Related papers: TreeOTU: Operational Taxonomic Unit Classification…
Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that…
Motivation: Predictive modelling of gene expression is a powerful framework for the in silico exploration of transcriptional regulatory interactions through the integration of high-throughput -omics data. A major limitation of previous…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
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…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
Recent advancements in aligning large language models via reinforcement learning have achieved remarkable gains in solving complex reasoning problems, but at the cost of expensive on-policy rollouts and limited exploration of diverse…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
How a single fertilized cell gives rise to a complex array of specialized cell types in development is a central question in biology. The cells grow, divide, and acquire differentiated characteristics through poorly understood molecular…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…
When studying ecosystems, hierarchical trees are often used to organize entities based on proximity criteria, such as the taxonomy in microbiology, social classes in geography, or product types in retail businesses, offering valuable…
Recently program learning techniques have been proposed to process source code based on syntactical structures (e.g., Abstract Syntax Trees) and/or semantic information (e.g., Dependency Graphs). Although graphs may be better at capturing…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…