Related papers: Phylotrack: C++ and Python libraries for in silico…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
Multi-objective evolutionary algorithms (MOEAs) have emerged as powerful tools for solving complex optimization problems characterized by multiple, often conflicting, objectives. While advancements have been made in computational efficiency…
Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
We introduce BioTrove, the largest publicly accessible dataset designed to advance AI applications in biodiversity. Curated from the iNaturalist platform and vetted to include only research-grade data, BioTrove contains 161.9 million…
We present POLO --- a C++ library for large-scale parallel optimization research that emphasizes ease-of-use, flexibility and efficiency in algorithm design. It uses multiple inheritance and template programming to decompose algorithms into…
Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…
The integration of bioinformatics predictions and experimental validation plays a pivotal role in advancing biological research, from understanding molecular mechanisms to developing therapeutic strategies. Bioinformatics tools and methods…
Visual data is used in numerous different scientific workflows ranging from remote sensing to ecology. As the amount of observation data increases, the challenge is not just to make accurate predictions but also to understand the underlying…
PINSKY is a system for open-ended learning through neuroevolution in game-based domains. It builds on the Paired Open-Ended Trailblazer (POET) system, which originally explored learning and environment generation for bipedal walkers, and…
Understanding the evolution of complexity is an important topic in a wide variety of academic fields. Implications of better understanding complexity include increased knowledge of major evolutionary transitions and the properties of living…
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the…
Evolutionary sparse learning (ESL) uses a supervised machine learning approach, Least Absolute Shrinkage and Selection Operator (LASSO), to build models explaining the relationship between a hypothesis and the variation across genomic…
We describe BayesMix, a C++ library for MCMC posterior simulation for general Bayesian mixture models. The goal of BayesMix is to provide a self-contained ecosystem to perform inference for mixture models to computer scientists,…
Designing effective control policies for autonomous systems remains a fundamental challenge, traditionally addressed through reinforcement learning or manual engineering. While reinforcement learning has achieved remarkable success, it…
Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution,…
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…
A deductive program synthesis tool takes a specification as input and derives a program that satisfies the specification. The drawback of this approach is that search spaces for such correct programs tend to be enormous, making it difficult…