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Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…

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).…

Given two phylogenetic trees with the $\{1, \ldots, n\}$ leaf-set the maximum agreement subtree problem asks what is the maximum size of the subset $A \subseteq \{1, \ldots, n\}$ such that the two trees are equivalent when restricted to…

Let $T$ be an oriented tree on $n$ vertices with maximum degree at most $e^{o(\sqrt{\log n})}$. If $G$ is a digraph on $n$ vertices with minimum semidegree $\delta^0(G)\geq(\frac12+o(1))n$, then $G$ contains $T$ as a spanning tree, as…

We introduce left and right-layered trees as trees with a specific representation and define the excess of a tree. Applying these ideas, we show a range-relaxed graceful labeling which improves on the upper bound for maximum vertex label…

An \emph{adjacency labeling scheme} for a given class of graphs is an algorithm that for every graph $G$ from the class, assigns bit strings (labels) to vertices of $G$ so that for any two vertices $u,v$, whether $u$ and $v$ are adjacent…

This note presents an encoding and a decoding algorithms for a forest of (labelled) rooted uniform hypertrees and hypercycles in linear time, by using as few as $n - 2$ integers in the range $[1,n]$. It is a simple extension of the…

Suppose we label the vertices of a tree by positive integers. The weight of an edge is defined by a monotonically increasing function of the absolute value of the difference of the labels of its endpoints. We define the total cost of the…

Arthur Cayley famously proved that there are n to the power n-2 labeled trees on n vertices. Here we go much further and show how to enumerate, fully automatically, labeled trees such that every vertex has a number of neighbors that belongs…

In this paper, we consider the minimum spanning tree problem (for short, MSTP) on an arbitrary set of $n$ points of $d$-dimensional space in $l_1$-norm. For this problem, for each fixed $d\geq 2$, there is a known algorithm of the…

Individual tree species labels are particularly hard to acquire due to the expert knowledge needed and the limitations of photointerpretation. Here, we present a methodology to automatically mine species labels from public forest inventory…

Decision trees are one of the most popular methods for solving classification problems, mainly because of their good interpretability properties. Moreover, due to advances in recent years in mixed-integer optimization, several models have…

We provide a short combinatorial proof of Cayley's formula by means of a bijective map to an outcome space of an urn-drawing problem. Furthermore we introduce an algebraic structure on the set of labeled trees, which provides a more…

We combine two methods for the lossless compression of unlabeled graphs - entropy compressing adjacency lists and computing canonical names for vertices - and solve an ensuing novel optimisation problem: Minimum-Entropy Tree-Extraction…

'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…

The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a. the weighted ancestor problem, has been extensively…

Data augmentation is widely used for training a neural network given little labeled data. A common practice of augmentation training is applying a composition of multiple transformations sequentially to the data. Existing augmentation…

In the online labeling problem with parameters n and m we are presented with a sequence of n keys from a totally ordered universe U and must assign each arriving key a label from the label set {1,2,...,m} so that the order of labels…

It is shown that for a given ordered node-labelled tree of size $n$ and with $s$ many different node labels, one can construct in linear time a top dag of height $O(\log n)$ and size $O(n / \log_\sigma n) \cap O(d \cdot \log n)$, where…

In this paper we propose a graph-based data clustering algorithm which is based on exact clustering of a minimum spanning tree in terms of a minimum isoperimetry criteria. We show that our basic clustering algorithm runs in $O(n \log n)$…