as it always happens with duality) and deeper understanding. An interesting feature of our approach is that its recursive nature requires a generality that bioinformaticians attempting to solve a particular problem usually avoid.

We study four problems: put $n$ distinguishable/non-distinguishable balls into $k$ non-empty distinguishable/non-distinguishable boxes randomly. What is the threshold function $k=k(n) $ to make almost sure that no two boxes contain the same number of balls? The non-distinguishable ball problems are very close to the Erd\H os--Lehner asymptotic formula for the number of partitions of the integer $n$ into $k$ parts with $k=o(n^{1/3})$. The problem is motivated by the statistics of an experiment, where we only can tell whether outcomes are identical or different.

Aydinian et al. [J. Combinatorial Theory A 118(2)(2011), 702-725] substituted the usual BLYM inequality for L-Sperner families with a set of M inequalities for $(m_1,m_2,...,m_M;L_1,L_2,...,L_M)$ type M-part Sperner families and showed that if all inequalities hold with equality, then the family is homogeneous. Aydinian et al. [Australasian J. Comb. 48(2010), 133-141] observed that all inequalities hold with equality if and only if the transversal of the Sperner family corresponds to a simple mixed orthogonal array with constraint M, strength M-1, using $m_i+1$ symbols in the $i^{\text{th}}$ column. In this paper we define $k$-dimensional $M$-part Sperner multi-families with parameters $L_P: P\in\binom{[M]}{k}$ and prove $\binom{M}{k}$ BLYM inequalities for them. We show that if k

P.L. Erdos and L.A. Szekely [Adv. Appl. Math. 10(1989), 488-496] gave a bijection between rooted semilabeled trees and set partitions. L.H. Harper's results [Ann. Math. Stat. 38(1967), 410-414] on the asymptotic normality of the Stirling numbers of the second kind translates into asymptotic normality of rooted semilabeled trees with given number of vertices, when the number of internal vertices varies. The Erdos-Szekely bijection specializes to a bijection between phylogenetic trees and set partitions with classes of size \geq 2. We consider modified Stirling numbers of the second kind that enumerate partitions of a fixed set into a given number of classes of size \geq 2, and obtain their asymptotic normality as the number of classes varies. The Erdos- Szekely bijection translates this result into the asymptotic normality of the number of phylogenetic trees with given number of vertices, when the number of leaves varies. We also obtain asymptotic normality of the number of phylogenetic trees with given number of leaves and varying number of internal vertices, which make more sense to students of phylogeny. By the Erdos-Szekely bijection this means the asymptotic normality of the number of partitions of n + m elements into m classes of size \geq 2, when n is fixed and m varies. The proofs are adaptations of the techniques of L.H. Harper [ibid.]. We provide asymptotics for the relevant expectations and variances with error term O(1/n).

Degree-based graph construction is an ubiquitous problem in network modeling, ranging from social sciences to chemical compounds and biochemical reaction networks in the cell. This problem includes existence, enumeration, exhaustive construction and sampling questions with aspects that are still open today. Here we give necessary and sufficient conditions for a sequence of nonnegative integers to be realized as a simple graph's degree sequence, such that a given (but otherwise arbitrary) set of connections from a arbitrarily given node are avoided. We then use this result to present a swap-free algorithm that builds {\em all} simple graphs realizing a given degree sequence. In a wider context, we show that our result provides a greedy construction method to build all the $f$-factor subgraphs embedded within $K_n\setminus S_k$, where $K_n$ is the complete graph and $S_k$ is a star graph centered on one of the nodes., Comment: 12 pages, 1 figure

Our previous paper applied a lopsided version of the Lov\'asz Local Lemma that allows negative dependency graphs to the space of random injections from an $m$-element set to an $n$-element set. Equivalently, the same story can be told about the space of random matchings in $K_{n,m}$. Now we show how the cited version of the Lov\'asz Local Lemma applies to the space of random matchings in $K_{2n}$. We also prove tight upper bounds that asymptotically match the lower bound given by the Lov\'asz Local Lemma. As a consequence, we give new proofs to results on the enumeration of $d$-regular graphs. The tight upper bounds can be modified to the space of matchings in $K_{n,m}$, where they yield as application asymptotic formulas for permutation and Latin rectangle enumeration problems. The strength of the method is shown by a new result: enumeration of graphs by degree sequence or bipartite degree sequence and girth. As another application, we provide a new proof to the classical probabilistic result of Erd\H os that showed the existence of graphs with arbitrary large girth and chromatic number. If the degree sequence satisfies some mild conditions, almost all graphs with this degree sequence and prescribed girth have high chromatic number.

We improve the lower bound on the extremal version of the Maximum Agreement Subtree problem. Namely we prove that two binary trees on the same $n$ leaves have subtrees with the same $\geq c\log\log n$ leaves which are homeomorphic, such that homeomorphism is identity on the leaves., Comment: 5 pages, 1 figure

Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following question: is the amount of sequence data required to accurately reconstruct a tree significantly more than the amount required to test whether or not a candidate tree was the `true' tree? By `significantly', we mean that the two quantities behave the same way as a function of the number of species being considered. We prove that, for a certain type of model, the amount of information required is not significantly different; while for another type of model, the information required to test a tree is independent of the number of leaves, while that required to reconstruct it grows with this number. Our results combine probabilistic and combinatorial arguments., Comment: 15 pages, 3 figures

This paper continues our earlier investigations into the inversion of random functions in a general (abstract) setting. In Section 2 we investigate a concept of invertibility and the invertibility of the composition of random functions. In Section 3 we resolve some questions concerning the number of samples required to ensure the accuracy of parametric maximum likelihood estimation (MLE). A direct application to phylogeny reconstruction is given.