Related papers: Algorithms of self-synchronizing single-deletion-c…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…
Different choices of quantum error-correcting codes can reduce the demands on the physical hardware needed to build a quantum computer. To achieve the full potential of a code, we must develop practical decoding algorithms that can correct…
A new class of exact-repair regenerating codes is constructed by combining two layers of erasure correction codes together with combinatorial block designs, e.g., Steiner systems, balanced incomplete block designs and t-designs. The…
Polar codes can be decoded with the low-complexity successive-cancellation flip (SCF) algorithm. To improve error-correction performance, the dynamic successive-cancellation flip (DSCF) variant was proposed, where the resulting…
Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…
Erasure coding techniques are getting integrated in networked distributed storage systems as a way to provide fault-tolerance at the cost of less storage overhead than traditional replication. Redundancy is maintained over time through…
Error correction codes are a crucial part of the physical communication layer, ensuring the reliable transfer of data over noisy channels. The design of optimal linear block codes capable of being efficiently decoded is of major concern,…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
Sequence generation applications require satisfying semantic constraints, such as ensuring that programs are correct, using certain keywords, or avoiding undesirable content. Language models, whether fine-tuned or prompted with few-shot…
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
In this paper, we propose a new erasure decoding algorithm for convolutional codes using the generator matrix. This implies that our decoding method also applies to catastrophic convolutional codes in opposite to the classic approach using…
In this paper, we propose a partitioning technique that decomposes a pair of sequences with overlapping $t$-deletion $s$-substitution balls into sub-pairs, where the $^{\leq}t$-burst-deletion balls of each sub-pair intersect. This…
This work introduces self-infilling code generation, a general framework that incorporates infilling operations into auto-regressive decoding. Our approach capitalizes on the observation that recent infilling-capable code language models…
Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…
Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and…
Construction of capacity achieving deletion correcting codes has been a baffling challenge for decades. A recent breakthrough by Brakensiek $et~al$., alongside novel applications in DNA storage, have reignited the interest in this…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
In this paper, we present a novel communication channel, called the absorption channel, inspired by information transmission in neurons. Our motivation comes from in-vivo nano-machines, emerging medical applications, and brain-machine…