Related papers: Phylotrack: C++ and Python libraries for in silico…
Reliable localization is essential for sustainable forest management, as it allows robots or sensor systems to revisit and monitor the status of individual trees over long periods. In modern forestry, this management is structured around…
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…
This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a…
forqs is a forward-in-time simulation of recombination, quantitative traits, and selection. It was designed to investigate haplotype patterns resulting from scenarios where substantial evolutionary change has taken place in a small number…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples…
Detecting microbial biomarkers used to predict disease phenotypes and clinical outcomes is crucial for disease early-stage screening and diagnosis. Most methods for biomarker identification are linear-based, which is very limited as…
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…
Bibliometric analysis is a critical tool for understanding the structure, dynamics, and impact of scientific research. Traditional methods often fall short in capturing the intricate relationships and evolving trends within scientific…
In this paper we introduce the phylogenetic scan test (PhyloScan) for investigating cross-group differences in microbiome compositions using the Dirichlet-tree multinomial (DTM) model. DTM models the microbiome data through a cascade of…
The simplicity of Python and the power of C++ force stark choices on a scientific software stack. There have been multiple developments to mitigate language boundaries by implementing language bindings, but the impedance mismatch between…
Computational notebooks are notoriously prone to reproducibility failures. By permitting out-of-order cell execution, notebooks accumulate hidden state and implicit dependencies that cause interactive executions to silently diverge from…
We report on the process of taking an early 2000's mathematical library, the Small Phylogenetic Trees, and transforming it into a FAIR, modern, and sustainable repository for data from algebraic phylogenetics. This process is based on a…
A promising paradigm for achieving highly efficient deep neural networks is the idea of evolutionary deep intelligence, which mimics biological evolution processes to progressively synthesize more efficient networks. A crucial design factor…
We propose ClusPath, a novel algorithm for detecting general evolution tendencies in a population of entities. We show how abstract notions, such as the Swedish socio-economical model (in a political dataset) or the companies fiscal…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
Experimental evolution has yielded surprising insights into human history and evolution by shedding light on the roles of chance and contingency in history and evolution, and on the deep evolutionary roots of cooperation, conflict and kin…
Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a…
GitHub Copilot, an extension for the Visual Studio Code development environment powered by the large-scale language model Codex, makes automatic program synthesis available for software developers. This model has been extensively studied in…
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…