Related papers: On the quartet distance given partial information

We give algorithms to compute the Fr\'echet distance of trees and graphs with bounded tree width. Our algorithms run in $O(n^2)$ time for trees of bounded degree, and $O(n^2\sqrt{n \log n})$ time for trees of arbitrary degree. For graphs of…

It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

We apply classical quartet techniques to the problem of phylogenetic decisiveness and find a value $k$ such that all collections of at least $k$ quartets are decisive. Moreover, we prove that this bound is optimal and give a lower-bound on…

Let $T$ be an $n$-node tree of maximum degree 4, and let $P$ be a set of $n$ points in the plane with no two points on the same horizontal or vertical line. It is an open question whether $T$ always has a planar drawing on $P$ such that…

We show that the expected size of the maximum agreement subtree of two $n$-leaf trees, uniformly random among all trees with the shape, is $\Theta(\sqrt{n})$. To derive the lower bound, we prove a global structural result on a decomposition…

The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…

Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site…

In rendezvous, two agents traverse network edges in synchronous rounds and have to meet at some node. In treasure hunt, a single agent has to find a stationary target situated at an unknown node of the network. We study tradeoffs between…

A tree $T$ on $2^n$ vertices is called set-sequential if the elements in $V(T)\cup E(T)$ can be labeled with distinct nonzero $(n+1)$-dimensional $01$-vectors such that the vector labeling each edge is the component-wise sum modulo $2$ of…

We propose a preferential attachment model for network growth where new entering nodes have a partial information about the state of the network. Our main result is that the presence of bounded information modifies the degree distribution…

The necessary information for specifying a complex system may not be completely accessible to us, i.e., to mathematical treatments. This is not to be confounded with the incompleteness of our knowledge about whatever systems or nature,…

An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…

Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…

In this paper, we study the distribution of distances in random Apollonian network structures (RANS), a family of graphs which has a one-to-one correspondence with planar ternary trees. Using multivariate generating functions that express…

Phylogenetic trees in genetics and biology in general are all binary. We make an attempt to answer one fundamental question: Is such binary branching from the coarsest to the finest scales sustained by data? We convert this question into an…

The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…

Stochastic modeling of phylogenies raises five questions that have received varying levels of attention from quantitatively inclined biologists. 1) How large do we expect (from the model) the ration of maximum historical diversity to…

The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…

A pseudo-polynomial time $(1 + \varepsilon)$-approximation algorithm is presented for computing the integral and average Fr\'{e}chet distance between two given polygonal curves $T_1$ and $T_2$. In particular, the running time is…