Frequency Coding over Noisy Sampling

Abstract

DNA molecules are so small that it might be practical to use their frequency vectors to encode messages. More precisely, a sender can inject $M_X$ copies of the string $X =$ CATCATCAT into a pool and the receiver can recover $M_X$ by sequencing the pool. There are, however, two sources of uncertainty: (a) $M_X$ is usually too big to be counted exactly, but is estimated by sampling. (b) The DNA sequencer could be noisy; it may have difficulty distinguishing CATCATCAT from CATGATCAT. Recently, Tamir, Weinberger, and Guill\'en i F\`abregas clarified the amount of information the frequency vector can carry under (a). They showed that each string can carry about $\log_4 R$ bits, where $R$ is the average number of times each string is read. They also showed that $\log_4 R$ bits can be achieved by a low-complexity uncoded scheme under the condition that there are at least $\sqrt R$ distinct strings. In this paper, we show that a low-complexity coded scheme can achieve the same $\log_4 R$ bits unconditionally. We then generalize the scheme to handle sequencing noise, (b), and show that the noise penalizes the total number of bits by $\log_2 \det W$, together with a linear term due to the use of Fourier transforms in our proof. The former penalty $\log_2 \det W$ is asymptotically the same as that obtained by Gerzon, Shomorony, and Weinberger; our scheme trades a small amount of rate for practical complexity.