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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,…

We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the…

A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…

Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…

Reading comprehension models are based on recurrent neural networks that sequentially process the document tokens. As interest turns to answering more complex questions over longer documents, sequential reading of large portions of text…

The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…

One of the key problems in tensor network based quantum circuit simulation is the construction of a contraction tree which minimizes the cost of the simulation, where the cost can be expressed in the number of operations as a proxy for the…

Mixture models are traditionally represented and learned by adding several distributions as components. Allowing mixtures to subtract probability mass or density can drastically reduce the number of components needed to model complex…

Regression trees and their ensemble methods are popular methods for nonparametric regression: they combine strong predictive performance with interpretable estimators. To improve their utility for locally smooth response surfaces, we study…

Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…

We present methods to serialize and deserialize tree ensembles that optimize inference latency when models are not already loaded into memory. This arises whenever models are larger than memory, but also systematically when models are…

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…

Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…

Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common…

Tree shape statistics quantify some aspect of the shape of a phylogenetic tree. They are commonly used to compare reconstructed trees to evolutionary models and to find evidence of tree reconstruction bias. Historically, to find a useful…

Reliable detection and quantification of quantum entanglement, particularly in high-spin or many-body systems, present significant computational challenges for traditional methods. This study examines the effectiveness of ensemble machine…

We introduce in this paper a runtime-efficient tree hashing algorithm for the identification of isomorphic subtrees, with two important applications in genetic programming for symbolic regression: fast, online calculation of population…

Quantum architecture search (QAS) is desired to construct a powerful and general QAS platform which can significantly accelerate quantum advantages in error-prone and depth limited quantum circuits in today Noisy Intermediate-Scale Quantum…

With increased access to data and the advent of computers, the use of statistical tools and numerical simulations is becoming commonplace for ecologists. These approaches help improve our understanding of ecological phenomena and their…

We apply the theory of Bruhat-Tits trees to the study of optimal embeddings of two and three dimensional commutative orders into quaternion algebras. Specifically, we determine how many conjugacy classes of global Eichler orders in a…