Related papers: Iterative DNA Coding Scheme With GC Balance and Ru…
In this paper, we study a model, which was first presented by Bunte and Lapidoth, that mimics the programming operation of memory cells. Under this paradigm we assume that cells are programmed sequentially and individually. The programming…
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,…
Motivated by recent work on stochastic gradient descent methods, we develop two stochastic variants of greedy algorithms for possibly non-convex optimization problems with sparsity constraints. We prove linear convergence in expectation to…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing…
One of the important problems in multiprocessor systems is Task Graph Scheduling. Task Graph Scheduling is an NP-Hard problem. Both learning automata and genetic algorithms are search tools which are used for solving many NP-Hard problems.…
Greedy algorithms are popular in compressive sensing for their high computational efficiency. But the performance of current greedy algorithms can be degenerated seriously by noise (both multiplicative noise and additive noise). A robust…
This paper proposes Genetic Algorithm with Border Trades (GAB), a novel modification of the standard genetic algorithm that enhances exploration by incorporating new chromosome patterns in the breeding process. This approach significantly…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Deoxyribonucleic Acid (DNA) as a storage medium with high density and long-term preservation properties can satisfy the requirement of archival storage for rapidly increased digital volume. The read and write processes of DNA storage are…
The fields of signal and image processing have been deeply influenced by the introduction of deep neural networks. These are successfully deployed in a wide range of real-world applications, obtaining state of the art results and surpassing…
Increasingly more attention is paid to the privacy in online applications due to the widespread data collection for various analysis purposes. Sensitive information might be mined from the raw data during the analysis, and this led to a…
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…
This paper has two contributions. First, we propose a novel coded matrix multiplication technique called Generalized PolyDot codes that advances on existing methods for coded matrix multiplication under storage and communication…
The compact genetic algorithm is an Estimation of Distribution Algorithm for binary optimisation problems. Unlike the standard Genetic Algorithm, no cross-over or mutation is involved. Instead, the compact Genetic Algorithm uses a virtual…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Iterative methods on irregular grids have been used widely in all areas of comptational science and engineering for solving partial differential equations with complex geometry. They provide the flexibility to express complex shapes with…
In real-time trajectory planning for unmanned vehicles, on-board sensors, radars and other instruments are used to collect information on possible obstacles to be avoided and pathways to be followed. Since, in practice, observations of the…
Contracting tensor networks is often computationally demanding. Well-designed contraction sequences can dramatically reduce the contraction cost. We explore the performance of simulated annealing and genetic algorithms, two common discrete…
DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…