arXiv subjects

Leon Anavy

Publications and source records attributed to Leon Anavy.

3 recordsLinked to original sources

arXiv2026

Error characterization and error correction approaches in combinatorial DNA-based storage

Data storage in DNA has recently emerged as a promising archival solution, offering space-efficient and long-lasting digital storage. Combinatorial DNA encoding enhances this potential by increasing the logical density through combinations of DNA shortmers, where each sequence position is represented by a set of predefined short DNA fragments, allowing more data to be encoded using fewer synthesis cycles. However, this method introduces unique synthesis and sequencing errors. In this study, we characterize errors in combinatorial DNA-based storage systems. We reveal that asymmetric combinatorial erasure errors, defined as the omission of a single shortmer from the set defining the combinatorial letter, are a prevalent error type, particularly in large-scale systems where read coverage is limited. In two previously published datasets, we observed a high frequency of erasure errors, where missing sequences obstruct the reconstruction of combinatorial letters. We conducted a large-scale experimental proof-of-concept and confirmed that erasure errors become increasingly prominent with reduced sequencing depth: below 50 reads per sequence, their frequency sharply increased. We developed an asymmetric error-correcting code for these errors, utilizing tensor-product codes to integrate standard erasure and substitution-correcting codes (such as Reed-Solomon (RS) codes) with asymmetric Varshamov-Tenengolts codes. We validated its performance in simulations and in a second large-scale experiment directly comparing it with the more straightforward 2D RS scheme. Our method consistently outperformed 2D RS, particularly in erasure-dominated scenarios, and demonstrated superior decoding accuracy under low coverage conditions where 2D RS struggled to decode the data. Our findings demonstrate the importance of error correction schemes tailored to the asymmetric nature of errors in combinatorial DNA.

cs.IT↗

arXiv2024

Error-Correcting Codes for Combinatorial Composite DNA

Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This approach extends the DNA alphabet by harnessing short DNA fragment reagents, known as shortmers. The shortmers are building blocks of the alphabet symbols, consisting of a fixed number of shortmers. Thus, when information is read, it is possible that one of the shortmers that forms part of the composition of a symbol is missing and therefore the symbol cannot be determined. In this paper, we model this type of error as a type of asymmetric error and propose code constructions that can correct such errors in this setup. We also provide a lower bound on the redundancy of such error-correcting codes and give an explicit encoder and decoder pair for our construction. Our suggested error model is also supported by an analysis of data from actual experiments that produced DNA according to the combinatorial scheme. Lastly, we also provide a statistical evaluation of the probability of observing such error events, as a function of read depth.

cs.IT↗

arXiv2021

Single-Read Reconstruction for DNA Data Storage Using Transformers

As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential solution for the future of data storage. Several studies introduced DNA based storage systems with high information density (petabytes/gram). However, DNA synthesis and sequencing technologies yield erroneous outputs. Algorithmic approaches for correcting these errors depend on reading multiple copies of each sequence and result in excessive reading costs. The unprecedented success of Transformers as a deep learning architecture for language modeling has led to its repurposing for solving a variety of tasks across various domains. In this work, we propose a novel approach for single-read reconstruction using an encoder-decoder Transformer architecture for DNA based data storage. We address the error correction process as a self-supervised sequence-to-sequence task and use synthetic noise injection to train the model using only the decoded reads. Our approach exploits the inherent redundancy of each decoded file to learn its underlying structure. To demonstrate our proposed approach, we encode text, image and code-script files to DNA, produce errors with high-fidelity error simulator, and reconstruct the original files from the noisy reads. Our model achieves lower error rates when reconstructing the original data from a single read of each DNA strand compared to state-of-the-art algorithms using 2-3 copies. This is the first demonstration of using deep learning models for single-read reconstruction in DNA based storage which allows for the reduction of the overall cost of the process. We show that this approach is applicable for various domains and can be generalized to new domains as well.

cs.ET↗