Related papers: Progress on Constructing Phylogenetic Networks for…
Owing to the influence of real-world networks both in science and society, numerous mathematical models have been developed to understand the structure and evolution of these systems, particularly in a temporal context. Recent advancements…
Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial persistence. To understand the strategy to control such…
The probing methodology allows one to obtain a partial representation of linguistic phenomena stored in the inner layers of the neural network, using external classifiers and statistical analysis. Pre-trained transformer-based language…
We introduce Holmes, a new benchmark designed to assess language models (LMs) linguistic competence - their unconscious understanding of linguistic phenomena. Specifically, we use classifier-based probing to examine LMs' internal…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
We propose a model of the evolution of a matrix along a phylogenetic tree, in which transformations affect either entire rows or columns of the matrix. This represents the change of both lexical and phonological aspects of linguistic data,…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
A core part of linguistic typology is the classification of languages according to linguistic properties, such as those detailed in the World Atlas of Language Structure (WALS). Doing this manually is prohibitively time-consuming, which is…
Evolutionary methods have long been useful for analysis and explanation in genetics, biology, ecology, and related fields. In this work, we extend these methods to neural networks, specifically large language models (LLMs), to better…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
The phylogenetic network emerged in the 1990s as a new model to represent the evolution of species in the case where coexisting species transfer genetic information through hybridization, recombination, lateral gene transfer, etc. As is…
Neural language models (LMs) have shown to benefit significantly from enhancing word vectors with subword-level information, especially for morphologically rich languages. This has been mainly tackled by providing subword-level information…
We investigate the nature of written human language within the framework of complex network theory. In particular, we analyse the topology of Orwell's \textit{1984} focusing on the local properties of the network, such as the properties of…
Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
Social influence cannot be identified from purely observational data on social networks, because such influence is generically confounded with latent homophily, i.e., with a node's network partners being informative about the node's…
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Morphological analysis involves predicting the syntactic traits of a word (e.g. {POS: Noun, Case: Acc, Gender: Fem}). Previous work in morphological tagging improves performance for low-resource languages (LRLs) through cross-lingual…