Disturbance-based Discretization, Differentiable IDS Channel, and an IDS-Correcting Code for DNA-based Storage

TL;DR

This paper introduces THEA-code, an autoencoder-based method that designs tailored IDS error-correcting codes for DNA storage by using a disturbance-based discretization and a differentiable IDS channel, improving code performance.

Contribution

The paper presents a novel autoencoder framework with disturbance-based discretization and a differentiable IDS channel for creating customized IDS-correcting codes in DNA storage.

Findings

Codes perform well across complex IDS channels

Effective convergence of the autoencoder achieved

Demonstrates applicability to realistic DNA storage channels

Abstract

With recent advancements in next-generation data storage, especially in biological molecule-based storage, insertion, deletion, and substitution (IDS) error-correcting codes have garnered increased attention. However, a universal method for designing tailored IDS-correcting codes across varying channel settings remains underexplored. We present an autoencoder-based approach, THEA-code, aimed at efficiently generating IDS-correcting codes for complex IDS channels. In the work, a disturbance-based discretization is proposed to discretize the features of the autoencoder, and a simulated differentiable IDS channel is developed as a differentiable alternative for IDS operations. These innovations facilitate the successful convergence of the autoencoder, producing channel-customized IDS-correcting codes that demonstrate commendable performance across complex IDS channels, particularly in realistic DNA-based storage channels.