Related papers: Progress on Constructing Phylogenetic Networks for…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
To fully exploit the potential of computational phylogenetic methods for cognate data one needs to leverage specific (complex) models an machine learning-based techniques. However, both approaches require datasets that are substantially…
Human history leaves fingerprints in human languages. Little is known over language evolution and its study is of great importance. Here, we construct a simple stochastic model and compare its results to statistical data of real languages.…
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…
The evolution of language has been a hotly debated subject with contradicting hypotheses and unreliable claims. Drawing from signalling games, dynamic population mechanics, machine learning and algebraic topology, we present a method for…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
This paper introduces how human languages can be studied in light of recent development of network theories. There are two directions of exploration. One is to study networks existing in the language system. Various lexical networks can be…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
This chapter critically examines the potential contributions of modern language models to theoretical linguistics. Despite their focus on engineering goals, these models' ability to acquire sophisticated linguistic knowledge from mere…
The network characteristics based on the phonological similarities in the lexicons of several languages were examined. These languages differed widely in their history and linguistic structure, but commonalities in the network…
Is it possible to develop a `physics of language' which can explain the spatial, temporal and social patterns we see, and which can predict future change like we forecast the weather? Such a theory is likely to involve ideas from…
Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…
Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
Inflection is an essential part of every human language's morphology, yet little effort has been made to unify linguistic theory and computational methods in recent years. Methods of string manipulation are used to infer inflectional…
We investigate the diffusion of linguistic innovations on a fully connected network in order to understand the emergence of linguistic diversity. We employ an agent-based dynamics based on the Axelrod model, where interactions between…
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…