Related papers: EvoZip: Efficient Compression of Large Collections…

In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…

In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

We present VBPI-Mixtures, an algorithm designed to enhance the accuracy of phylogenetic posterior distributions, particularly for tree-topology and branch-length approximations. Despite the Variational Bayesian Phylogenetic Inference…

Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…

Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…

Cultural phylogenies, or "trees" of culture, are typically built using methods from biology that use similarities and differences in artifacts to infer the historical relationships between the populations that produced them. While these…

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…

Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…

The problem of selecting small groups of itemsets that represent the data well has recently gained a lot of attention. We approach the problem by searching for the itemsets that compress the data efficiently. As a compression technique we…

Tree ensembles are powerful models that achieve excellent predictive performances, but can grow to unwieldy sizes. These ensembles are often post-processed (pruned) to reduce memory footprint and improve interpretability. We present…

We present a new universal source code for distributions of unlabeled binary and ordinal trees that achieves optimal compression to within lower order terms for all tree sources covered by existing universal codes. At the same time, it…

Fuzzy rule-based systems have been mostly used in interpretable decision-making because of their interpretable linguistic rules. However, interpretability requires both sensible linguistic partitions and small rule-base sizes, which are not…

Data-efficient image classification is a challenging task that aims to solve image classification using small training data. Neural network-based deep learning methods are effective for image classification, but they typically require…

We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…

Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…

Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…

Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of…

In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…