Related papers: Finite Blocklength Performance Bound for the DNA S…
Channels with synchronization errors, exhibiting deletion and insertion errors, find practical applications in DNA storage, data reconstruction, and various other domains. Presence of insertions and deletions render the channel with memory,…
This article considers the performance of digital communication systems transmitting messages over finite-state erasure channels with memory. Information bits are protected from channel erasures using error-correcting codes; successful…
We derive the optimum second-order coding rates, known as second-order capacities, for erasure and list decoding. For erasure decoding for discrete memoryless channels, we show that second-order capacity is $\sqrt{V}\Phi^{-1}(\epsilon_t)$…
Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently…
Synthetic DNA can in principle be used for the archival storage of arbitrary data. Because errors are introduced during DNA synthesis, storage, and sequencing, an error-correcting code (ECC) is necessary for error-free recovery of the data.…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
We derive novel upper and lower finite-length bounds of the error probability in joint source-channel coding when the source obeys an ergodic Markov process and the channel is a Markovian additive channel or a Markovian conditional additive…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
This paper tackles two problems that fall under the study of coding for insertions and deletions. These problems are motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm,…
Predictive coding (PC) is a biologically plausible alternative to standard backpropagation (BP) that minimises an energy function with respect to network activities before updating weights. Recent work has improved the training stability of…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…
In this paper we estimate the fidelity of stabilizer and CSS codes. First, we derive a lower bound on the fidelity of a stabilizer code via its quantum enumerator. Next, we find the average quantum enumerators of the ensembles of finite…
Performance evaluation of particular channel coding has been a significant topic in coding theory, often involving the use of bounding techniques. This paper focuses on the new family of capacity-achieving codes, Spinal codes, to provide a…
Molecular communication is set to play an important role in the design of complex biological and chemical systems. An important class of molecular communication systems is based on the timing channel, where information is encoded in the…
Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
We consider data transmission across discrete memoryless channels (DMCs) using variable-length codes with feedback. We consider the family of such codes whose rates are $\rho_N$ below the channel capacity $C$, where $\rho_N$ is a positive…
We consider binary input deletion/substitution channels, which model certain types of synchronization errors encountered in practice. Specifically, we focus on the regime of small deletion and substitution probabilities, and by extending an…
DNA based storage systems received attention by many researchers. This includes archival and re-writable random access DNA based storage systems. In this work, we have developed an efficient technique to encode the data into DNA sequence by…
This paper studies the capacities of input-driven finite-state channels, i.e., channels whose current state is a time-invariant deterministic function of the previous state and the current input. We lower bound the capacity of such a…