Related papers: Making mathematical online resources FAIR: at the …

Fair clustering has gained increasing attention in recent years, especially in applications involving socially sensitive attributes. However, existing fair clustering methods often lack interpretability, limiting their applicability in…

The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…

Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…

In recent years, randomized algorithms have established themselves as fundamental tools in computational linear algebra, with applications in scientific computing, machine learning, and quantum information science. Many randomized matrix…

A thesaurus is one, out of many, possible representations of term (or word) connectivity. The terms of a thesaurus are seen as the nodes and their relationship as the links of a directed graph. The directionality of the links retains all…

We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…

This paper describes a method for creating structure from heterogeneous sources, as part of an information database, or more specifically, a 'concept base'. Structures called 'concept trees' can grow from the semi-structured sources when…

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…

We consider the design of adaptive data structures for searching elements of a tree-structured space. We use a natural generalization of the rotation-based online binary search tree model in which the underlying search space is the set of…

In computational science and in computer science, research software is a central asset for research. Computational science is the application of computer science and software engineering principles to solving scientific problems, whereas…

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…

The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…

One initial goal for the DRMF is to seed our digital compendium with fundamental orthogonal polynomial formulae. We had used the data from the NIST Digital Library of Mathematical Functions (DLMF) as initial seed for our DRMF project. The…

Cultural phylogenies, or "trees" of culture, are typically built using methods from biology that use similarities and differences in artifacts to infer the historical relationships between the populations that produced them. While these…

Phylogenetic trees are the primary framework for conveying evolutionary relationships. While many tools exist for visualizing phylogenetic trees, most are limited to static graphics, require coding expertise, or are developed for a specific…

In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…

Machine learning (ML) is an increasingly important scientific tool supporting decision making and knowledge generation in numerous fields. With this, it also becomes more and more important that the results of ML experiments are…

Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…

Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…