Related papers: Efficient Constraining of Transcoding in DNA-Based…
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…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
Motivation: High-throughput sequencing (HTS) enables population-scale genomics but generates massive datasets, creating bottlenecks in storage, transfer, and analysis. FASTQ, the standard format for over two decades, stores one byte per…
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…
Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in…
With the growing size of deep neural networks and datasets, the computational costs of training have significantly increased. The layer-freezing technique has recently attracted great attention as a promising method to effectively reduce…
Sonography techniques use multiple transducer elements for tissue visualization. Signals detected at each element are sampled prior to digital beamforming. The sampling rates required to perform high resolution digital beamforming are…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
Data compression has been widely applied in many data processing areas. Compression methods use variable-size codes with the shorter codes assigned to symbols or groups of symbols that appear in the data frequently. Fibonacci coding, as a…
Computational cost of training state-of-the-art deep models in many learning problems is rapidly increasing due to more sophisticated models and larger datasets. A recent promising direction for reducing training cost is dataset…
Compressed sensing is an image reconstruction technique to achieve high-quality results from limited amount of data. In order to achieve this, it utilizes prior knowledge about the samples that shall be reconstructed. Focusing on image…
Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In…
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…
Real-world data typically contain repeated and periodic patterns. This suggests that they can be effectively represented and compressed using only a few coefficients of an appropriate basis (e.g., Fourier, Wavelets, etc.). However, distance…
The rapid growth of digital data has heightened the demand for efficient lossless compression methods. However, existing algorithms exhibit trade-offs: some achieve high compression ratios, others excel in encoding or decoding speed, and…
Private inference using homomorphic encryption has gained a great attention to leverage powerful predictive models, e.g., deep convolutional neural networks (CNNs), in the area where data privacy is crucial, such as in healthcare or medical…
Resampling detection plays an important role in identifying image tampering, such as image splicing. Currently, the resampling detection is still difficult in recompressed images, which are yielded by applying resampling followed by…