Related papers: Combinatorial properties of phylogenetic diversity…
Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research…
Several indices that measure the degree of balance of a rooted phylogenetic tree have been proposed so far in the literature. In this work we define and study a new index of this kind, which we call the total cophenetic index: the sum, over…
The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One…
The Colless index for bifurcating phylogenetic trees, introduced by Colless (1982), is defined as the sum, over all internal nodes $v$ of the tree, of the absolute value of the difference of the sizes of the clades defined by the children…
Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…
Shapley Values (SV) are widely used in explainable AI, but their estimation and interpretation can be challenging, leading to inaccurate inferences and explanations. As a starting point, we remind an invariance principle for SV and derive…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
Evolution by Natural Selection is a process by which progeny inherit some properties from their progenitors with small variation. These properties are subject to Natural Selection and are called adaptive traits and carriers of the latter…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
Phytoplankton plays an important role in marine ecosystem. It is defined as a biological factor to assess marine quality. The identification of phytoplankton species has a high potential for monitoring environmental, climate changes and for…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
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,…
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…
Federated learning paradigm to utilize datasets across multiple data providers. In FL, cross-silo data providers often hesitate to share their high-quality dataset unless their data value can be fairly assessed. Shapley value (SV) has been…
Interpreting predictions from tree ensemble methods such as gradient boosting machines and random forests is important, yet feature attribution for trees is often heuristic and not individualized for each prediction. Here we show that…
A wide variety of stochastic models of cladogenesis (based on speciation and extinction) lead to an identical distribution on phylogenetic tree shapes once the edge lengths are ignored. By contrast, the distribution of the tree's edge…
The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…