Related papers: Tractable Maximization of Budgeted Phylogenetic Di…

Query evaluation on probabilistic databases is generally intractable (#P-hard). Existing dichotomy results have identified which queries are tractable (or safe), and connected them to tractable lineages. In our previous work, using…

We introduce a new parameter, called stretch-width, that we show sits strictly between clique-width and twin-width. Unlike the reduced parameters [BKW '22], planar graphs and polynomial subdivisions do not have bounded stretch-width. This…

Treewidth and hypertree width have proven to be highly successful structural parameters in the context of the Constraint Satisfaction Problem (CSP). When either of these parameters is bounded by a constant, then CSP becomes solvable in…

The traditional approach to network robustness, is based on comparing network parameters before and after an event of nodes removal, such as the change in network diameter, the change in giant component size and the existence of giant…

Given a budget and arbitrary cost for selecting each node, the budgeted influence maximization (BIM) problem concerns selecting a set of seed nodes to disseminate some information that maximizes the total number of nodes influenced (termed…

We consider two capacity problems in P2P networks. In the first one, the nodes have an infinite amount of data to send and the goal is to optimally allocate their uplink bandwidths such that the demands of every peer in terms of receiving…

In this paper, we present fixed-parameter tractability algorithms for both the undirected and directed versions of the Spanning Tree Isomorphism Problem, parameterized by the size $k$ of a redundant set. A redundant set is a collection of…

Sparse decision trees are one of the most common forms of interpretable models. While recent advances have produced algorithms that fully optimize sparse decision trees for prediction, that work does not address policy design, because the…

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…

It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…

Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

In this study, we investigate the application of Semidefinite Programming (SDP) to phylogenetics. SDP is a powerful optimization framework that seeks to optimize a linear objective function over the cone of positive semidefinite matrices.…

We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the…

Parameterized algorithms are a way to solve hard problems more efficiently, given that a specific parameter of the input is small. In this paper, we apply this idea to the field of answer set programming (ASP). To this end, we propose two…

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…

While much of network design focuses mostly on cost (number or weight of edges), node degrees have also played an important role. They have traditionally either appeared as an objective, to minimize the maximum degree (e.g., the Minimum…

Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…

It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…

Arising from structural graph theory, treewidth has become a focus of study in fixed-parameter tractable algorithms in various communities including combinatorics, integer-linear programming, and numerical analysis. Many NP-hard problems…