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Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

Text-to-image models are powerful tools for image creation. However, the generation process is akin to a dice roll and makes it difficult to achieve a single image that captures everything a user wants. In this paper, we propose a framework…

Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…

We consider the problems of computing maximal palindromes and distinct palindromes in a trie. A trie is a natural generalization of a string, which can be seen as a single-path tree. There is a linear-time offline algorithm to compute…

In many modern applications, including analysis of gene expression and text documents, the data are noisy, high-dimensional, and unordered--with no particular meaning to the given order of the variables. Yet, successful learning is often…

Discovering the underlying structures present in large real world graphs is a fundamental scientific problem. In this paper we show that a graph's clique tree can be used to extract a hyperedge replacement grammar. If we store an ordering…

We demonstrate NeedleDB, an open-source, deployment-ready database system for answering complex natural language queries over image data. Unlike existing approaches that rely on contrastive-learning embeddings (e.g., CLIP), which degrade on…

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…

treePL uses a penalised likelihood approach to produce a dated phylogeny in a maximum likelihood framework. Since its publication in 2012, few resources have been developed to explain how to use it properly. In this guide, I provide a…

Dynamic regression trees are an attractive option for automatic regression and classification with complicated response surfaces in on-line application settings. We create a sequential tree model whose state changes in time with the…

The Fenwick tree is a classical implicit data structure that stores an array in such a way that modifying an element, accessing an element, computing a prefix sum and performing a predecessor search on prefix sums all take logarithmic time.…

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…

PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…

Most phylogenetic analyses result in a sample of trees, but summarizing and visualizing these samples can be challenging. Consensus trees often provide limited information about a sample, and so methods such as consensus networks,…

We present TripNet, a method for constructing phylogenetic networks from triplets. We will present the motivations behind our approach and its theoretical and empirical justification. To demonstrate the accuracy and efficiency of TripNet,…

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…