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In Chapter 1 we fully characterise pairs of finite graphs which form a gap in the full homomorphism order. This leads to a simple proof of the existence of generalised duality pairs. We also discuss how such results can be carried to…
True slime mould Physarum polycephalum approximates a range of complex computations via growth and adaptation of its proto- plasmic transport network, stimulating a large body of recent research into how such a simple organism can perform…
We develop a general theory of cluster categories, applying to a 2-Calabi-Yau extriangulated category $\mathcal{C}$ and cluster-tilting subcategory $\mathcal{T}$ satisfying only mild finiteness conditions. We show that the structure theory…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
In this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating many phylogenetic invariants. We prove that we obtain all invariants for any tree for the binary…
A numerical evidence for the dependence of the substructure abundance of cluster halos on the orientation coherence of the surrounding tidal fields is presented. Applying the adapted minimal spanning tree (MST) algorithm to the cluster…
Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and…
The species scale provides an upper bound for the ultraviolet cutoff of effective theories of gravity coupled to a number of light particle species. We point out that modular invariant (super-)potentials provide a simple and computable…
For a given set $\mathcal{L}$ of species and a set $\mathcal{T}$ of triplets on $\mathcal{L}$, one wants to construct a phylogenetic network which is consistent with $\mathcal{T}$, i.e which represents all triplets of $\mathcal{T}$. The…
Let $R$ be a semilocal principal ideal domain. Two algebraic objects over $R$ in which scalar extension makes sense (e.g. quadratic spaces) are said to be of the same genus if they become isomorphic after extending scalars to all…
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples…
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…
We consider random arrays indexed by the leaves of an infinitary rooted tree of finite depth, with the distribution invariant under the rearrangements that preserve the tree structure. We call such arrays hierarchically exchangeable and…
Let $A$ be a quasi-hereditary algebra. We prove that in many cases, a tilting module is rigid (i.e. has identical radical and socle series) if it does not have certain subquotients whose composition factors extend more than one layer in the…
We show that for any two values $\alpha, \beta >0 $ for which $\alpha+\beta>1$ then there is a value $N$ so that for all $n \geq N$ the following holds. For any binary phylogenetic tree $T$ on $n$ leaves there is a set of $\lfloor n^\alpha…
In this paper we investigate the geometry of a discrete Bayesian network whose graph is a tree all of whose variables are binary and the only observed variables are those labeling its leaves. We provide the full geometric description of…
Support $\tau$-tilting modules correspond to some classes of categorical objects bijectively, such as two-term tilting complexes for any finite dimensional symmetric algebra. This fact motivates us to classify support $\tau$-tilting modules…
Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of species), it is possible to determine in polynomial time whether there exists a level-1…