15 papers · ranked by Valyu relevance
Luka Skorić, Dan E. Browne, Kenton M. Barnes, Neil I. Gillespie + 1 more
'Earl T. Campbell'] Large-scale quantum computers have the potential to hold computational capabilities beyond conventional computers for certain problems. However, the physical qubits within a quantum computer are prone to noise and decoherence, which must be corrected in order to perform reliable, fault-tolerant…
Zihui Yan, Guanjin Qu, Xin Chen, Gang Zheng + 1 more
DNA-based data storage is a promising solution to the challenges of large-scale data storage. However, the low throughput of the mainstream inkjet-based DNA synthesis method has hindered its widespread adoption. In contrast, high-throughput electrochemical synthesis provides higher throughput but with more nucleotide…
Cody Rivera, Sheng Di, Jiannan Tian, Xiaodong Yu + 2 more
'Franck Cappello'] Cody Rivera? , Sheng Di‡ , Jiannan Tian† , Xiaodong Yu‡ , Dingwen Tao†? , Franck Cappello‡ ?Department of Computer Science, University of Alabama, Tuscaloosa, AL, USA †School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA ‡Mathematics and Computer…
Fangzheng Lin, Kasidis Arunruangsirilert, Heming Sun, Jiro Katto
Entropy coding is essential to data compression, image and video coding, etc. The Range variant of Asymmetric Numeral Systems (rANS) is a modern entropy coder, featuring superior speed and compression rate. As rANS is not designed for parallel execution, the conventional approach to parallel rANS partitions the input…
Andrea Di Giusto, Wim van Houtum, Alberto Ravagnani, Yan Wu
—Motivated by applications to digital audio broadcasting (DAB) systems, we study the a-posteriori probabilities (APPs) of the coded and information bits of the serial concatenation of multiple convolutional codewords. The main result of this paper is a proof that the APPs of the input bits do not change when…
Amir Said, Hoang Le, Farzad Farhadzadeh
—Video compression systems must support increasing bandwidth and data throughput at low cost and power, and can be limited by entropy coding bottlenecks. Efficiency can be greatly improved by parallelizing coding, which can be done at much larger scales with new neural-based codecs, but with some compression loss…
Kevin D. Volkel, Paul W. Hook, Albert Keung, Winston Timp + 1 more
As nanopore technology reaches ever higher throughput and accuracy, it becomes an increasingly viable candidate for reading out DNA data storage. Nanopore sequencing offers considerable flexibility by allowing long reads, real-time signal analysis, and the ability to read both DNA and RNA. We need flexible and…
Ramy Khabbaz, Jérémy Mateos, Marc Antonini, Serge Kas Hanna
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level dropouts, occur and pose major challenges for reliable data retrieval. Here we introduce…
Rob Patro, Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal + 2 more
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compressed fastq.gz files has become a substantial scalability bottleneck in the modern world of fast and massively parallel…
G. Kandemir, D. H. Duncan, D. van Moorselaar, J. Theeuwes
For almost half a century, target-distractor similarity has been known to induce different visual search modes. When a target is highly salient, it can pop out, suggesting parallel processing of all items irrespective of set size. By contrast, high similarity among items requires item-by-item comparison with an…
Mohammed Mensouri, Mustapha Eddahibi
In this paper, we introduce a new coding and decoding structure for enhancing the reliability and performance of polar codes, specifically at low error rates. We achieve this by concatenating two polar codes in series to create robust error-correcting codes. The primary objective here is to optimize the behavior of…
Hamid Saber, Homayoon Hatami, Jung Hyun Bae
—Polar codes are the first class of structured channel codes that achieve the symmetric capacity of binary channels with efficient encoding and decoding. In 2019, Arikan proposed a new polar coding scheme referred to as polarization-adjusted convolutional (PAC) codes. In contrast to polar codes, PAC codes precode the…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
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With the ever-increasing demand for atomistic structures representative of real-life systems as well as the ad-vent of exascale computers, it has now become necessary and possible to use advanced global optimization (GO) techniques to intelligently sample the potential energy surface (PES). Given the previous studies…
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Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…