| 1. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Strategies to improve usability and preserve accuracy in biological sequence databases
- 2016
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 16:18, s. 2454-2460
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Tidskriftsartikel (refereegranskat)abstract
- Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identifications of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate post-submission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.
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| 2. |
- Fitzek, David, 1993, et al.
(författare)
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Optimizing Variational Quantum Algorithms with qBang: Efficiently Interweaving Metric and Momentum to Navigate Flat Energy Landscapes
- 2024
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Ingår i: Quantum. - 2521-327X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Variational quantum algorithms (VQAs) represent a promising approach to utilizing current quantum computing infrastructures. VQAs are based on a parameterized quantum circuit optimized in a closed loop via a classical algorithm. This hybrid approach reduces the quantum processing unit load but comes at the cost of a classical optimization that can feature a flat energy landscape. Existing optimization techniques, including either imaginary time -propagation, natural gradient, or momentum -based approaches, are promising candidates but place either a significant burden on the quantum device or suffer frequently from slow convergence. In this work, we propose the quantum Broyden adaptive natural gradient (qBang) approach, a novel optimizer that aims to distill the best aspects of existing approaches. By employing the Broyden approach to approximate updates in the Fisher information matrix and combining it with a momentumbased algorithm, qBang reduces quantumresource requirements while performing better than more resource -demanding alternatives. Benchmarks for the barren plateau, quantum chemistry, and the maxcut problem demonstrate an overall stable performance with a clear improvement over existing techniques in the case of flat (but not exponentially flat) optimization landscapes. qBang introduces a new development strategy for gradient -based VQAs with a plethora of possible improvements.
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| 3. |
- Jonsson, Robert, 1987, et al.
(författare)
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Communication through quantum fields near a black hole
- 2020
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Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 2470-0010 .- 2470-0029. ; 101:12
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Tidskriftsartikel (refereegranskat)abstract
- We study the quantum channel between two localized first-quantized systems that communicate in 3 + 1 dimensional Schwarzschild spacetime via a quantum field. We analyze the information carrying capacity of direct and black hole-orbiting null geodesics as well as of the timelike contributions that arise because the strong Huygens principle does not hold on the Schwarzschild background. We find, in particular, that the nondirect-null and timelike contributions, which do not possess an analog on Minkowski spacetime, can dominate over the direct null contributions. We cover the cases of both geodesic and accelerated emitters. Technically, we apply tools previously designed for the study of wave propagation in curved spacetimes to a relativistic quantum information communication setup, first for generic spacetimes, and then for the case of Schwarzschild spacetime in particular.
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| 4. |
- Jonsson, Robert, 1987
(författare)
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Quantum signaling in relativistic motion and across acceleration horizons
- 2017
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Ingår i: Journal of Physics A: Mathematical and Theoretical. - : IOP Publishing. - 1751-8121 .- 1751-8113. ; 50:35, s. Article no 355401 -
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Tidskriftsartikel (refereegranskat)abstract
- The quantum channel between two particle detectors provides a prototype framework for the study of wireless quantum communication via relativistic quantum fields. In this article we calculate the classical channel capacity between two Unruh-DeWitt detectors arising from couplings within the perturbative regime. To this end, we identify the detector states which achieve maximal signal strength. We use these results to investigate the impact of relativistic effects on signaling between detectors in inertial and uniformly accelerated motion which communicate via a massless field in Minkowski spacetime.
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| 5. |
- Jonsson, Robert, 1987, et al.
(författare)
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Transmitting qubits through relativistic fields
- 2018
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Ingår i: Journal of Physics A: Mathematical and Theoretical. - : IOP Publishing. - 1751-8121 .- 1751-8113. ; 51:48
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Tidskriftsartikel (refereegranskat)abstract
- Wireless communication derives its power from the simultaneous emission of signals in multiple directions. However, in the context of quantum communication, this phenomenon must be reconciled carefully with the no-cloning principle. In this context, we here study how wireless communication of quantum information can be realized via relativistic fields. To this end, we extend existing frameworks to allow for a non-perturbative description of, e.g. quantum state transfer. We consider, in particular, the case of 1+1 spacetime dimensions, which already allows for a number of interesting scenarios, pointing to, for example, new methods for tasks similar to quantum secret sharing.
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| 6. |
- Osipov, George, 1994-
(författare)
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On Infinite-Domain CSPs Parameterized by Solution Cost
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis we study the computational complexity of MinCSP - an optimization version of the Constraint Satisfaction Problem (CSP). The input to a MinCSP is a set of variables and constraints applied to these variables, and the goal is to assign values (from a fixed domain) to the variables while minimizing the solution cost, i.e. the number of unsatisfied constraints. We are specifically interested in MinCSP with infinite domains of values. Infinite-domain MinCSPs model fundamental optimization problems in computer science and are of particular relevance to artificial intelligence, especially temporal and spatial reasoning. The usual way to study computational complexity of CSPs is to restrict the types of constraints that can be used in the inputs, and either construct fast algorithms or prove lower bounds on the complexity of the resulting problems.The vast majority of interesting MinCSPs are NP-hard, so standard complexity-theoretic assumptions imply that we cannot find exact solutions to all inputs of these problems in polynomial time with respect to the input size. Hence, we need to relax at least one of the three requirements above, opting for either approximate solutions, solving some inputs, or using super-polynomial time. Parameterized algorithms exploits the latter two relaxations by identifying some common structure of the interesting inputs described by some parameter, and then allowing super-polynomial running times with respect to that parameter. Such algorithms are feasible for inputs of any size whenever the parameter value is small. For MinCSP, a natural parameter is optimal solution cost. We also study parameterized approximation algorithms, where the requirement for exact solutions is also relaxed.We present complete complexity classifications for several important classes of infinite-domain constraints. These are simple temporal constraints and interval constraints, which have notable applications in temporal reasoning in AI, linear equations over finite and infinite fields as well as some commutative rings (e.g., the rationals and the integers), which are of fundamental theoretical importance, and equality constraints, which are closely related to connectivity problems in undirected graphs and form the basis of studying first-order definable constraints over infinite domains. In all cases, we prove results as follows: we fix a (possibly infinite) set of allowed constraint types C, and for every finite subset of C, determine whether MinCSP(), i.e., MinCSP restricted to the constraint types in , is fixed-parameter tractable, i.e. solvable in f(k) · poly(n) time, where k is the parameter, n is the input size, and f is any function that depends solely on k. To rule out such algorithms, we prove lower bounds under standard assumptions of parameterized complexity. In all cases except simple temporal constraints, we also provide complete classifications for fixed-parameter time constant-factor approximation.
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