Related papers: Quantum Simulation of Phylogenetic Trees
Variational quantum circuits have arisen as an important method in quantum computing. A crucial step of it is parameter optimization, which is typically tackled through gradient-descent techniques. We advantageously explore instead the use…
Simulations of weighted tree automata (wta) are considered. It is shown how such simulations can be decomposed into simpler functional and dual functional simulations also called forward and backward simulations. In addition, it is shown in…
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…
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…
When confined to a topological environment consisting of a cycle coupled with a half-line, quantum walks exhibit long-term statistical tendencies which differ dramatically from the tendencies of classical random walks in the same…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
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…
An overview of a quantum algorithm application for the identification of causal singular configurations of multiloop Feynman diagrams is presented. The quantum algorithm is implemented in two different quantum simulators, the output…
The treewidth of a graph is a useful combinatorial measure of how close the graph is to a tree. We prove that a quantum circuit with $T$ gates whose underlying graph has treewidth $d$ can be simulated deterministically in…
Several structural learning algorithms for staged tree models, an asymmetric extension of Bayesian networks, have been defined. However, they do not scale efficiently as the number of variables considered increases. Here we introduce the…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known…
Quantum walks are a well-established model for the study of coherent transport phenomena and provide a universal platform in quantum information theory. Dynamically influencing the walker's evolution gives a high degree of flexibility for…
Probabilistic cellular automata with deterministic updating are quantum systems. We employ the quantum formalism for an investigation of random probabilistic cellular automata, which start with a probability distribution over initial…
We introduce complex-valued tensor network models for sequence processing motivated by correspondence to probabilistic graphical models, interpretability and resource compression. Inductive bias is introduced to our models via network…
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
As simulations of quantum systems cross the limits of classical computability, both quantum and classical approaches become hard to verify. Scaling predictions are therefore based on local structure and asymptotic assumptions, typically…
The quantum random walk is a possible approach to construct new quantum algorithms. Several groups have investigated the quantum random walk and experimental schemes were proposed. In this paper we present the experimental implementation of…