Related papers: phylo2vec: a library for vector-based phylogenetic…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
In the last decade, some algebraic tools have been successfully applied to phylogenetic reconstruction. These tools are mainly based on the knowledge of equations describing algebraic varieties associated to phylogenetic trees evolving…
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\cal…
Real-world data usually have high dimensionality and it is important to mitigate the curse of dimensionality. High-dimensional data are usually in a coherent structure and make the data in relatively small true degrees of freedom. There are…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
A phylogenetic variety is an algebraic variety parameterized by a statistical model of the evolution of biological sequences along a tree. Understanding this variety is an important problem in the area of algebraic statistics with…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
In recent years, the explosion of malware and extensive code reuse have formed complex evolutionary connections among malware specimens. The rapid pace of development makes it challenging for existing studies to characterize recent…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Human migration and mobility drives major societal phenomena including epidemics, economies, innovation, and the diffusion of ideas. Although human mobility and migration have been heavily constrained by geographic distance throughout the…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
Large scale contextual representation models have significantly advanced NLP in recent years, understanding the semantics of text to a degree never seen before. However, they need to process large amounts of data to achieve high-quality…
Programming language processing (similar to natural language processing) is a hot research topic in the field of software engineering; it has also aroused growing interest in the artificial intelligence community. However, different from a…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
Rapid digitalisation spurred by the Covid-19 pandemic has resulted in more cyber crime. Malware-as-a-service is now a booming business for cyber criminals. With the surge in malware activities, it is vital for cyber defenders to understand…
Relationships in scientific data, such as the numerical and spatial distribution relations of features in univariate data, the scalar-value combinations' relations in multivariate data, and the association of volumes in time-varying and…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…