Data-Driven Bee Identification for DNA Strands

Abstract: We study a data-driven approach to the bee identification problem for DNA strands. The bee-identification problem, introduced by Tandon et al. (2019), requires one to identify $M$ bees, each tagged by a unique barcode, via a set of $M$ noisy measurements. Later, Chrisnata et al. (2022) extended the model to case where one observes $N$ noisy measurements of each bee, and applied the model to address the unordered nature of DNA storage systems. In such systems, a unique address is typically prepended to each DNA data block to form a DNA strand, but the address may possibly be corrupted. While clustering is usually used to identify the address of a DNA strand, this requires $\mathcal{M}^2$ data comparisons (when $\mathcal{M}$ is the number of reads). In contrast, the approach of Chrisnata et al. (2022) avoids data comparisons completely. In this work, we study an intermediate, data-driven approach to this identification task. For the binary erasure channel, we first show that we can almost surely correctly identify all DNA strands under certain mild assumptions. Then we propose a data-driven pruning procedure and demonstrate that on average the procedure uses only a fraction of $\mathcal{M}^2$ data comparisons. Specifically, for $\mathcal{M}= 2^n$ and erasure probability $p$, the expected number of data comparisons performed by the procedure is $\kappa\mathcal{M}^2$, where $\left(\frac{1+2p-p^2}{2}\right)^n \leq \kappa \leq \left(\frac{1+p}{2}\right)^n $.