Searched for: author%3A%22Bertels%2C+K.L.M.%22
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Sarkar, A. (author), Al-Ars, Z. (author), Bertels, K.L.M. (author)
In this research, we extend the universal reinforcement learning agent models of artificial general intelligence to quantum environments. The utility function of a classical exploratory stochastic Knowledge Seeking Agent, KL-KSA, is generalized to distance measures from quantum information theory on density matrices. Quantum process...
conference paper 2023
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Khammassi, N. (author), Ashraf, I. (author), van Someren, J. (author), Nane, R. (author), Krol, A.M. (author), Rol, M.A. (author), Lao, L. (author), Bertels, K.L.M. (author), Almudever, Carmen G. (author)
With the potential of quantum algorithms to solve intractable classical problems, quantum computing is rapidly evolving, and more algorithms are being developed and optimized. Expressing these quantum algorithms using a high-level language and making them executable on a quantum processor while abstracting away hardware details is a...
journal article 2022
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Krol, A.M. (author), Sarkar, A. (author), Ashraf, I. (author), Al-Ars, Z. (author), Bertels, K.L.M. (author)
Unitary decomposition is a widely used method to map quantum algorithms to an arbitrary set of quantum gates. Efficient implementation of this decomposition allows for the translation of bigger unitary gates into elementary quantum operations, which is key to executing these algorithms on existing quantum computers. The decomposition can be used...
journal article 2022
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Sarkar, A. (author), Al-Ars, Z. (author), Almudever, Carmen G. (author), Bertels, K.L.M. (author)
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors in a few years are expected to scale up and be more robust for efficiently computing important algorithms in various fields. In this paper, we propose a quantum algorithm to address the challenging field of data processing...
journal article 2021
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Sarkar, A. (author), Al-Ars, Z. (author), Bertels, K.L.M. (author)
Inferring algorithmic structure in data is essential for discovering causal generative models. In this research, we present a quantum computing framework using the circuit model, for estimating algorithmic information metrics. The canonical computation model of the Turing machine is restricted in time and space resources, to make the target...
journal article 2021
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Sarkar, A. (author), Al-Ars, Z. (author), Bertels, K.L.M. (author)
In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. This is the first time this important application in bioinformatics is modeled using quantum computation. Each one of the four steps of the implementation (TSP, QUBO,...
journal article 2021
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Yu, J. (author), Nane, R. (author), Ashraf, I. (author), Taouil, M. (author), Hamdioui, S. (author), Corporaal, Henk (author), Bertels, K.L.M. (author)
Memristor-based Computation-in-Memory (CIM) is one of the emerging architectures for next-generation Big Data problems. Its design requires a radically new synthesis flow as the memristor is a passive device that uses resistances to encode its logic values. This article proposes a synthesis flow for mapping parallel applications on memristor...
journal article 2020
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Moueddene, A.A. (author), Khammassi, Nader (author), Bertels, K.L.M. (author), Almudever, Carmen G. (author)
The implementation and practicality of quantum algorithms hinge largely on the quality of operations within a quantum processor. Therefore, including realistic error models in quantum computing simulation platforms is crucial for testing these algorithms. Existing classical simulation techniques of quantum information processing devices...
journal article 2020
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Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
The seeding heuristic is widely used in many DNA analysis applications to speed up the analysis time. In many applications, seeding takes a substantial amount of the total execution time. In this paper, we present an efficient GPU implementation for computing maximal exact matching (MEM) seeds in long DNA reads. We applied various...
conference paper 2020
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Ahmed, N. (author), Qiu, T.D. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
BACKGROUND: In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can be used for de novo...
journal article 2020
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Ahmed, N. (author), Lévy, Jonathan (author), Ren, S. (author), Mushtaq, Hamid (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
Following publication of the original article [1], the author requested changes to the figures 4, 7, 8, 9, 12 and 14 to align these with the text. The corrected figures are supplied below. The original article [1] has been corrected. [Typesetter, please insert new supplied figure in package].
journal article 2019
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Ahmed, N. (author), Lévy, Jonathan (author), Ren, S. (author), Mushtaq, Hamid (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
BACKGROUND: Due the computational complexity of sequence alignment algorithms, various accelerated solutions have been proposed to speedup this analysis. NVBIO is the only available GPU library that accelerates sequence alignment of high-throughput NGS data, but has limited performance. In this article we present GASAL2, a GPU library for...
journal article 2019
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Vuillot, C. (author), Lao, L. (author), Criger, D.B. (author), Almudever, Carmen G. (author), Bertels, K.L.M. (author), Terhal, B.M. (author)
The large-scale execution of quantum algorithms requires basic quantum operations to be implemented fault-tolerantly. The most popular technique for accomplishing this, using the devices that can be realized in the near term, uses stabilizer codes which can be embedded in a planar layout. The set of fault-tolerant operations which can be...
journal article 2019
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Correale, G. (author), Cerrone, Gianluca (author), Al-Ars, Z. (author), Bertels, K.L.M. (author)
The exploitation of quantum physics and of quantum states superposition and entanglement properties for computing applications has been studied since 1980s [1] [2] for their disrupting potential in the evolution of information theory. Although quantum computing is still in its infancy, experiments have been carried out and proto-types have...
abstract 2019
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Ren, S. (author), Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
Background: Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself. In GATK HaplotypeCaller (HC), the semi-global pairwise sequence alignment with traceback has so far<br/...
journal article 2019
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Lao, L. (author), van Wee, B. (author), Ashraf, I. (author), van Someren, J. (author), Khammassi, N. (author), Bertels, K.L.M. (author), Almudever, Carmen G. (author)
Quantum error correction (QEC) and fault-tolerant (FT) mechanisms are essential for reliable quantum computing. However, QEC considerably increases the computation size up to four orders of magnitude. Moreover, FT implementation has specific requirements on qubit layouts, causing both resource and time overhead. Reducing spatial-temporal costs...
journal article 2019
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Xie, L. (author), Du Nguyen, H.A. (author), Taouil, M. (author), Hamdioui, S. (author), Bertels, K.L.M. (author)
Alternatives to CMOS logic circuit implementations are under research for future scaled electronics. Memristor crossbar-based logic circuit is one of the promising candidates to at least partially replace CMOS technology, which is facing many challenges such as reduced scalability, reliability, and performance gain. Memristor crossbar offers...
journal article 2018
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Fu, X. (author), Rol, M.A. (author), Bultink, C.C. (author), van Someren, J. (author), Khammassi, N. (author), Ashraf, I. (author), Vermeulen, R.F.L. (author), de Sterke, J.C. (author), Vlothuizen, W.J. (author), Schouten, R.N. (author), Almudever, Carmen G. (author), DiCarlo, L. (author), Bertels, K.L.M. (author)
This article proposes a quantum microarchitecture, QuMA. Flexible programmability of a quantum processor is achieved by multilevel instructions decoding, abstracting analog control into digital control, and translating instruction execution with non-deterministic timing into event trigger with precise timing. QuMA is validated by several...
journal article 2018
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Houtgast, E.J. (author), Sima, V.M. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
We present our work on hardware accelerated genomics pipelines, using either FPGAs or GPUs to accelerate execution of BWA-MEM, a widely-used algorithm for genomic short read mapping. The mapping stage can take up to 40% of overall processing time for genomics pipelines. Our implementation offloads the Seed Extension function, one of the main...
journal article 2018
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Ren, S. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to...
journal article 2018
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