Related papers: Quantum Field Theory and Phylogenetic Branching
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
We give a relativistically covariant, wave-functional formulation of Bohm's quantum field theory for the scalar field based on a general foliation of space-time by space-like hypersurfaces. The wave functional, which guides the evolution of…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
Given a group-based Markov model on a tree, one can compute the vertex representation of a polytope which describes the associated toric variety. The half-space representation, however, is not easily computable. In the case of…
Semiclassical approximation based on extracting a c-number classical component from quantum field is widely used in the quantum field theory. Semiclassical states are considered then as Gaussian wave packets in the functional Schrodinger…
We construct the classical and canonically quantized theories of a massless scalar field on a background lattice in which the number of points--and hence the number of modes--may grow in time. To obtain a well-defined theory certain…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…
This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units…
In this series of papers we aim to provide a mathematically comprehensive framework to the Hamiltonian pictures of quantum field theory in curved spacetimes. Our final goal is to study the kinematics and the dynamics of the theory from the…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
We derive machine learning algorithms from discretized Euclidean field theories, making inference and learning possible within dynamics described by quantum field theory. Specifically, we demonstrate that the $\phi^{4}$ scalar field theory…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
The precise equivalence between discretized Euclidean field theories and a certain class of probabilistic graphical models, namely the mathematical framework of Markov random fields, opens up the opportunity to investigate machine learning…
We present a local framework for investigating non-unitary evolution groups pertinent to effective field theories in general semi-classical spacetimes. Our approach is based on a rigorous local stability analysis of the algebra of…
We introduce a framework for non-linear time evolution in quantum mechanics as a natural non-linear generalization of the Schrodinger equation. Within our framework, we derive simple toy models of dynamical geometry on finite graphs. Along…
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…
Canonical quantization of abelian BF-type topological field theory coupled to extended sources on generic d-dimensional manifolds and with curved line bundles is studied. Sheaf cohomology is used to construct the appropriate topological…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
Let $q$ be a quadratic form over a field $F$ and let $L$ be a field extension of $F$ of odd degree. It is a classical result that if $q_L$ is isotropic (resp. hyperbolic) then $q$ is isotropic (resp. hyperbolic). In turn, given two…