Related papers: On Achievable Rates Over Noisy Nanopore Channels
Nanopore sequencing is an emerging DNA sequencing technology that has been proposed for use in DNA storage systems. We propose the noisy nanopore channel model for nanopore sequencing. This model captures duplications, inter-symbol…
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…
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…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
We investigate the capacity of noisy frequency-based channels, motivated by DNA data storage in the short-molecule regime, where information is encoded in the frequency of items types rather than their order. The channel output is a…
In this paper, we formally define and analyze the class of noisy permutation channels. The noisy permutation channel model constitutes a standard discrete memoryless channel (DMC) followed by an independent random permutation that reorders…
The noisy permutation channel is a useful abstraction introduced by Makur for point-to-point communication networks and biological storage. While the asymptotic capacity results exist for this model, the characterization of the second-order…
Channels with noisy duplications have recently been used to model the nanopore sequencer. This paper extends some foundational information-theoretic results to this new scenario. We prove the asymptotic equipartition property (AEP) for…
In this paper, we first consider a channel that is contaminated by two independent Gaussian noises $S ~ N(0,Q)$ and $Z_0 ~ N(0,N_0)$. The capacity of this channel is computed when independent noisy versions of $S$ are known to the…
This paper presents a comparison of several Convolutional Neural Network (CNN) models for extracting target signals in highly noisy measurement conditions. Four CNN architectures were investigated. The first comprises six consecutive…
To model printing noise a binary noisy channel and a set of controlled gates are introduced. The channel input is an image created by a halftoning algorithm and its output is the printed picture. Using this channel robustness to noise…
Motivated by DNA-based storage, we study the noisy shuffling channel, which can be seen as the concatenation of a standard noisy channel (such as the BSC) and a shuffling channel, which breaks the data block into small pieces and shuffles…
This paper introduces a novel neural network-based speech coding system that can process noisy speech effectively. The proposed source-aware neural audio coding (SANAC) system harmonizes a deep autoencoder-based source separation model and…
Binary-input memoryless channels with a runlength constrained input are considered. Upper bounds to the capacity of such noisy runlength constrained channels are derived using the dual capacity method with Markov test distributions…
In this paper, a diffusion-based molecular communication channel between two nano-machines is considered. The effect of the amount of memory on performance is characterized, and a simple memory-limited decoder is proposed and its…
We establish the capacity of a class of communication channels introduced in [1]. The $n$-letter input from a finite alphabet is passed through a discrete memoryless channel $P_{Z|X}$ and then the output $n$-letter sequence is uniformly…
Random Linear Network Coding (RLNC) has been proved to offer an efficient communication scheme, leveraging an interesting robustness against packet losses. However, it suffers from a high computational complexity and some novel approaches,…
We study the capacity of discrete memoryless many-to-one interference channels, i.e., K user interference channels where only one receiver faces interference. For a class of many-to-one interference channels, we identify a noisy…