Related papers: Coding for Synthesis Defects
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
Despite their significant advantages over competing technologies, nanopore sequencers are plagued by high error rates, due to physical characteristics of the nanopore and inherent noise in the biological processes. It is thus paramount not…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
In this paper, we show that the code-trellis and the error-trellis for a convolutional code can be reduced simultaneously, if reduction is possible. Assume that the error-trellis can be reduced using shifted error-subsequences. In this…
In this paper, we investigate the problem of designing $(n, N; \mathcal{B})$-reconstruction codes for $N\in \{14,11,9,5\}$, where $\mathcal{B}$ is the single-deletion single-substitution ball function that maps a sequence to the set of all…
Program synthesis is the task of automatically generating a program consistent with a specification. Recent years have seen proposal of a number of neural approaches for program synthesis, many of which adopt a sequence generation paradigm…
In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…
Defect-adaptive surface-code methods have substantially advanced the construction of valid logical patches on imperfect hardware, but fault-tolerant computation also requires executable logical oper ations on the resulting irregular…
Automated defect inspection is critical for effective and efficient maintenance, repair, and operations in advanced manufacturing. On the other hand, automated defect inspection is often constrained by the lack of defect samples, especially…
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…
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…
We construct deletion error-correcting codes in the oblivious model, where errors are adversarial but oblivious to the encoder's randomness. Oblivious errors bridge the gap between the adversarial and random error models, and are motivated…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
We present a new program synthesis approach that combines an encoder-decoder based synthesis architecture with a differentiable program fixer. Our approach is inspired from the fact that human developers seldom get their program correct on…
Quantum error correction requires accurate and efficient decoding to optimally suppress errors in the encoded information. For concatenated codes, where one code is embedded within another, optimal decoding can be achieved using a…
Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate…
Data-hunger and data-imbalance are two major pitfalls in many deep learning approaches. For example, on highly optimized production lines, defective samples are hardly acquired while non-defective samples come almost for free. The defects…
In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA…