Related papers: On the Weighted Quartet Consensus problem
The Consensus Clustering problem has been introduced as an effective way to analyze the results of different microarray experiments. The problem consists of looking for a partition that best summarizes a set of input partitions (each…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…
We study the complexity of approximating solution structure of the bijective weighted sentence alignment problem of DeNero and Klein (2008). In particular, we consider the complexity of finding an alignment that has a significant overlap…
Solving fastest distributed consensus averaging problem (i.e., finding weights on the edges to minimize the second-largest eigenvalue modulus of the weight matrix) over networks with different topologies is one of the primary areas of…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
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…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…
We consider the problem of optimally compressing and caching data across a communication network. Given the data generated at edge nodes and a routing path, our goal is to determine the optimal data compression ratios and caching decisions…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
The problem of nearest neighbor condensing has enjoyed a long history of study, both in its theoretical and practical aspects. In this paper, we introduce the problem of weighted distance nearest neighbor condensing, where one assigns…
Treewidth is a useful tool in designing graph algorithms. Although many NP-hard graph problems can be solved in linear time when the input graphs have small treewidth, there are problems which remain hard on graphs of bounded treewidth. In…
The problems discussed in this paper are motivated by general ratio consensus algorithms, introduced by Kempe, Dobra, and Gehrke (2003) in a simple form as the push-sum algorithm, later extended by B\'en\'ezit et al. (2010) under the name…
Let $G$ be a complete edge-weighted graph on $n$ vertices. To each subset of vertices of $G$ assign the cost of the minimum spanning tree of the subset as its weight. Suppose that $n$ is a multiple of some fixed positive integer $k$. The…
We resolve a long-standing open question, about the existence of a constant-factor approximation algorithm for the average-case \textsc{Decision Tree} problem with uniform probability distribution over the hypotheses. We answer the question…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…
We study complexity of rearrangement problems in the generalized breakpoint model and settle several open questions. The model was introduced by Tannier et al. (2009) who showed that the median problem is solvable in polynomial time in the…
Distributed quantized weight-balancing and average consensus over fixed digraphs are considered. A digraph with non-negative weights associated to its edges is weight-balanced if, for each node, the sum of the weights of its out-going edges…