Circular Trace Reconstruction

TL;DR

This paper introduces circular trace reconstruction, analyzing how to recover circular strings from noisy, randomly shifted traces, with new bounds on the number of traces needed for reconstruction.

Contribution

It establishes the first bounds for circular trace reconstruction, including upper bounds for arbitrary and random strings, and a new lower bound for the problem.

Findings

Reconstruction of arbitrary circular strings with exp(O(n^{1/3})) traces for prime or product-of-two-primes lengths.

High-probability reconstruction of random circular strings with polynomially many traces.

Lower bound of ~Ω(n^3) traces for arbitrary circular strings, exceeding standard trace reconstruction bounds.

Abstract

Trace reconstruction is the problem of learning an unknown string $x$ from independent traces of $x$, where traces are generated by independently deleting each bit of $x$ with some deletion probability $q$. In this paper, we initiate the study of Circular trace reconstruction, where the unknown string $x$ is circular and traces are now rotated by a random cyclic shift. Trace reconstruction is related to many computational biology problems studying DNA, which is a primary motivation for this problem as well, as many types of DNA are known to be circular. Our main results are as follows. First, we prove that we can reconstruct arbitrary circular strings of length $n$ using $\exp\big(\tilde{O}(n^{1/3})\big)$ traces for any constant deletion probability $q$, as long as $n$ is prime or the product of two primes. For $n$ of this form, this nearly matches what was the best known bound of $\exp\big(O(n^{1/3})\big)$ for standard trace reconstruction when this paper was initially released. We note, however, that Chase very recently improved the standard trace reconstruction bound to $\exp\big(\tilde{O}(n^{1/5})\big)$. Next, we prove that we can reconstruct random circular strings with high probability using $n^{O(1)}$ traces for any constant deletion probability $q$. Finally, we prove a lower bound of $\tilde{\Omega}(n^3)$ traces for arbitrary circular strings, which is greater than the best known lower bound of $\tilde{\Omega}(n^{3/2})$ in standard trace reconstruction.