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There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Many natural language processing (NLP) applications require the computation of similarities between pairs of syntactic or semantic trees. Many researchers have used tree edit distance for this task, but this technique suffers from the…
Most Machine Learning (ML) methods, from clustering to classification, rely on a distance function to describe relationships between datapoints. For complex datasets it is hard to avoid making some arbitrary choices when defining a distance…
The Weisfeiler-Lehman graph kernels are among the most prevalent graph kernels due to their remarkable time complexity and predictive performance. Their key concept is based on an implicit comparison of neighborhood representing trees with…
Although random cell complexes occur throughout the physical sciences, there does not appear to be a standard way to quantify their statistical similarities and differences. The various proposals in the literature are usually motivated by…
A merge tree is a topological descriptor of a real-valued function. Merge trees are used in visualization and topological data analysis, either directly or as a means to another end: computing a 0-dimensional persistence diagram,…
Recent advances in self-supervised learning and neural network scaling have enabled the creation of large models, known as foundation models, which can be easily adapted to a wide range of downstream tasks. The current paradigm for…
In graph theory, a tree is one of the more popular families of graphs with a wide range of applications in computer science as well as many other related fields. While there are several distance measures over the set of all trees, we…
We study the problem of how well a tree metric is able to preserve the sum of pairwise distances of an arbitrary metric. This problem is closely related to low-stretch metric embeddings and is interesting by its own flavor from the line of…
Community structure is of paramount importance for the understanding of complex networks. Consequently, there is a tremendous effort in order to develop efficient community detection algorithms. Unfortunately, the issue of a fair assessment…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…
We transfer distances on clusterings to the building process of decision trees, and as a consequence extend the classical ID3 algorithm to perform modifications based on the global distance of the tree to the ground truth--instead of…
In this empirical study, I compare various tree distance measures -- originally developed in computational biology for the purpose of tree comparison -- for the purpose of parser evaluation. I will control for the parser setting by…
We introduce a topology on the space of all isomorphism types represented in a given class of countable models, and use this topology as an aid in classifying the isomorphism types. This mixes ideas from effective descriptive set theory and…
In this paper, we propose a concept to design, track, and compare application-specific feature definitions expressed as sets of critical points. Our work has been inspired by the observation that in many applications a large variety of…
Modelling semantic similarity plays a fundamental role in lexical semantic applications. A natural way of calculating semantic similarity is to access handcrafted semantic networks, but similarity prediction can also be anticipated in a…
Local feature matching aims at establishing sparse correspondences between a pair of images. Recently, detector-free methods present generally better performance but are not satisfactory in image pairs with large scale differences. In this…
Different types of graphs and complex networks have been characterized, analyzed, and modeled based on measurements of their respective topology. However, the available networks may constitute approximations of the original structure as a…
Firing a gun leaves marks on cartridge cases which purportedly uniquely identify the gun. Firearms examiners typically use a visual examination to evaluate if two cartridge cases were fired from the same gun, and this is a subjective…
1. Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. 2. Over time, sensor technology for measuring movement patterns has…