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Rectangular layouts, subdivisions of an outer rectangle into smaller rectangles, have many applications in visualizing spatial information, for instance in rectangular cartograms in which the rectangles represent geographic or political…

Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…

Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…

A brick is a 3-connected graph such that the graph obtained from it by deleting any two distinct vertices has a perfect matching. A brick is minimal if for every edge e the deletion of e results in a graph that is not a brick. We prove a…

A graph is rectilinear planar if it admits a planar orthogonal drawing without bends. While testing rectilinear planarity is NP-hard in general (Garg and Tamassia, 2001), it is a long-standing open problem to establish a tight upper bound…

A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…

We consider finite trees with edges labeled by letters on a finite alphabet $\varSigma$. Each pair of nodes defines a unique labeled path whose trace is a word of the free monoid $\varSigma^*$. The set of all such words defines the language…

A flip in a plane spanning tree $T$ is the operation of removing one edge from $T$ and adding another edge such that the resulting structure is again a plane spanning tree. For trees on a set of points in convex position we study two…

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 often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…

Language models generate reasoning sequentially, preventing them from decoupling irrelevant exploration paths during search. We introduce Tree-Structured Language Modeling (TSLM), which uses special tokens to encode branching structure,…

This paper studies Minimum Spanning Trees under incomplete information for its vertices. We assume that no information is available on the precise placement of vertices so that it is only known that vertices belong to some neighborhoods…

Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…

It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to…

Tree decompositions of graphs are of fundamental importance in structural and algorithmic graph theory. Planar decompositions generalise tree decompositions by allowing an arbitrary planar graph to index the decomposition. We prove that…

Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard…

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…

Dynamic programming is a powerful technique that is, unfortunately, often inherently sequential. That is, there exists no unified method to parallelize algorithms that use dynamic programming. In this paper, we attempt to address this issue…

For a set of red and blue points in the plane, a minimum bichromatic spanning tree (MinBST) is a shortest spanning tree of the points such that every edge has a red and a blue endpoint. A MinBST can be computed in $O(n\log n)$ time where…