Related papers: Deletion Correcting Codes for Efficient DNA Synthe…
Erasure codes are an efficient means of storing data across a network in comparison to data replication, as they tend to reduce the amount of data stored in the network and offer increased resilience in the presence of node failures. The…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Already in the 1960s, Levenshtein and others studied error-correcting codes that protect against synchronization errors, such as symbol insertions and deletions. However, despite significant efforts, progress on designing such codes has…
An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
Synthesis is a particularly challenging problem for concurrent programs. At the same time it is a very promising approach, since concurrent programs are difficult to get right, or to analyze with traditional verification techniques. This…
This work presents a theoretical analysis of the probability of successfully retrieving data encoded with MDS codes (e.g., Reed-Solomon codes) in DNA storage systems. We study this probability under independent and identically distributed…
We investigate the fundamental limits of the recently proposed random access coverage depth problem for DNA data storage. Under this paradigm, it is assumed that the user information consists of $k$ information strands, which are encoded…
Regenerating codes are a class of codes proposed for providing reliability of data and efficient repair of failed nodes in distributed storage systems. In this paper, we address the fundamental problem of handling errors and erasures during…
Defect segmentation is crucial for quality control in advanced manufacturing, yet data scarcity poses challenges for state-of-the-art supervised deep learning. Synthetic defect data generation is a popular approach for mitigating data…
Motivated by applications in DNA-based storage, we introduce the new problem of code design in the Damerau metric. The Damerau metric is a generalization of the Levenshtein distance which, in addition to deletions, insertions and…
In modern age, the increasing complexity of computation and communication technology is leading us towards the necessity of new paradigm. As a result, unconventional approach like DNA coding theory is gaining considerable attention. The…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…
The problem of designing codes for deletion-correction and synchronization has received renewed interest due to applications in DNA-based data storage systems that use nanopore sequencers as readout platforms. In almost all instances,…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
The use of deep learning techniques has achieved significant progress for program synthesis from input-output examples. However, when the program semantics become more complex, it still remains a challenge to synthesize programs that are…
DNA-based data storage systems face practical challenges due to the high cost of DNA synthesis. A strategy to address the problem entails encoding data via topological modifications of the DNA sugar-phosphate backbone. The DNA Punchcards…