Related papers: On the locality of the Pr\"ufer code
Neighborhood algorithms may take a considerable percentage of computer time in discrete element methods (DEM). While the sort-and-sweep algorithm is ideal in some ways, as it only deal with particles whose relative positions change in one…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
In this paper we provide a novel mathematical optimization based methodology to perturb the features of a given observation to be re-classified, by a tree ensemble classification rule, to a certain desired class. The method is based on…
Accessibility percolation is a new type of percolation problem inspired by evolutionary biology. To each vertex of a graph a random number is assigned and a path through the graph is called accessible if all numbers along the path are in…
A permutation $\boldsymbol w$ gives rise to a graph $G_{\boldsymbol w}$; the vertices of $G_{\boldsymbol w}$ are the letters in the permutation and the edges of $G_{\boldsymbol w}$ are the inversions of $\boldsymbol w$. We find that the…
While obtaining optimal algorithms for the most important problems in the LOCAL model has been one of the central goals in the area of distributed algorithms since its infancy, tight complexity bounds are elusive for many problems even when…
There is a deep connection between permutations and trees. Certain sub-structures of permutations, called sub-permutations, bijectively map to sub-trees of binary increasing trees. This opens a powerful tool set to study enumerative and…
In the infinite regular tree $\mathbb{T}_{q+1}$ with $q \in \mathbb{Z}_{\ge 2}$, we consider families $\{\mu_u^n\}$, indexed by vertices $u$ and nonnegative integers ("discrete time steps") $n$, of probability measures such that $\mu_u^n(v)…
I describe an `oct-tree' N-body code which randomly shifts, reorients, and resizes the root cell at each time step. Averaging over a plurality of root cell positions and orientations statistically restores translational and rotational…
We study local modifications of the graph distance in large random triangulations. Our main results show that, in large scales, the modified distance behaves like a deterministic constant $\mathbf{c}~\in~(0,\infty)$ times the usual graph…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
We study the relation between the minimal spanning tree (MST) on many random points and the "near-minimal" tree which is optimal subject to the constraint that a proportion $\delta$ of its edges must be different from those of the MST.…
We describe a new Pr\"ufer code which works also for infinite trees.
We show that for every hereditary permutation property P and every eps>0, there exists an integer M such that if a permutation p is eps-far from P in the Kendall's tau distance, then a random subpermutation of p of order M has the property…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
Explaining why and how a tree $t$ structurally differs from another tree $t^\star$ is a question that is encountered throughout computer science, including in understanding tree-structured data such as XML or JSON data. In this article, we…
The {\em edit distance} between two ordered trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as…
Every encoding has priori information if the encoding represents any semantic information of the unverse or object. Encoding means mapping from the unverse to the string or strings of digits. The semantic here is used in the model-theoretic…