Related papers: Quantum Simulation of Phylogenetic Trees
Machine learning is a promising application of quantum computing, but challenges remain as near-term devices will have a limited number of physical qubits and high error rates. Motivated by the usefulness of tensor networks for machine…
Quantum computers are the promising candidates for simulation of large quantum systems, which is a daunting task to perform in a classical computer. Here, we report the experimental realization of quantum tunneling of a single particle…
The characterisation of quantum networks is fundamental to understanding how energy and information propagates through complex systems, with applications in control, communication, error mitigation and energy transfer. In this work, we…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
Recurrent neurons, or "simulated" qubits, can store simultaneous true and false with probabilistic behaviors usually reserved for the qubits of quantum physics. Although possible to construct artificially, simulated qubits are intended to…
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…
Quantum walks constitute a rich area of quantum information science, where multipartite entanglement plays a central role in the dynamics and scalability of quantum advantage over classical simulators. In this work, we study the…
Continuous-time quantum walks are natural tools for spatial search, where one searches for a marked vertex in a graph. Sometimes, the structure of the graph causes the walker to get trapped, such that the probability of finding the marked…
In recent years, tree tensor network methods have proven capable of simulating quantum many-body and other high-dimensional systems. This work is a user guide to our Python library PyTreeNet. It includes code examples and exercises to…
Latent tree analysis seeks to model the correlations among a set of random variables using a tree of latent variables. It was proposed as an improvement to latent class analysis --- a method widely used in social sciences and medicine to…
Existing genetic programming (GP) methods are typically designed based on a certain representation, such as tree-based or linear representations. These representations show various pros and cons in different domains. However, due to the…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
We make and generalize the observation that summing of probability amplitudes of a discrete-time quantum walk over partitions of the walking graph consistent with the step operator results in a unitary evolution on the reduced graph which…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Monitored many-body systems fall broadly into two dynamical phases, ``entangling'' or ``disentangling'', separated by a transition as a function of the rate at which measurements are made on the system. Producing an analytical theory of…
Simulating quantum systems constructively furthers our understanding of qualitative and quantitative features which may be analytically intractable. In this letter, we directly simulate and explore the entanglement structure present in a…
A universal quantum simulator would enable efficient simulation of quantum dynamics by implementing quantum-simulation algorithms on a quantum computer. Specifically the quantum simulator would efficiently generate qubit-string states that…
The time process of transport on randomly evolving trees is investigated. By introducing the notions of living and dead nodes a model of random tree evolution is constructed which describes the spreading in time of objects corresponding to…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…