4,905 research outputs found
Coordinating virus research: The Virus Infectious Disease Ontology
The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects
Quantum Kolmogorov complexity and quantum correlations in deterministic-control quantum Turing machines
This work presents a study of Kolmogorov complexity for general quantum states from the perspective of deterministic-control quantum Turing Machines (dcq-TM). We extend the dcq-TM model to incorporate mixed state inputs and outputs, and define dcq-computable states as those that can be approximated by a dcq-TM. Moreover, we introduce (conditional) Kolmogorov complexity of quantum states and use it to study three particular aspects of the algorithmic information contained in a quantum state: a comparison of the information in a quantum state with that of its classical representation as an array of real numbers, an exploration of the limits of quantum state copying in the context of algorithmic complexity, and study of the complexity of correlations in quantum systems, resulting in a correlation-aware definition for algorithmic mutual information that satisfies symmetry of information property
LIPIcs, Volume 251, ITCS 2023, Complete Volume
LIPIcs, Volume 251, ITCS 2023, Complete Volum
From G\"odel's Incompleteness Theorem to the completeness of bot beliefs (Extended abstract)
Hilbert and Ackermann asked for a method to consistently extend incomplete
theories to complete theories. G\"odel essentially proved that any theory
capable of encoding its own statements and their proofs contains statements
that are true but not provable. Hilbert did not accept that G\"odel's
construction answered his question, and in his late writings and lectures,
G\"odel agreed that it did not, since theories can be completed incrementally,
by adding axioms to prove ever more true statements, as science normally does,
with completeness as the vanishing point. This pragmatic view of validity is
familiar not only to scientists who conjecture test hypotheses but also to real
estate agents and other dealers, who conjure claims, albeit invalid, as
necessary to close a deal, confident that they will be able to conjure other
claims, albeit invalid, sufficient to make the first claims valid. We study the
underlying logical process and describe the trajectories leading to testable
but unfalsifiable theories to which bots and other automated learners are
likely to converge.Comment: 19 pages, 13 figures; version updates: changed one word in the title,
expanded Introduction, improved presentation, tidied up some diagram
Functional completeness of planar Rydberg blockade structures
The construction of Hilbert spaces that are characterized by local
constraints as the low-energy sectors of microscopic models is an important
step towards the realization of a wide range of quantum phases with long-range
entanglement and emergent gauge fields. Here we show that planar structures of
trapped atoms in the Rydberg blockade regime are functionally complete: Their
ground state manifold can realize any Hilbert space that can be characterized
by local constraints in the product basis. We introduce a versatile framework,
together with a set of provably minimal logic primitives as building blocks, to
implement these constraints. As examples, we present lattice realizations of
the string-net Hilbert spaces that underlie the surface code and the Fibonacci
anyon model. We discuss possible optimizations of planar Rydberg structures to
increase their geometrical robustness.Comment: 33 pages, 14 figures, v2: fixed typos, added additional references
and comment
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