Capacity Upper Bounds for Deletion-Type Channels

We develop a systematic approach, based on convex programming and real analysis, for obtaining upper bounds on the capacity of the binary deletion channel and, more generally, channels with i.i.d. insertions and deletions. Other than the classical deletion channel, we give a special attention to the Poisson-repeat channel introduced by Mitzenmacher and Drinea (IEEE Transactions on Information Theory, 2006). Our framework can be applied to obtain capacity upper bounds for any repetition distribution (the deletion and Poisson-repeat channels corresponding to the special cases of Bernoulli and Poisson distributions). Our techniques essentially reduce the task of proving capacity upper bounds to maximizing a univariate, real-valued, and often concave function over a bounded interval. We show the following: 1. The capacity of the binary deletion channel with deletion probability $d$ is at most $(1-d)\log\varphi$ for $d\geq 1/2$, and, assuming the capacity function is convex, is at most $1-d\log(4/\varphi)$ for $d<1/2$, where $\varphi=(1+\sqrt{5})/2$ is the golden ratio. This is the first nontrivial capacity upper bound for any value of $d$ outside the limiting case $d\to 0$ that is fully explicit and proved without computer assistance. 2. We derive the first set of capacity upper bounds for the Poisson-repeat channel. 3. We derive several novel upper bounds on the capacity of the deletion channel. All upper bounds are maximums of efficiently computable, and concave, univariate real functions over a bounded domain. In turn, we upper bound these functions in terms of explicit elementary and standard special functions, whose maximums can be found even more efficiently (and sometimes, analytically, for example for $d=1/2$). Along the way, we develop several new techniques of potentially independent interest in information theory, probability, and mathematical analysis.Comment: Minor edits, In Proceedings of 50th Annual ACM SIGACT Symposium on the Theory of Computing (STOC), 201

Models and information-theoretic bounds for nanopore sequencing

Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore sequencers can acquire long reads, the high error rates (20%-30%) pose a technical challenge. In a nanopore sequencer, a DNA is migrated through a nanopore and current variations are measured. The DNA sequence is inferred from this observed current pattern using an algorithm called a base-caller. In this paper, we propose a mathematical model for the "channel" from the input DNA sequence to the observed current, and calculate bounds on the information extraction capacity of the nanopore sequencer. This model incorporates impairments like (non-linear) inter-symbol interference, deletions, as well as random response. These information bounds have two-fold application: (1) The decoding rate with a uniform input distribution can be used to calculate the average size of the plausible list of DNA sequences given an observed current trace. This bound can be used to benchmark existing base-calling algorithms, as well as serving a performance objective to design better nanopores. (2) When the nanopore sequencer is used as a reader in a DNA storage system, the storage capacity is quantified by our bounds

Secrecy Through Synchronization Errors

In this paper, we propose a transmission scheme that achieves information theoretic security, without making assumptions on the eavesdropper's channel. This is achieved by a transmitter that deliberately introduces synchronization errors (insertions and/or deletions) based on a shared source of randomness. The intended receiver, having access to the same shared source of randomness as the transmitter, can resynchronize the received sequence. On the other hand, the eavesdropper's channel remains a synchronization error channel. We prove a secrecy capacity theorem, provide a lower bound on the secrecy capacity, and propose numerical methods to evaluate it.Comment: 5 pages, 6 figures, submitted to ISIT 201