Related papers: On Computing the Maximum Parsimony Score of a Phyl…

Machine learning is increasingly used to guide branch-and-cut (B&C) for mixed-integer linear programming by learning score-based policies for selecting branching variables and cutting planes. Many approaches train on local signals from…

There exist several methods dealing with the reconstruction of rooted phylogenetic networks explaining different evolutionary histories given by rooted binary phylogenetic trees. In practice, however, due to insufficient information of the…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…

Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is…

Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted binary phylogenetic trees on taxon set X in time (6r)^r.poly(n), where n=|X|. The novelty of this approach is that it avoids the…

Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…

Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…

The robustness of deep neural networks is crucial to modern AI-enabled systems and should be formally verified. Sigmoid-like neural networks have been adopted in a wide range of applications. Due to their non-linearity, Sigmoid-like…

With the development of connected filters for the last decade, many algorithms have been proposed to compute the max-tree. Max-tree allows to compute the most advanced connected operators in a simple way. However, no fair comparison of…

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…

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…

We give a 2-approximation algorithm for Non-Uniform Sparsest Cut that runs in time $n^{O(k)}$, where $k$ is the treewidth of the graph. This improves on the previous $2^{2^k}$-approximation in time $\poly(n) 2^{O(k)}$ due to Chlamt\'a\v{c}…

The recently introduced graph parameter tree-cut width plays a similar role with respect to immersions as the graph parameter treewidth plays with respect to minors. In this paper, we provide the first algorithmic applications of tree-cut…

In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…

We seek to develop network algorithms for function computation in sensor networks. Specifically, we want dynamic joint aggregation, routing, and scheduling algorithms that have analytically provable performance benefits due to in-network…

An instance of the Connected Maximum Cut problem consists of an undirected graph G = (V, E) and the goal is to find a subset of vertices S $\subseteq$ V that maximizes the number of edges in the cut \delta(S) such that the induced graph…

Here we show that, given a set of clusters C on a set of taxa X, where |X|=n, it is possible to determine in time f(k).poly(n) whether there exists a level-<= k network (i.e. a network where each biconnected component has reticulation…

Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…