Related papers: Additive Approximation for Near-Perfect Phylogeny …
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
The Euclidean Steiner tree problem asks to find a min-cost metric graph that connects a given set of \emph{terminal} points $X$ in $\mathbb{R}^d$, possibly using points not in $X$ which are called Steiner points. Even though near-linear…
Uniform cost-distance Steiner trees minimize the sum of the total length and weighted path lengths from a dedicated root to the other terminals. They are applied when the tree is intended for signal transmission, e.g. in chip design or…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
We consider the problem of constructing optimal decision trees: given a collection of tests which can disambiguate between a set of $m$ possible diseases, each test having a cost, and the a-priori likelihood of the patient having any…
{\em Reoptimization} is a setting in which we are given an (near) optimal solution of a problem instance and a local modification that slightly changes the instance. The main goal is that of finding an (near) optimal solution of the…
An optimal binary search tree for an access sequence on elements is a static tree that minimizes the total search cost. Constructing perfectly optimal binary search trees is expensive so the most efficient algorithms construct almost…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
We give an algorithm that computes a $(1+\epsilon)$-approximate Steiner forest in near-linear time $n \cdot 2^{(1/\epsilon)^{O(ddim^2)} (\log \log n)^2}$. This is a dramatic improvement upon the best previous result due to Chan et al., who…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
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 present a new exact algorithm for the Steiner tree problem in edge-weighted graphs. Our algorithm improves the classical dynamic programming approach by Dreyfus and Wagner. We achieve a significantly better practical performance via…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
For a metric graph $G=(V,E)$ and $R\subset V$, the internal Steiner minimum tree problem asks for a minimum weight Steiner tree spanning $R$ such that every vertex in $R$ is not a leaf. This note shows a simple polynomial-time…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
We consider the following general network design problem on directed graphs. The input is an asymmetric metric $(V,c)$, root $r^{*}\in V$, monotone submodular function $f:2^V\rightarrow \mathbb{R}_+$ and budget $B$. The goal is to find an…