Coding Schemes for the Noisy Torn Paper Channel

TL;DR

This paper introduces coding schemes for a probabilistic noisy torn paper channel modeled for DNA data storage, focusing on sequence reconstruction despite corruption and fragmentation, with high accuracy demonstrated through simulations.

Contribution

It proposes novel coding strategies using static and data-dependent markers to improve sequence reconstruction in noisy torn paper channels for DNA storage.

Findings

Static markers perform better at higher substitution probabilities.

Data-dependent markers excel at lower noise levels.

Achieved over 99% reconstruction rates with no false decodings.

Abstract

To make DNA a suitable medium for archival data storage, it is essential to consider the decay process of the strands observed in DNA storage systems. This paper studies the decay process as a probabilistic noisy torn paper channel (TPC), which first corrupts the bits of the transmitted sequence in a probabilistic manner by substitutions, then breaks the sequence into a set of noisy unordered substrings. The present work devises coding schemes for the noisy TPC by embedding markers in the transmitted sequence. We investigate the use of static markers and markers connected to the data in the form of hash functions. These two tools have also been recently exploited to tackle the noiseless TPC. Simulations show that static markers excel at higher substitution probabilities, while data-dependent markers are superior at lower noise levels. Both approaches achieve reconstruction rates exceeding $99\%$ with no false decodings observed, primarily limited by computational resources.