Related papers: GC+ Code: A Systematic Short Blocklength Code for …
We study data structures in the presence of adversarial noise. We want to encode a given object in a succinct data structure that enables us to efficiently answer specific queries about the object, even if the data structure has been…
We present a Compression Tool, "GenBit Compress", for genetic sequences based on our new proposed "GenBit Compress Algorithm". Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
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…
To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit…
Efficiently realizing logical operations on general stabilizer codes remains a long-standing challenge in fault tolerant quantum computing. While code surgery provides a general framework with provable guarantees by joint logical…
Synthetic data generation is widely known to boost the accuracy of neural grammatical error correction (GEC) systems, but existing methods often lack diversity or are too simplistic to generate the broad range of grammatical errors made by…
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…
Nowadays, data augmentation through synthetic data has been widely used in the field of Grammatical Error Correction (GEC) to alleviate the problem of data scarcity. However, these synthetic data are mainly used in the pre-training phase…
In Search Based Software Engineering, Genetic Programming has been used for bug fixing, performance improvement and parallelisation of programs through the modification of source code. Where an evolutionary computation algorithm, such as…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
In recent years, the emergence of DNA storage systems has led to a widespread focus on the research of codes correcting insertions, deletions, and classic substitutions. During the initial investigation, Levenshtein discovered the VT codes…
We consider the problem of designing low-redundancy codes in settings where one must correct deletions in conjunction with substitutions or adjacent transpositions; a combination of errors that is usually observed in DNA-based data storage.…
Performing active quantum error correction to protect fragile quantum states highly depends on the correctness of error information--error syndromes. To obtain reliable error syndromes using imperfect physical circuits, we propose the idea…
Program synthesis aims to {\it automatically} find programs from an underlying programming language that satisfy a given specification. While this has the potential to revolutionize computing, how to search over the vast space of programs…
Concatenated coding provides a general strategy to achieve the desired level of noise protection in quantum information storage and transmission. We report the implementation of a concatenated quantum error-correcting code able to correct…
The exponential increase in storage demand and low lifespan of data storage devices has resulted in long-term archival and preservation emerging as a critical bottlenecks in data storage. In order to meet this demand, researchers are now…
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…