Related papers: Progress on Constructing Phylogenetic Networks for…

Stochasticity and spatial heterogeneity are of great interest recently in studying the spread of an infectious disease. The presented method solves an inverse problem to discover the effectively decisive topology of a heterogeneous network…

We show that short-range phoneme dependencies encode large-scale patterns of linguistic relatedness, with direct implications for quantitative typology and evolutionary linguistics. Specifically, using an information-theoretic framework, we…

Large language models (LLMs) are increasingly used as substitutes for human subjects in behavioral simulations, including synthetic social network generation. Yet it remains unclear how their relational outputs depend on prompt design,…

How do neural language models acquire a language's structure when trained for next-token prediction? We address this question by deriving theoretical scaling laws for neural network performance on synthetic datasets generated by the Random…

In this paper we review some recent results that shed light on a fundamental question in molecular systematics: how much phylogenetic `signal' can we expect from characters that have evolved under some Markov process? There are many sides…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

Computer model has been extensively adopted to overcome the time limitation of language evolution by transforming language theory into physical modeling mechanism, which helps to explore the general laws of the evolution. In this paper, a…

Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…

Syntax connects words to each other in very specific ways. Two words are syntactically connected if they depend directly on each other. Syntactic connections usually happen within a sentence. Gathering all those connection across several…

Social networks exhibit strikingly systematic patterns across a wide range of human contexts. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric…

A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…

A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…

Generative models defining joint distributions over parse trees and sentences are useful for parsing and language modeling, but impose restrictions on the scope of features and are often outperformed by discriminative models. We propose a…

Stochastic models of evolution (Markov random fields on trivalent trees) generally assume that different characters (different runs of the stochastic process) are independent and identically distributed. In this paper we take the first…

In this research, we advanced a spoken language recognition system, moving beyond traditional feature vector-based models. Our improvements focused on effectively capturing language characteristics over extended periods using a specialized…

Generating synthetic languages aids in the testing and validation of future computational linguistic models and methods. This thesis extends the BEAST2 phylogenetic framework to add linguistic sequence generation under multiple models. The…

The association of a given human phenotype to a genetic variant remains a critical challenge for biology. We present a novel system called PhenoLinker capable of associating a score to a phenotype-gene relationship by using heterogeneous…

Morphosyntactic lexicons and word vector representations have both proven useful for improving the accuracy of statistical part-of-speech taggers. Here we compare the performances of four systems on datasets covering 16 languages, two of…

n this paper, we attempt to explain the emergence of the linguistic diversity that exists across the consonant inventories of some of the major language families of the world through a complex network based growth model. There is only a…

The success of large pretrained language models (LMs) such as BERT and RoBERTa has sparked interest in probing their representations, in order to unveil what types of knowledge they implicitly capture. While prior research focused on…