Related papers: Checking Phylogenetic Decisiveness in Theory and i…
In molecular systematics, evolutionary trees are reconstructed from sequences at the tips under simple models of site substitution. A central question is how much sequence data is required to reconstruct a tree accurately? The answer…
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…
We say that a collection $\Cc$ of subsets of $X$ is {\em bureaucratic} if every maximal hierarchy on $X$ contained in $\Cc$ is also maximum. We characterise bureaucratic set systems and show how they arise in phylogenetics. This framework…
Genetic Programming (GP) has found various applications. Understanding this type of algorithm from a theoretical point of view is a challenging task. The first results on the computational complexity of GP have been obtained for problems…
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…
Scatterplot selection is an effective approach to represent essential portions of multidimensional data in a limited display space. Various metrics for evaluation of scatterplots such as scagnostics have been presented and applied to…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
Decision trees and systems of decision rules are widely used as classifiers, as a means for knowledge representation, and as algorithms. They are among the most interpretable models for data analysis. The study of the relationships between…
For any fixed surface Sigma of genus g, we give an algorithm to decide whether a graph G of girth at least five embedded in Sigma is colorable from an assignment of lists of size three in time O(|V(G)|). Furthermore, we can allow a subgraph…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
We study the problem of detecting planted solutions in a random satisfiability formula. Adopting the formalism of hypothesis testing in statistical analysis, we describe the minimax optimal rates of detection. Our analysis relies on the…
A first step in exploring population structure in crop plants and other organisms is to define the number of subpopulations that exist for a given data set. The genetic marker data sets being generated have become increasingly large over…
Existing algorithms for explaining the outputs of image classifiers are based on a variety of approaches and produce explanations that frequently lack formal rigour. On the other hand, logic-based explanations are formally and rigorously…
Suppose we have a family ${\cal F}$ of sets. For every $S \in {\cal F}$, a set $D \subseteq S$ is a {\sf defining set} for $({\cal F},S)$ if $S$ is the only element of $\cal{F}$ that contains $D$ as a subset. This concept has been studied…
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…
How should we gather information to make effective decisions? We address Bayesian active learning and experimental design problems, where we sequentially select tests to reduce uncertainty about a set of hypotheses. Instead of minimizing…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
We explore the connection between an agent's decision problem and her ranking of information structures. We find that a finite amount of ordinal data on the agent's ranking of experiments is enough to identify her (finite) set of…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…