Related papers: A simple fixed parameter tractable algorithm for c…
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…
In the Steiner Tree problem we are given an undirected edge-weighted graph as input, along with a set $K$ of vertices called terminals. The task is to output a minimum-weight connected subgraph that spans all the terminals. The famous…
Inspired by [4] we present a new algorithm for uniformly random generation of ordered trees in which all occuring outdegrees can be specified by a given sequence of numbers. The method can be used for random generation of binary or n-ary…
We introduce and study the {\em orderly spanning trees} of plane graphs. This algorithmic tool generalizes {\em canonical orderings}, which exist only for triconnected plane graphs. Although not every plane graph admits an orderly spanning…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…
We propose to prune a random forest (RF) for resource-constrained prediction. We first construct a RF and then prune it to optimize expected feature cost & accuracy. We pose pruning RFs as a novel 0-1 integer program with linear constraints…
We consider the problem of constructing an an optimal-weight tree from the 3*(n choose 4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologiesis optimal (so it can be the…
In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Optimal Morse matchings reveal essential structures of cell complexes which lead to powerful tools to study discrete geometrical objects, in particular discrete 3-manifolds. However, such matchings are known to be NP-hard to compute on…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
Higher-order unification has been shown to be undecidable. Miller discovered the pattern fragment and subsequently showed that higher-order pattern unification is decidable and has most general unifiers. We extend the algorithm to…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
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 herein introduce a new method of interpretable clustering that uses unsupervised binary trees. It is a three-stage procedure, the first stage of which entails a series of recursive binary splits to reduce the heterogeneity of the data…
We present a comprehensive classical and parameterized complexity analysis of decision tree pruning operations, extending recent research on the complexity of learning small decision trees. Thereby, we offer new insights into the…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
Given an edge-weighted graph $G$ on $n$ nodes, the NP-hard Max-Cut problem asks for a node bipartition such that the sum of edge weights joining the different partitions is maximized. We propose a fixed-parameter tractable algorithm…