Related papers: Analysis of Phylogeny Tracking Algorithms for Seri…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
Diffusion Models have become a cornerstone of modern generative AI for their exceptional generation quality and controllability. However, their inherent \textit{multi-step iterations} and \textit{complex backbone networks} lead to…
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our…
Identifying similar documents within extensive volumes of data poses a significant challenge. To tackle this issue, researchers have developed a variety of effective distributed computing techniques. With the advancement of computing power…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
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 phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Radio propagation modeling is essential in telecommunication research, as radio channels result from complex interactions with environmental objects. Recently, Machine Learning has been attracting attention as a potential alternative to…
Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on…
Diffusion models, widely used in image generation, rely on iterative refinement to generate images from noise. Understanding this data evolution is important for model development and interpretability, yet challenging due to its…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…