Related papers: RECKONER: Read Error Corrector Based on KMC
Quantum error correction offers a promising path for performing quantum computations with low errors. Although a fully fault-tolerant execution of a quantum algorithm remains unrealized, recent experimental developments, along with…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
Analog computing has reemerged as a promising avenue for accelerating deep neural networks (DNNs) due to its potential to overcome the energy efficiency and scalability challenges posed by traditional digital architectures. However,…
Lowering the resource overhead needed to achieve fault-tolerant quantum computation is crucial to building scalable quantum computers. We show that adapting conventional maximum likelihood (ML) decoders to a small subset of efficiently…
Quantum error correction plays an important role in fault-tolerant quantum information processing. It is usually difficult to experimentally realize quantum error correction, as it requires multiple qubits and quantum gates with high…
We present the results of an R&D study of a specialized processor capable of precisely reconstructing events with hundreds of charged-particle tracks in pixel detectors at 40 MHz, thus suitable for processing LHC events at the full crossing…
A robust real-world deployment of autonomous edge devices requires on-chip adaptation to user-, environment- and task-induced variability. Due to on-chip memory constraints, prior learning devices were limited to static stimuli with no…
Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference introduces significant latency, limiting their utility in…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
The persistent storage of big data requires advanced error correction schemes. The classical approach is to use error correcting codes (ECCs). This work studies an alternative approach, which uses the redundancy inherent in data itself for…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
We propose a frame-based representation of k-mers for detecting sequencing errors and rare variants in next generation sequencing data obtained from populations of closely related genomes. Frames are sets of non-orthogonal basis functions,…
Synthetic DNA can in principle be used for the archival storage of arbitrary data. Because errors are introduced during DNA synthesis, storage, and sequencing, an error-correcting code (ECC) is necessary for error-free recovery of the data.…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a…
Neural network decoders are becoming essential for achieving fault-tolerant quantum computations. However, their internal mechanisms are poorly understood, hindering our ability to ensure their reliability and security against adversarial…
The realization of fault-tolerant quantum computers hinges on the construction of high-speed, high-accuracy, real-time decoding systems. The persistent challenge lies in the fundamental trade-off between speed and accuracy: efforts to…
Error correction code is a major part of the communication physical layer, ensuring the reliable transfer of data over noisy channels. Recently, neural decoders were shown to outperform classical decoding techniques. However, the existing…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…