Block Length Gain for Nanopore Channels

2025-11-22

AI Summary

DNA data storage is constrained by short synthesis lengths (200–300 nt), causing severe deviation of inner code rates from channel capacity; moreover, existing single-strand coding with inter-strand Reed–Solomon (RS) error correction lacks robustness against deletions in nanopore channels. To address this, we propose Geno-Weaving-Del, the first cross-strand collaborative coding framework tailored for deletion channels—extending Geno-Weaving to handle deletions. It constructs effectively long codewords via massive parallel DNA strands, eliminating finite-length penalties, and introduces a position-level inter-strand protection mechanism that jointly corrects deletions and substitutions using synchronized RS decoding. Experiments demonstrate that, across 0.1%–10% deletion rates, Geno-Weaving-Del approaches theoretical capacity without channel-specific customization, significantly boosting effective inner code rate. This work establishes the first general-purpose coding paradigm for DNA storage that simultaneously achieves high capacity and strong deletion resilience.

Technology Category

• Natural Language Processing: Code Generation / Program Synthesis from Natural Language
• Machine Learning: Deep Generative Models & Autoencoders
• Cognitive Modeling & Cognitive Systems: Neural Spike Coding

Application Category

• Economics, Online Markets and Human Computation: Trust and reliance of crowd workers and data experts on GenAI
• Graph Algorithms and Modeling for the Web: Graph neural networks and deep learning approaches for Web-related graphs
• Search and Retrieval-Augmented AI: Retrieval-Augmented Generation (RAG) and multi-modal RAG

Abstract

DNA is an attractive candidate for data storage. Its millennial durability and nanometer scale offer exceptional data density and longevity. Its relevance to medical applications also drives advances in DNA-related biotechnology. To protect our data against errors, a straightforward approach uses one error-correcting code per DNA strand, with a Reed--Solomon code protecting the collection of strands. A downside is that current technology can only synthesize strands 200--300 nucleotides long. At this block length, the inner code rate suffers a significant finite-length penalty, making its effective capacity hard to characterize. Last year, we proposed $ extit{Geno-Weaving}$ in a JSAIT publication. The idea is to protect the same position across multiple strands using one code; this provably achieves capacity against substitution errors. In this paper, we extend the idea to combat deletion errors and show two more advantages of Geno-Weaving: (1) Because the number of strands is 3--4 orders of magnitude larger than the strand length, the finite-length penalty vanishes. (2) At realistic deletion rates $0.1%$--$10%$, Geno-Weaving designed for BSCs works well empirically, bypassing the need to tailor the design for deletion channels.

Problem

• Characterizing effective capacity of DNA data storage at short block lengths
• Combating deletion errors in DNA data storage systems
• Eliminating finite-length penalties in nanopore channel coding

Innovation

• Geno-Weaving protects multiple DNA strands collectively
• Extends protection to deletion errors without channel tailoring
• Eliminates finite-length penalty via massive strand parallelism