Bounds on the Capacity of Random Insertion and Deletion-Additive Noise Channels

We develop several analytical lower bounds on the capacity of binary insertion and deletion channels by considering independent uniformly distributed (i.u.d.) inputs and computing lower bounds on the mutual information between the input and output sequences. For the deletion channel, we consider two different models: independent and identically distributed (i.i.d.) deletion-substitution channel and i.i.d. deletion channel with additive white Gaussian noise (AWGN). These two models are considered to incorporate effects of the channel noise along with the synchronization errors. For the insertion channel case we consider the Gallager's model in which the transmitted bits are replaced with two random bits and uniform over the four possibilities independently of any other insertion events. The general approach taken is similar in all cases, however the specific computations differ. Furthermore, the approach yields a useful lower bound on the capacity for a wide range of deletion probabilities for the deletion channels, while it provides a beneficial bound only for small insertion probabilities (less than 0.25) for the insertion model adopted. We emphasize the importance of these results by noting that 1) our results are the first analytical bounds on the capacity of deletion-AWGN channels, 2) the results developed are the best available analytical lower bounds on the deletion-substitution case, 3) for the Gallager insertion channel model, the new lower bound improves the existing results for small insertion probabilities.Comment: Accepted for publication in IEEE Transactions on Information Theor

On Asynchronous Communication Systems: Capacity Bounds and Relaying Schemes

abstract: Practical communication systems are subject to errors due to imperfect time alignment among the communicating nodes. Timing errors can occur in different forms depending on the underlying communication scenario. This doctoral study considers two different classes of asynchronous systems; point-to-point (P2P) communication systems with synchronization errors, and asynchronous cooperative systems. In particular, the focus is on an information theoretic analysis for P2P systems with synchronization errors and developing new signaling solutions for several asynchronous cooperative communication systems. The first part of the dissertation presents several bounds on the capacity of the P2P systems with synchronization errors. First, binary insertion and deletion channels are considered where lower bounds on the mutual information between the input and output sequences are computed for independent uniformly distributed (i.u.d.) inputs. Then, a channel suffering from both synchronization errors and additive noise is considered as a serial concatenation of a synchronization error-only channel and an additive noise channel. It is proved that the capacity of the original channel is lower bounded in terms of the synchronization error-only channel capacity and the parameters of both channels. On a different front, to better characterize the deletion channel capacity, the capacity of three independent deletion channels with different deletion probabilities are related through an inequality resulting in the tightest upper bound on the deletion channel capacity for deletion probabilities larger than 0.65. Furthermore, the first non-trivial upper bound on the 2K-ary input deletion channel capacity is provided by relating the 2K-ary input deletion channel capacity with the binary deletion channel capacity through an inequality. The second part of the dissertation develops two new relaying schemes to alleviate asynchronism issues in cooperative communications. The first one is a single carrier (SC)-based scheme providing a spectrally efficient Alamouti code structure at the receiver under flat fading channel conditions by reducing the overhead needed to overcome the asynchronism and obtain spatial diversity. The second one is an orthogonal frequency division multiplexing (OFDM)-based approach useful for asynchronous cooperative systems experiencing excessive relative delays among the relays under frequency-selective channel conditions to achieve a delay diversity structure at the receiver and extract spatial diversity.Dissertation/ThesisPh.D. Electrical Engineering 201

An Upper Bound on the Capacity of non-Binary Deletion Channels

We derive an upper bound on the capacity of non-binary deletion channels. Although binary deletion channels have received significant attention over the years, and many upper and lower bounds on their capacity have been derived, such studies for the non-binary case are largely missing. The state of the art is the following: as a trivial upper bound, capacity of an erasure channel with the same input alphabet as the deletion channel can be used, and as a lower bound the results by Diggavi and Grossglauser are available. In this paper, we derive the first non-trivial non-binary deletion channel capacity upper bound and reduce the gap with the existing achievable rates. To derive the results we first prove an inequality between the capacity of a 2K-ary deletion channel with deletion probability $d$, denoted by $C_{2K}(d)$, and the capacity of the binary deletion channel with the same deletion probability, $C_2(d)$, that is, $C_{2K}(d)\leq C_2(d)+(1-d)\log(K)$. Then by employing some existing upper bounds on the capacity of the binary deletion channel, we obtain upper bounds on the capacity of the 2K-ary deletion channel. We illustrate via examples the use of the new bounds and discuss their asymptotic behavior as $d \rightarrow 0$.Comment: accepted for presentation in ISIT 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

A Note on the Deletion Channel Capacity

Memoryless channels with deletion errors as defined by a stochastic channel matrix allowing for bit drop outs are considered in which transmitted bits are either independently deleted with probability $d$ or unchanged with probability $1-d$. Such channels are information stable, hence their Shannon capacity exists. However, computation of the channel capacity is formidable, and only some upper and lower bounds on the capacity exist. In this paper, we first show a simple result that the parallel concatenation of two different independent deletion channels with deletion probabilities $d_1$ and $d_2$, in which every input bit is either transmitted over the first channel with probability of $\lambda$ or over the second one with probability of $1-\lambda$, is nothing but another deletion channel with deletion probability of $d=\lambda d_1+(1-\lambda)d_2$. We then provide an upper bound on the concatenated deletion channel capacity $C(d)$ in terms of the weighted average of $C(d_1)$, $C(d_2)$ and the parameters of the three channels. An interesting consequence of this bound is that $C(\lambda d_1+(1-\lambda))\leq \lambda C(d_1)$ which enables us to provide an improved upper bound on the capacity of the i.i.d. deletion channels, i.e., $C(d)\leq 0.4143(1-d)$ for $d\geq 0.65$. This generalizes the asymptotic result by Dalai as it remains valid for all $d\geq 0.65$. Using the same approach we are also able to improve upon existing upper bounds on the capacity of the deletion/substitution channel.Comment: Submitted to the IEEE Transactions on Information Theor