Related papers: Progress on Constructing Phylogenetic Networks for…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
In this paper, we tackle the problem of convolutional neural network design. Instead of focusing on the design of the overall architecture, we investigate a design space that is usually overlooked, i.e. adjusting the channel configurations…
Although linguistic typology has a long history, computational approaches have only recently gained popularity. The use of distributed representations in computational linguistics has also become increasingly popular. A recent development…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
We consider character sequences evolving on a phylogenetic tree under the TKF91 model. We show that as the sequence lengths tend to infinity the the topology of the phylogenetic tree and the edge lengths are determined by any one of (a) the…
Investigating linguistic relationships on a global scale requires analyzing diverse features such as syntax, phonology and prosody, which evolve at varying rates influenced by internal diversification, language contact, and sociolinguistic…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
Deep neural networks are inherently opaque and challenging to interpret. Unlike hand-crafted feature-based models, we struggle to comprehend the concepts learned and how they interact within these models. This understanding is crucial not…
The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…
Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
This paper presents a statistically sound method for using likelihood to assess potential models of network evolution. The method is tested on data from five real networks. Data from the internet autonomous system network, from two photo…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
Understanding how individual learning behavior and structural dynamics interact is essential to modeling emergent phenomena in socioeconomic networks. While bounded rationality and network adaptation have been widely studied, the role of…
The Naming Game is an agent-based model where individuals communicate to name an initially unnamed object. On a large class of networks continual pairwise interactions lead the system to an ultimate consensus state, in which agents converge…
Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…
We use the persistent homology method of topological data analysis and dimensional analysis techniques to study data of syntactic structures of world languages. We analyze relations between syntactic parameters in terms of dimensionality,…
The application of phylogenetic techniques to the documentation of cultural history can present a distorted picture due to horizontal transmission and blending. Moreover, the units of cultural transmission must be communicable concepts,…
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…