Related papers: Complete intersection for equivariant models
The rates-across-sites assumption in phylogenetic inference posits that the rate matrix governing the Markovian evolution of a character on an edge of the putative phylogenetic tree is the product of a character-specific scale factor and a…
In nice cases, a zero-dimensional complete intersection ideal over a field of characteristic zero has a Shape Lemma. There are also cases where the ideal is generated by the resultant and first subresultant polynomials of the generators.…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees. The typical application is the visualization of the co-evolution of hosts and parasites in…
Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…
A quasispecies is a set of interrelated genotypes that have reached a situation of equilibrium while evolving according to the usual Darwinian principles of selection and mutation. Quasispecies studies invariably assume that it is possible…
Exactly solvable models are essential in physics. For many-body spin-1/2 systems, an important class of such models consists of those that can be mapped to free fermions hopping on a graph. We provide a complete characterization of models…
Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…
We define a new family of open Gromov-Witten type invariants based on intersection theory on the moduli space of pseudoholomorphic curves of arbitrary genus with boundary in a Lagrangian submanifold. We assume the Lagrangian submanifold…
We study when the derived intersection of two smooth subvarieties of a smooth variety is formal. As a consequence we obtain a derived base change theorem for non-transversal intersections. We also obtain applications to the study of the…
A variety is rationally connected if two general points can be joined by a rational curve. A higher version of this notion is rational simple connectedness, which requires suitable spaces of rational curves through two points to be…
Fossil-based palaeoclimate reconstruction is an important area of ecological science that has gained momentum in the backdrop of the global climate change debate. The hierarchical Bayesian paradigm provides an interesting platform for…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
Richardson varieties play an important role in intersection theory and in the geometric interpretation of the Littlewood-Richardson Rule for flag varieties. We discuss three natural generalizations of Richardson varieties which we call…
We obtain a perfect sampling characterization of weak ergodicity for backward products of finite stochastic matrices, and equivalently, simultaneous tail triviality of the corresponding nonhomogeneous Markov chains. Applying these ideas to…
A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus…
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…
We introduce a general Bayesian framework for graph matching grounded in a new theory of exchangeable random permutations. Leveraging the cycle representation of permutations and the literature on exchangeable random partitions, we define,…
We use tropical and non-archimedean geometry to study the generic number of solutions of families of polynomial equations over a parameter space $Y$. In particular, we are interested in the choices of parameters for which the generic root…
Lotka-Volterra (LV) equations play a key role in the mathematical modeling of various ecological, biological and chemical systems. When the number of species (or, depending on the viewpoint, chemical components) becomes large, basic but…