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Solid-state nanopores have received substantial attention in the past years owing to their simplicity and potential applications expected in genomics, sensing, archival information storage, and computing. The underlying sensing technique of…
This paper considers the derivative of the entropy rate of a hidden Markov process with respect to the observation probabilities. The main result is a compact formula for the derivative that can be evaluated easily using Monte Carlo…
We consider a real-time communication system with noisy feedback consisting of a Markov source, a forward and a backward discrete memoryless channels, and a receiver with finite memory. The objective is to design an optimal communication…
This paper investigates the decentralized detection of Hidden Markov Processes using the Neyman-Pearson test. We consider a network formed by a large number of distributed sensors. Sensors' observations are noisy snapshots of a Markov…
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…
To make DNA a suitable medium for archival data storage, it is essential to consider the decay process of the strands observed in DNA storage systems. This paper studies the decay process as a probabilistic noisy torn paper channel (TPC),…
The objective of this article is to study the asymptotic behavior of a new particle filtering approach in the context of hidden Markov models (HMMs). In particular, we develop an algorithm where the latent-state sequence is segmented into…
We review recent advances in the DNA sequencing based on the measurement of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major…
Recent progress in the application of color centers to nanoscale spin sensing makes the combined use of noise spectroscopy and scanning probe imaging an attractive route for the characterization of arbitrary material systems. Unfortunately,…
Molecular communication (MC) can enable the transfer of information between nanomachines using molecules as the information carrier. In MC systems, multiple receiver nanomachines often co-exist in the same communication channel to serve…
Nanopore resistive pulse techniques are based on analysis of current or voltage spikes in the recorded signal. These spikes result from translocation of nanometer sized analytes through a nanopore. The most important information that needs…
We present a new method for inferring hidden Markov models from noisy time sequences without the necessity of assuming a model architecture, thus allowing for the detection of degenerate states. This is based on the statistical prediction…
The field of speech recognition is in the midst of a paradigm shift: end-to-end neural networks are challenging the dominance of hidden Markov models as a core technology. Using an attention mechanism in a recurrent encoder-decoder…
This paper describes the conversion of a Hidden Markov Model into a sequential transducer that closely approximates the behavior of the stochastic model. This transformation is especially advantageous for part-of-speech tagging because the…
We consider multi-state capture-recapture-recovery data where observed individuals are recorded in a set of possible discrete states. Traditionally, the Arnason-Schwarz model has been fitted to such data where the state process is modeled…
We study universal decoding over unknown discrete additive channels determined by a finite-state (unifilar) random process. Aiming at low-complexity decoders, we study variants of noise-guessing decoders that use estimators for the…
We present a tight-binding model study of a two-terminal graphene nanopore device for sequential determination of DNA bases. Using Green's function technique we investigate the changes in electronic transport properties of the device due to…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
Nanopore sensing is a versatile technique for the analysis of molecules on the single-molecule level. However, extracting information from data with established algorithms usually requires time-consuming checks by an experienced researcher…
Searches for persistent gravitational radiation from nonpulsating neutron stars in young supernova remnants (SNRs) are computationally challenging because of rapid stellar braking. We describe a practical, efficient, semi-coherent search…