Related papers: Beyond cognacy
Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
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,…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Most current word prediction systems make use of n-gram language models (LM) to estimate the probability of the following word in a phrase. In the past years there have been many attempts to enrich such language models with further…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
We describe a set of new methods to partially automate linguistic phylogenetic inference given (1) cognate sets with their respective protoforms and sound laws, (2) a mapping from phones to their articulatory features and (3) a typological…
Ranking functions in information retrieval are often used in search engines to recommend the relevant answers to the query. This paper makes use of this notion of information retrieval and applies onto the problem domain of cognate…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper,…
The Phylogenetic Genome Annotator (PGA) is a computer program that enables real-time comparison of 'gene trees' versus 'species trees' obtained from predicted open reading frames of whole genome data. The gene phylogenies are inferred for…
Phylogenetic comparative methods are new in our field and are shrouded, for most linguists, in at least a little mystery. Yet the path that led to their discovery in comparative biology is so similar to the methodological history of…
We describe an "embarrassingly parallel" method for Bayesian phylogenetic inference, annealed Sequential Monte Carlo, based on recent advances in the Sequential Monte Carlo literature such as adaptive determination of annealing parameters.…
Automaton-based representations of task knowledge play an important role in control and planning for sequential decision-making problems. However, obtaining the high-level task knowledge required to build such automata is often difficult.…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Semantic search technology has received more attention in the last years. Compared with the keyword based search, semantic search is used to excavate the latent semantics information and help users find the information items that they want…
We present an extension of Felsenstein's algorithm to indel models defined on entire sequences, without the need to condition on one multiple alignment. The algorithm makes use of a generalization from probabilistic substitution matrices to…