arXiv subjects

Tom Niklas Hamann

Publications and source records attributed to Tom Niklas Hamann.

3 recordsLinked to original sources

arXiv2026

A height-based metaconcept for rooted tree balance and its implications for the $B_1$ index

Tree balance has received considerable attention in recent years, both in phylogenetics and in other areas. Numerous (im)balance indices have been proposed to quantify the (im)balance of rooted trees. A recent comprehensive survey summarized this literature and showed that many existing indices are based on similar underlying principles. To unify these approaches, three general metaconcepts were introduced, providing a framework to classify, analyze, and extend imbalance indices. In this context, a metaconcept is a function $Φ_f$ that depends on another function $f$ capturing some aspect of tree shape. In this manuscript, we extend this line of research by introducing a new metaconcept based on the heights of the pending subtrees of all inner vertices. We provide a thorough analysis of this metaconcept and use it to answer open questions concerning the well-known $B_1$ balance index. In particular, we characterize the tree shapes that maximize the $B_1$ index in two cases: (i) arbitrary rooted trees and (ii) binary rooted trees. For both cases, we also determine the corresponding maximum values of the index. Finally, while the $B_1$ index is induced by a so-called third-order metaconcept, we explicitly introduce three new (im)balance indices derived from the first- and second-order height metaconcepts, respectively, thereby demonstrating that pending subtree heights give rise to a variety of novel (im)balance indices.

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arXiv2025

Metaconcepts of rooted tree balance

Measures of tree balance play an important role in many different research areas such as mathematical phylogenetics or theoretical computer science. Typically, tree balance is quantified by a single number which is assigned to the tree by a balance or imbalance index, of which several exist in the literature. Most of these indices are based on structural aspects of tree shape, such as clade sizes or leaf depths. For instance, indices like the Sackin index, total cophenetic index, and $\widehat{s}$-shape statistic all quantify tree balance through clade sizes, albeit with different definitions and properties. In this paper, we formalize the idea that many tree (im)balance indices are functions of similar underlying tree shape characteristics by introducing metaconcepts of tree balance. A metaconcept is a function $Φ_f$ that depends on a function $f$ capturing some aspect of tree shape, such as balance values, clade sizes, or leaf depths. These metaconcepts encompass existing indices but also provide new means of measuring tree balance. The versatility and generality of metaconcepts allow for the systematic study of entire families of (im)balance indices, providing deeper insights that extend beyond index-by-index analysis.

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arXiv2022

How far is my network from being edge-based? Proximity measures for edge-basedness of unrooted phylogenetic networks

Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into account, they are relatively rare, which implies that biologically relevant networks are often assumed to be similar to trees in the sense that they can be obtained by taking a tree and adding some additional edges. This observation led to the concept of so-called tree-based networks, which recently gained substantial interest in the literature. Unfortunately, though, identifying such networks in the unrooted case is an NP-complete problem. Therefore, classes of networks for which tree-basedness can be guaranteed are of the utmost interest. The most prominent such class is formed by so-called edge-based networks, which have a close relationship to generalized series-parallel graphs known from graph theory. They can be identified in linear time and are in some regards biologically more plausible than general tree-based networks. While concerning the latter proximity measures for general networks have already been introduced, such measures are not yet available for edge-basedness. This means that for an arbitrary unrooted network, the "distance" to the nearest edge-based network could so far not be determined. The present manuscript fills this gap by introducing two classes of proximity measures for edge-basedness, one based on the given network itself and one based on its so-called leaf shrink graph (LS graph). Both classes contain four different proximity measures, whose similarities and differences we study subsequently.

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