Related papers: Finite-State Semi-Markov Channels for Nanopore Seq…
In this paper, we consider a discrete memoryless point to point channel with noisy feedback, where there is a sender with a private message that she wants to communicate to a receiver by sequentially transmitting symbols over a noisy…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
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…
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…
Rapid sequencing of individual human genome is prerequisite to genomic medicine, where diseases will be prevented by preemptive cures. Quantum-mechanical tunneling through single-stranded DNA in a solid-state nanopore has been proposed for…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
The problem of detection and possible estimation of a signal generated by a dynamic system when a variable number of noisy measurements can be taken is here considered. Assuming a Markov evolution of the system (in particular, the pair…
Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost, and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and…
We propose two-terminal devices for DNA sequencing which consist of a metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its interior through which the DNA molecule is translocated. Using the nonequilibrium Green…
Miniature DNA sequencing hardware has begun to succeed in mobile contexts, driving demand for efficient machine learning at the edge. This domain leverages deep learning techniques familiar from speech and time-series analysis for both…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
Noisy labels can significantly affect the performance of deep neural networks (DNNs). In medical image segmentation tasks, annotations are error-prone due to the high demand in annotation time and in the annotators' expertise. Existing…
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. We have created a method for…
In numerous systems in biophysics and related fields, scientists measure (with very smart methods) individual molecules (e.g. biopolymers (proteins, DNA, RNA, etc), nano - crystals, ion channels), aiming at finding a model from the data.…
Motivated by the concept of probe storage, we study the problem of information retrieval using a large array of N nano-mechanical probes, N ~ 4000. At the nanometer scale it is impossible to avoid errors in the positioning of the array,…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
Ionic transport in nanopores or nanochannels is key to many cellular processes and is now being explored as a method for DNA/polymer sequencing and detection. Although apparently simple in its scope, the study of ionic dynamics in confined…
Diffusion is a prominent source of noise affecting nuclear magnetic resonance at the nanometer scale (nano-NMR), preventing high resolution studies of unpolarized liquid samples. Actively managing diffusion noise through, for example,…
Solid-state nanopores offer a powerful platform for nanoscale analysis of individual analytes, including biomolecules and functionalized nanoparticles, by confining them within a precisely defined sensing region. However, their inherently…
Dynamic watermarking, as an active intrusion detection technique, can potentially detect replay attacks, spoofing attacks, and deception attacks in the feedback channel for control systems. In this paper, we develop a novel dynamic…