Related papers: Rotation Distance is Fixed-Parameter Tractable
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…
Recently it was shown that, if the subtree and chain reduction rules have been applied exhaustively to two unrooted phylogenetic trees, the reduced trees will have at most 15k-9 taxa where k is the TBR (Tree Bisection and Reconnection)…
Every finite metric tree has generalized roundness strictly greater than one. On the other hand, some countable metric trees have generalized roundness precisely one. The purpose of this paper is to identify some large classes of countable…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
In this paper, we present a novel heuristic algorithm for the stable but NP-complete deformation-based edit distance on merge trees. Our key contribution is the introduction of a user-controlled look-ahead parameter that allows to trade off…
We study the problem of how well a tree metric is able to preserve the sum of pairwise distances of an arbitrary metric. This problem is closely related to low-stretch metric embeddings and is interesting by its own flavor from the line of…
We consider the well-studied problem of finding a spanning tree with minimum average distance between vertex pairs (called a MAD tree). This is a classic network design problem which is known to be NP-hard. While approximation algorithms…
A flip in a plane spanning tree $T$ is the operation of removing one edge from $T$ and adding another edge such that the resulting structure is again a plane spanning tree. For trees on a set of points in convex position we study two…
The matching distance is a computationally tractable topological measure to compare multi-filtered simplicial complexes. We design efficient algorithms for approximating the matching distance of two bi-filtered complexes to any desired…
Metrics for merge trees that are simultaneously stable, informative, and efficiently computable have so far eluded researchers. We show in this work that it is possible to devise such a metric when restricting merge trees to ordered domains…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
An order-theoretic forest is a countable partial order such that the set of elements larger than any element is linearly ordered. It is an order-theoretic tree if any two elements have an upper-bound. The order type of a branch can be any…
Tree rearrangement operations typically induce a metric on the space of phylogenetic trees. One important property of these metrics is the size of the neighbourhood, that is, the number of trees exactly one operation from a given tree. We…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
A rotor-router walk on a graph is a deterministic process, in which each vertex is endowed with a rotor that points to one of the neighbors. A particle located at some vertex first rotates the rotor in a prescribed order, and then it is…
We consider spanning trees of $n$ points in convex position whose edges are pairwise non-crossing. Applying a flip to such a tree consists in adding an edge and removing another so that the result is still a non-crossing spanning tree.…
This paper presents several new tractability results for planning based on macros. We describe an algorithm that optimally solves planning problems in a class that we call inverted tree reducible, and is provably tractable for several…
Geodesic distance, sometimes called shortest path length, has proven useful in a great variety of applications, such as information retrieval on networks including treelike networked models. Here, our goal is to analytically determine the…