Related papers: Evaluating Phylogenetic Comparative Methods under …
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…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks. To find bigger networks, one can attempt to combine small…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
Plant traits are a key to understanding and predicting the adaptation of ecosystems to environmental changes, which motivates the TRY project aiming at constructing a global database for plant traits and becoming a standard resource for the…
Quantum simulations constructing probability tensors of biological multi-taxa in phylogenetic trees are proposed, in terms of positive trace preserving maps, describing evolving systems of quantum walks with multiple walkers. Basic…
Recent generative learning models applied to protein multiple sequence alignment (MSA) datasets include simple and interpretable physics-based Potts covariation models and other machine learning models such as MSA-Transformer (MSA-T). The…
Many machine learning models have been proposed to classify phenotypes from gene expression data. In addition to their good performance, these models can potentially provide some understanding of phenotypes by extracting explanations for…
Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics,…
Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organisms carrying the trait. State-of-the-art methods assume that the trait evolves according to a…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
Phylogenetic comparative methods are new in our field and are shrouded, for most linguists, in at least a little mystery. Yet the path that led to their discovery in comparative biology is so similar to the methodological history of…
Divergence time estimation requires the reconciliation of two major sources of data. These are fossil and/or biogeographic evidence that give estimates of the absolute age of nodes (ancestors) and molecular estimates that give us estimates…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Geographic ranges of communities of species evolve in response to environmental, ecological, and evolutionary forces. Understanding the effects of these forces on species' range dynamics is a major goal of spatial ecology. Previous…
Prediction models based on deep neural networks are increasingly gaining attention for fast and accurate virtual screening systems. For decision makings in virtual screening, researchers find it useful to interpret an output of…