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In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
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,…
The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities…
Protoform reconstruction is the task of inferring what morphemes or words appeared like in the ancestral languages of a set of daughter languages. Meloni et al. (2021) achieved the state-of-the-art on Latin protoform reconstruction with an…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
Creating a new Ontology: a Modular Approach
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a. the weighted ancestor problem, has been extensively…
Historical linguists have long written a kind of incompletely formalized ''program'' that converts reconstructed words in an ancestor language into words in one of its attested descendants that consist of a series of ordered string rewrite…
We propose an unsupervised method for the reconstruction of protoforms i.e., ancestral word forms from which modern language forms are derived. While prior work has primarily relied on probabilistic models of phonological edits to infer…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
We present a computational model to reconstruct trees of ancestors for animals with sexual reproduction. Through a recursive algorithm combined with a random number generator, it is possible to reproduce the number of ancestors for each…
We probe the layers in multilingual BERT (mBERT) for phylogenetic and geographic language signals across 100 languages and compute language distances based on the mBERT representations. We 1) employ the language distances to infer and…
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…
A substantial thread of recent work on latent tree learning has attempted to develop neural network models with parse-valued latent variables and train them on non-parsing tasks, in the hope of having them discover interpretable tree…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
It is very costly to build up lexical resources and domain ontologies. Especially when confronted with a new application domain lexical gaps and a poor coverage of domain concepts are a problem for the successful exploitation of natural…
This work proposes an extension to Structured Grammatical Evolution (SGE) called Co-evolutionary Probabilistic Structured Grammatical Evolution (Co-PSGE). In Co-PSGE each individual in the population is composed by a grammar and a genotype,…
We calculate the density and expectation for the number of lineages in a reconstructed tree with $n$ extant species. This is done with conditioning on the age of the tree as well as with assuming a uniform prior for the age of the tree.