# Deep DNA Storage: Scalable and Robust DNA Storage via Coding Theory and Deep Learning

arXiv: https://arxiv.org/abs/2109.00031 · HTML: https://mlsanity.com/paper/2109.00031/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 5 of its 73 references that are in the map.
- First posted on arXiv 31 Aug 2021.

## Builds on (most cited first, 5 of 5)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Xception: Deep Learning with Depthwise Separable Convolutions](https://mlsanity.com/paper/1610.02357/) (2016)
- [Early Convolutions Help Transformers See Better](https://mlsanity.com/paper/2106.14881/) (2021)
- [Subpolynomial trace reconstruction for random strings and arbitrary deletion probability](https://mlsanity.com/paper/1801.04783/) (2018)
- [Average-case reconstruction for the deletion channel: subpolynomially many traces suffice](https://mlsanity.com/paper/1708.00854/) (2017)

## Built on by (most cited first, 3 of 3)

- [Single-Read Reconstruction for DNA Data Storage Using Transformers](https://mlsanity.com/paper/2109.05478/) (2021)
- [Transformer-Based Decoding in Concatenated Coding Schemes Under Synchronization Errors](https://mlsanity.com/paper/2511.00999/) (2025)
- [Beyond the Alphabet: Deep Signal Embedding for Enhanced DNA Clustering](https://mlsanity.com/paper/2410.06188/) (2024)

## Abstract (arXiv)

DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced data durability, and negligible power consumption to maintain data integrity. To access the data, an information retrieval process is employed, where some of the main bottlenecks are the scalability and accuracy, which have a natural tradeoff between the two. Here we show a modular and holistic approach that combines Deep Neural Networks (DNN) trained on simulated data, Tensor-Product (TP) based Error-Correcting Codes (ECC), and a safety margin mechanism into a single coherent pipeline. We demonstrated our solution on 3.1MB of information using two different sequencing technologies. Our work improves upon the current leading solutions by up to x3200 increase in speed, 40% improvement in accuracy, and offers a code rate of 1.6 bits per base in a high noise regime. In a broader sense, our work shows a viable path to commercial DNA storage solutions hindered by current information retrieval processes.