相关论文: A tight kernel for computing the tree bisection an…

Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…

In this experimental study we consider Steiner tree approximations that guarantee a constant approximation of ratio smaller than $2$. The considered greedy algorithms and approaches based on linear programming involve the incorporation of…

We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…

Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…

We study search trees with 2-way comparisons (2WCST's), which involve separate less-than and equal-to tests in their nodes, each test having two possible outcomes, yes and no. These trees have a much subtler structure than standard search…

Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for…

We study the natural problem of Triplet Reconstruction (also Rooted Triplets Consistency or Triplet Clustering), originally motivated in computational biology and relational databases (Aho, Sagiv, Szymanski, and Ullman, 1981): given $n$…

Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…

Phylogenetic networks allow modeling reticulate evolution, capturing events such as hybridization and horizontal gene transfer. A fundamental computational problem in this context is the Tree Containment problem, which asks whether a given…

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…

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…

Vertex deletion and edge deletion problems play a central role in Parameterized Complexity. Examples include classical problems like Feedback Vertex Set, Odd Cycle Transversal, and Chordal Deletion. Interestingly, the study of edge…

We revisit the \textsc{$k$-Secluded Tree} problem. Given a vertex-weighted undirected graph $G$, its objective is to find a maximum-weight induced subtree $T$ whose open neighborhood has size at most $k$. We present a fixed-parameter…

Orchard and tree-child networks share an important property with phylogenetic trees: they can be completely reduced to a single node by iteratively deleting cherries and reticulated cherries. As it is the case with phylogenetic trees, the…

Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…

Kernelization is a theoretical formalization of efficient preprocessing for NP-hard problems. Empirically, preprocessing is highly successful in practice, for example in state-of-the-art ILP-solvers like CPLEX. Motivated by this, previous…

It is a classical result that any finite tree with positively weighted edges, and without vertices of degree 2, is uniquely determined by the weighted path distance between each pair of leaves. Moreover, it is possible for a (small) strict…

This paper tightens the best known analysis of Hein's 1989 algorithm to infer the topology of a weighted tree based on the lengths of paths between its leaves. It shows that the number of length queries required for a degree-$k$ tree of $n$…

In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…

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…