Related papers: Combinatorial properties of phylogenetic diversity…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
Phylogenetic trees are important tools in the study of evolutionary relationships between species. Measures such as the index of Sackin, Colless, and Total Cophenetic have been extensively used to quantify tree balance, one key property of…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
Measures of tree balance play an important role in many different research areas such as mathematical phylogenetics or theoretical computer science. Typically, tree balance is quantified by a single number which is assigned to the tree by a…
Erikkson showed that singular value decomposition(SVD) of flattenings determined a partition of a phylogenetic tree to be a split. In this paper, based on his work, we develop new statistically consistent algorithms fit for grid computing…
Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
Trait allocations are a class of combinatorial structures in which data may belong to multiple groups and may have different levels of belonging in each group. Often the data are also exchangeable, i.e., their joint distribution is…
Originally introduced in cooperative game theory, Shapley values have become a very popular tool to explain machine learning predictions. Based on Shapley's fairness axioms, every input (feature component) gets a credit how it contributes…
Explainability and fairness have mainly been considered separately, with recent exceptions trying the explain the sources of unfairness. This paper shows that the Shapley value can be used to both define and explain unfairness, under…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
The Equivalent Effect Function (EEF) is defined as having the identical integral values on the control points of the original time series data; the EEF can be obtained from the derivative of the spline function passing through the integral…
Spatial mapping of biodiversity is crucial to investigate spatial variations in natural communities. Several indices have been proposed in the literature to represent biodiversity as a single statistic. However, these indices only provide…
In a deterministic or random tree, a notion of ancestral diversity can be defined as follows. Sample independently $n$ groups of $k$ leaves and count the number $N_n(k)$ of distinct most recent common ancestors of each of the groups. As $n$…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
Efficient Natural Evolution Strategies (eNES) is a novel alternative to conventional evolutionary algorithms, using the natural gradient to adapt the mutation distribution. Unlike previous methods based on natural gradients, eNES uses a…
Entropy measures of probability distributions are widely used measures in ecology, biology, genetics, and in other fields, to quantify species diversity of a community. Unfortunately, entropy-based diversity indices, or diversity indices…