Related papers: Are Sounds Sound for Phylogenetic Reconstruction?
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…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
In the first year of life, infants' speech perception becomes attuned to the sounds of their native language. Many accounts of this early phonetic learning exist, but computational models predicting the attunement patterns observed in…
Semantic matching is of central importance to many natural language tasks \cite{bordes2014semantic,RetrievalQA}. A successful matching algorithm needs to adequately model the internal structures of language objects and the interaction…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
Accented speech recognition and accent classification are relatively under-explored research areas in speech technology. Recently, deep learning-based methods and Transformer-based pretrained models have achieved superb performances in both…
To be able to interact better with humans, it is crucial for machines to understand sound - a primary modality of human perception. Previous works have used sound to learn embeddings for improved generic textual similarity assessment. In…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
The reconstruction mechanisms built by the human auditory system during sound reconstruction are still a matter of debate. The purpose of this study is to refine the auditory cortex model introduced in [9], and inspired by the geometrical…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…
Recent research has shown that language and the socio-cognitive phenomena associated with it can be aptly modeled and visualized through networks of linguistic entities. However, most of the existing works on linguistic networks focus only…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
Evolutionary models of languages are usually considered to take the form of trees. With the development of so-called tree constraints the plausibility of the tree model assumptions can be addressed by checking whether the moments of…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Spoken language evolves constrained by the economy of speech, which depends on factors such as the structure of the human mouth. This gives rise to local phonetic correlations in spoken words. Here we demonstrate that these local…
Bayesian approaches to reconstructing the evolutionary history of languages rely on the tree model, which assumes that these languages descended from a common ancestor and underwent modifications over time. However, this assumption can be…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino-acid usage at contacting sites. Because homologous proteins…