# Scaling up DNA digital data storage by efficiently predicting DNA hybridisation using deep learning

arXiv: https://arxiv.org/abs/2102.10131 · HTML: https://mlsanity.com/paper/2102.10131/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 7 of its 47 references that are in the map.
- First posted on arXiv 19 Feb 2021.

## Builds on (most cited first, 7 of 7)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Optuna: A Next-generation Hyperparameter Optimization Framework](https://mlsanity.com/paper/1907.10902/) (2019)
- [Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling](https://mlsanity.com/paper/1412.3555/) (2014)
- [HuggingFace's Transformers: State-of-the-art Natural Language Processing](https://mlsanity.com/paper/1910.03771/) (2019)

## Abstract (arXiv)

Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in solution, thus enabling search and pattern-matching capabilities. Being able to control and predict the process of DNA hybridisation is crucial for the ambitious future of Hybrid Molecular-Electronic Computing. Current tools are, however, limited in terms of throughput and applicability to large-scale problems. We present the first comprehensive study of machine learning methods applied to the task of predicting DNA hybridisation. For this purpose, we introduce an in silico-generated hybridisation dataset of over 2.5 million data points, enabling the use of deep learning. Depending on hardware, we achieve a reduction in inference time ranging from one to over two orders of magnitude compared to the state-of-the-art, while retaining high fidelity. We then discuss the integration of our methods in modern, scalable workflows.