Write Channel Model for Bit-Patterned Media Recording

We propose a new write channel model for bit-patterned media recording that reflects the data dependence of write synchronization errors. It is shown that this model accommodates both substitution-like errors and insertion-deletion errors whose statistics are determined by an underlying channel state process. We study information theoretic properties of the write channel model, including the capacity, symmetric information rate, Markov-1 rate and the zero-error capacity.Comment: 11 pages, 12 figures, journa

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

Detecting and Estimating Signals over Noisy and Unreliable Synapses: Information-Theoretic Analysis

The temporal precision with which neurons respond to synaptic inputs has a direct bearing on the nature of the neural code. A characterization of the neuronal noise sources associated with different sub-cellular components (synapse, dendrite, soma, axon, and so on) is needed to understand the relationship between noise and information transfer. Here we study the effect of the unreliable, probabilistic nature of synaptic transmission on information transfer in the absence of interaction among presynaptic inputs. We derive theoretical lower bounds on the capacity of a simple model of a cortical synapse under two different paradigms. In signal estimation, the signal is assumed to be encoded in the mean firing rate of the presynaptic neuron, and the objective is to estimate the continuous input signal from the postsynaptic voltage. In signal detection, the input is binary, and the presence or absence of a presynaptic action potential is to be detected from the postsynaptic voltage. The efficacy of information transfer in synaptic transmission is characterized by deriving optimal strategies under these two paradigms. On the basis of parameter values derived from neocortex, we find that single cortical synapses cannot transmit information reliably, but redundancy obtained using a small number of multiple synapses leads to a significant improvement in the information capacity of synaptic transmission

Achievable Rates for Noisy Channels with Synchronization Errors

Cataloged from PDF version of article.We develop several lower bounds on the capacity of binary input symmetric output channels with synchronization errors, which also suffer from other types of impairments such as substitutions, erasures, additive white Gaussian noise (AWGN), etc. More precisely, we show that if a channel suffering from synchronization errors as well as other type of impairments can be decomposed into a cascade of two component channels where the first one is another channel with synchronization errors and the second one is a memoryless channel (with no synchronization errors), a lower bound on the capacity of the original channel in terms of the capacity of the component synchronization error channel can be derived. A primary application of our results is that we can employ any lower bound derived on the capacity of the component synchronization error channel to find lower bounds on the capacity of the (original) noisy channel with synchronization errors. We apply the general ideas to several specific classes of channels such as synchronization error channels with erasures and substitutions, with symmetric q-ary outputs and with AWGN explicitly, and obtain easy-to-compute bounds. We illustrate that, with our approach, it is possible to derive tighter capacity lower bounds compared to the currently available bounds in the literature for certain classes of channels, e.g., deletion/substitution channels and deletion/AWGN channels (for certain signal-to-noise ratio (SNR) ranges). © 2014 IEEE

The Wiretap Channel with Feedback: Encryption over the Channel

In this work, the critical role of noisy feedback in enhancing the secrecy capacity of the wiretap channel is established. Unlike previous works, where a noiseless public discussion channel is used for feedback, the feed-forward and feedback signals share the same noisy channel in the present model. Quite interestingly, this noisy feedback model is shown to be more advantageous in the current setting. More specifically, the discrete memoryless modulo-additive channel with a full-duplex destination node is considered first, and it is shown that the judicious use of feedback increases the perfect secrecy capacity to the capacity of the source-destination channel in the absence of the wiretapper. In the achievability scheme, the feedback signal corresponds to a private key, known only to the destination. In the half-duplex scheme, a novel feedback technique that always achieves a positive perfect secrecy rate (even when the source-wiretapper channel is less noisy than the source-destination channel) is proposed. These results hinge on the modulo-additive property of the channel, which is exploited by the destination to perform encryption over the channel without revealing its key to the source. Finally, this scheme is extended to the continuous real valued modulo-$\Lambda$ channel where it is shown that the perfect secrecy capacity with feedback is also equal to the capacity in the absence of the wiretapper.Comment: Submitted to IEEE Transactions on Information Theor

Skip-Sliding Window Codes

Constrained coding is used widely in digital communication and storage systems. In this paper, we study a generalized sliding window constraint called the skip-sliding window. A skip-sliding window (SSW) code is defined in terms of the length $L$ of a sliding window, skip length $J$, and cost constraint $E$ in each sliding window. Each valid codeword of length $L + kJ$ is determined by $k+1$ windows of length $L$ where window $i$ starts at $(iJ + 1)$th symbol for all non-negative integers $i$ such that $i \leq k$; and the cost constraint $E$ in each window must be satisfied. In this work, two methods are given to enumerate the size of SSW codes and further refinements are made to reduce the enumeration complexity. Using the proposed enumeration methods, the noiseless capacity of binary SSW codes is determined and observations such as greater capacity than other classes of codes are made. Moreover, some noisy capacity bounds are given. SSW coding constraints arise in various applications including simultaneous energy and information transfer.Comment: 28 pages, 11 figure