Related papers: Progress on Constructing Phylogenetic Networks for…

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…

We study the self-organization of the consonant inventories through a complex network approach. We observe that the distribution of occurrence as well as cooccurrence of the consonants across languages follow a power-law behavior. The…

Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic…

Generative models, from diffusion models to large language models, achieve remarkable performance but at a cost in training data orders of magnitude larger than what biological learners require. An alternative paradigm has emerged in which…

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…

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…

Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…

Phylogenetic methods have broad potential in linguistics beyond tree inference. Here, we show how a phylogenetic approach opens the possibility of gaining historical insights from entirely new kinds of linguistic data--in this instance,…

Age estimation of unknown persons is a challenging pattern analysis task due to the lacking of training data and various aging mechanisms for different people. Label distribution learning-based methods usually make distribution assumptions…

Recent advances in language modeling using deep neural networks have shown that these models learn representations, that vary with the network depth from morphology to semantic relationships like co-reference. We apply pre-trained language…

In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…

This work examines the problem of topology inference over discrete-time nonlinear stochastic networked dynamical systems. The goal is to recover the underlying digraph linking the network agents, from observations of their state-evolution.…

The neutral theory of genetic and linguistic evolution holds that the relative frequencies of variants evolve by random drift. Neutral evolution remains a plausible null model of language change. In this paper we provide evidence against…

Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…

Character-level features are currently used in different neural network-based natural language processing algorithms. However, little is known about the character-level patterns those models learn. Moreover, models are often compared only…

Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…

Inference of network-like evolutionary relationships between species from genomic data must address the interwoven signals from both gene flow and incomplete lineage sorting. The heavy computational demands of standard approaches to this…

Language can be described as a network of interacting objects with different qualitative properties and complexity. These networks include semantic, syntactic, or phonological levels and have been found to provide a new picture of language…

The phenomenon of human language is widely studied from various points of view. It is interesting not only for social scientists, antropologists or philosophers, but also for those, interesting in the network dynamics. In several recent…