相关论文: Combinatorial properties of phylogenetic diversity…
Explainability in yield prediction helps us fully explore the potential of machine learning models that are already able to achieve high accuracy for a variety of yield prediction scenarios. The data included for the prediction of yields…
Random forests have been widely used for their ability to provide so-called importance measures, which give insight at a global (per dataset) level on the relevance of input variables to predict a certain output. On the other hand, methods…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Phylogenetic trees capture evolutionary relationships among species and reflect the forces that shaped them. While many studies rely on branch length information, the topology of phylogenetic trees (particularly their degree of imbalance)…
The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
We investigate the distribution of flavonoids, a major category of plant secondary metabolites, across species. Flavonoids are known to show high species specificity, and were once considered as chemical markers for understanding adaptive…
Phylogenetic invariants are not the only constraints on site-pattern frequency vectors for phylogenetic trees. A mutation matrix, by its definition, is the exponential of a matrix with non-negative off-diagonal entries; this positivity…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
A degree sequence is a sequence ${\bf s}=(N_i,i\geq 0)$ of non-negative integers satisfying $1+\sum_i iN_i=\sum_i N_i<\infty$. We are interested in the uniform distribution $\mathbb{P}_{{\bf s}}$ on rooted plane trees whose degree sequence…
Recognition of evolutionary units (species, populations) requires integrating several kinds of data such as genetic or phenotypic markers or spatial information, in order to get a comprehensive view concerning the differentiation of the…
We consider the problem of dividing items between individuals in a way that is fair both in the sense of distributional fairness and in the sense of not having disparate impact across protected classes. An important existing mechanism for…
The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
Shapley values have become increasingly popular in the machine learning literature thanks to their attractive axiomatisation, flexibility, and uniqueness in satisfying certain notions of `fairness'. The flexibility arises from the myriad…
Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least…
We consider the problem of payoff division in indivisible coalitional games, where the value of the grand coalition is a natural number. This number represents a certain quantity of indivisible objects, such as parliamentary seats, kidney…