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- Hesam, A.S. (author), Pijpers, Frank (author), Rademakers, Fons (author), Al-Ars, Z. (author) poster 2023
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Mokveld, T.O. (author), Al-Ars, Z. (author), Sistermans, Erik A. (author), Reinders, M.J.T. (author)Background<br/><br/>Non-Invasive Prenatal Testing is often performed by utilizing read coverage-based profiles obtained from shallow whole genome sequencing to detect fetal copy number variations. Such screening typically operates on a discretized binned representation of the genome, where (ab)normality of bins of a set size is judged relative...journal article 2023
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Reukers, Matthijs A. (author), Tian, Y. (author), Al-Ars, Z. (author), Hofstee, H.P. (author), Brobbel, M. (author), Peltenburg, J.W. (author), van Straten, J. (author)Tydi is an open specification for streaming dataflow designs in digital circuits, allowing designers to express how composite and variable-length data structures are transferred over streams using clear, data-centric types. These data types are extensively used in a many application domains, such as big data and SQL applications. This way,...journal article 2023
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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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Trentin, Vinicius (author), Ma, Chenxu (author), Villagra, Jorge (author), Al-Ars, Z. (author)Motion prediction is a key factor towards the full deployment of autonomous vehicles. It is fundamental in order to assure safety while navigating through highly interactive complex scenarios. In this work, the framework IAMP (Interaction-Aware Motion Prediction), producing multi-modal probabilistic outputs from the integration of a Dynamic...conference paper 2023
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Ji, M. (author), Al-Ars, Z. (author), Hofstee, H.P. (author), Chang, Yuchun (author), Zhang, Baolin (author)Convolutional neural networks (CNNs) are to be effective in many application domains, especially in the computer vision area. In order to achieve lower latency CNN processing, and reduce power consumption, developers are experimenting with using FPGAs to accelerate CNN processing in several applications. Current FPGA CNN accelerators usually use...journal article 2023
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Cromjongh, Casper (author), Tian, Y. (author), Hofstee, H.P. (author), Al-Ars, Z. (author)In spite of progress on hardware design languages, the design of high-performance hardware accelerators forces many design decisions specializing the interfaces of these accelerators in ways that complicate the understanding of the design and hinder modularity and collaboration. In response to this challenge, Tydi is presented as an open...conference paper 2023
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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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Mokveld, T.O. (author), Al-Ars, Z. (author), Sistermans, Erik A. (author), Reinders, M.J.T. (author)In prenatal diagnostics, NIPT screening utilizing read coverage-based profiles obtained from shallow WGS data is routinely used to detect fetal CNVs. From this same data, fragment size distributions of fetal and maternal DNA fragments can be derived, which are known to be different, and often used to infer fetal fractions. We argue that the...journal article 2022
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Ahmad, T. (author), Al-Ars, Z. (author), Hofstee, H.P. (author)Moving structured data between different big data frameworks and/or data warehouses/storage systems often cause significant overhead. Most of the time more than 80% of the total time spent in accessing data is elapsed in serialization/de-serialization step. Columnar data formats are gaining popularity in both analytics and transactional...conference paper 2022
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Abrahamse, Robin (author), Hadnagy, A. (author), Al-Ars, Z. (author)The concept of memory disaggregation has recently been gaining traction in research. With memory disaggregation, data center compute nodes can directly access memory on adjacent nodes and are therefore able to overcome local memory restrictions, introducing a new data management paradigm for distributed computing. This paper proposes and...conference paper 2022
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Arvanitis, P. (author), Betting, Jan Harm L.F. (author), Bosman, Laurens W.J. (author), Al-Ars, Z. (author), Strydis, C. (author)Mice and rats can rapidly move their whiskers when exploring the environment. Accurate description of these movements is important for behavioral studies in neuroscience. Whisker tracking is, however, a notoriously difficult task due to the fast movements and frequent crossings and juxtapositionings among whiskers. We have recently developed...conference paper 2022
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Park, Seongyeon (author), Kim, Hajin (author), Ahmad, T. (author), Ahmed, N. (author), Al-Ars, Z. (author), Hofstee, H.P. (author), Kim, Youngsok (author), Lee, Jinho (author)Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work has been conducted on GPU acceleration of a sequence alignment, we identify several shortcomings that limit...conference paper 2022
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Ahmad, T. (author), Ma, Chengxin (author), Al-Ars, Z. (author), Hofstee, H.P. (author)Current cluster scaled genomics data processing solutions rely on big data frameworks like Apache Spark, Hadoop and HDFS for data scheduling, processing and storage. These frameworks come with additional computation and memory overheads by default. It has been observed that scaling genomics dataset processing beyond 32 nodes is not efficient on...conference paper 2022
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Breitwieser, Lukas (author), Hesam, A.S. (author), De Montigny, Jean (author), Vavourakis, Vasileios (author), Iosif, Alexandros (author), Jennings, Jack (author), Kaiser, Marcus (author), Manca, Marco (author), Di Meglio, Alberto (author), Al-Ars, Z. (author), Rademakers, Fons (author), Mutlu, Onur (author), Bauer, Roman (author)Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulation platforms do not always take full advantage of modern hardware and often have a field-specific software design. Results: We present a novel simulation platform called BioDynaMo that alleviates both of these problems....journal article 2022
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Ahmad, T. (author), Al-Ars, Z. (author), Hofstee, H.P. (author)Background Recently many new deep learning–based variant-calling methods like DeepVariant have emerged as more accurate compared with conventional variant-calling algorithms such as GATK HaplotypeCaller, Sterlka2, and Freebayes albeit at higher computational costs. Therefore, there is a need for more scalable and higher performance workflows of...review 2021
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Peltenburg, J.W. (author), Hadnagy, A. (author), Brobbel, M. (author), Morrow, Robert (author), Al-Ars, Z. (author)JSON is a popular data interchange format for many web, cloud, and IoT systems due to its simplicity, human readability, and widespread support. However, applications must first parse and convert the data to a native in-memory format before being able to perform useful computations. Many big data applications with high performance requirements...conference paper 2021
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Hoozemans, J.J. (author), Tervo, Kati (author), Jaaskelainen, Pekka (author), Al-Ars, Z. (author)Many applications make extensive use of various forms of compression techniques for storing and communicating data. As decompression is highly regular and repetitive, it is a suitable candidate for acceleration. Examples are offloading (de)compression to a dedicated circuit on a heterogeneous System-on-Chip, or attaching FPGAs or ASICs...conference paper 2021
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Peltenburg, J.W. (author), Van Leeuwen, Lars T.J. (author), Hoozemans, J.J. (author), Fang, J. (author), Al-Ars, Z. (author), Hofstee, H.P. (author)In the domain of big data analytics, the bottleneck of converting storage-focused file formats to in-memory data structures has shifted from the bandwidth of storage to the performance of decoding and decompression software. Two widely used formats for big data storage and in-memory data are Apache Parquet and Apache Arrow, respectively. In...conference paper 2021
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Hoozemans, J.J. (author), Peltenburg, J.W. (author), Nonnenmacher, Fabian (author), Hadnagy, A. (author), Al-Ars, Z. (author), Hofstee, H.P. (author)The big data revolution has ushered an era with ever increasing volumes and complexity of data requiring ever faster computational analysis. During this very same era, CPU performance growth has been stagnating, pushing the industry to either scale their computation horizontally using multiple nodes in datacenters, or to scale vertically using...journal article 2021