Related papers: Constrained Coding for Composite DNA: Channel Capa…
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.…
Discrete diffusion models are a powerful, emerging paradigm for code generation. They construct programs through iterative refinement of partially corrupted token sequences and enable parallel token refinement. Importantly, this paradigm…
The coverage depth problem in DNA data storage is about minimizing the expected number of reads until all data is recovered. When they exist, MDS codes offer the best performance in this context. This paper focuses on the scenario where the…
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.…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
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…
In this paper, we present a novel communication channel, called the absorption channel, inspired by information transmission in neurons. Our motivation comes from in-vivo nano-machines, emerging medical applications, and brain-machine…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
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…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
We introduce a novel framework for implementing error-correction in constrained systems. The main idea of our scheme, called Quantized-Constraint Concatenation (QCC), is to employ a process of embedding the codewords of an error-correcting…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Constrained sequence (CS) codes, including fixed-length CS codes and variable-length CS codes, have been widely used in modern wireless communication and data storage systems. Sequences encoded with constrained sequence codes satisfy…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
This paper considers the problem of distributed source coding for a large network. A major obstacle that poses an existential threat to practical deployment of conventional approaches to distributed coding is the exponential growth of the…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Motivated by surveillance applications with wireless cameras or drones, we consider the problem of image retrieval over a wireless channel. Conventional systems apply lossy compression on query images to reduce the data that must be…
New directions in computing and algorithms has lead to some new applications that have tolerance to imprecision. Although, These applications are creating large volumes of data which exceeds the capability of today's computing systems.…