VT-Former: Efffcient Transformer-based Decoder for Varshamov-Tenengolts Codes

TL;DR

This paper introduces VT-Former, a Transformer-based decoder that significantly improves the correction of multiple insertion, deletion, and substitution errors in Varshamov-Tenengolts codes for DNA data storage.

Contribution

It presents a novel statistic-enhanced Transformer architecture that extends VT codes' capabilities to multi-error correction with improved accuracy and efficiency.

Findings

Achieves nearly 100% accuracy in single-error correction.

Improves frame and bit accuracy in multi-error decoding tasks.

Reduces decoding latency and computational overhead.

Abstract

In recent years, widespread attention has been drawn to the challenge of correcting insertion, deletion, and substitution (IDS) errors in DNA-based data storage. Among various IDS-correcting codes, Varshamov-Tenengolts (VT) codes, originally designed for single-error correction, have been established as a central research focus. While existing decoding methods demonstrate high accuracy for single-error correction, they are typically not applicable to the correction of multiple IDS errors. In this work, the latent capability of VT codes for multiple-error correction is investigated through a statistic-enhanced Transformer-based VT decoder (VT-Former), utilizing both symbol and statistic feature embeddings. Experimental results demonstrate that VT-Former achieves nearly 100\% accuracy on correcting single errors. For multi-error decoding tasks across various codeword lengths, improvements in both frame accuracy and bit accuracy are observed, compared to conventional hard-decision and soft-in soft-out decoding algorithms. Furthermore, while lower decoding latency is exhibited by the base model compared to traditional soft decoders, the architecture is further optimized in this study to enhance decoding efficiency and reduce computational overhead.