Related papers: Error-Correcting Codes for Labeled DNA Sequences
The task of assigning label sequences to a set of observed sequences is common in computational linguistics. Several models for sequence labeling have been proposed over the last few years. Here, we focus on discriminative models for…
In coding theory, handling errors that occur when symbols are inserted or deleted from a transmitted message is a long-standing challenge. Optimising redundancy for insertion and deletion channels remains a key open problem with significant…
The paper presents a solution for endcoding/decoding DNA information in 2D barcodes. First part focuses on the existing techniques and symbologies in 2D barcodes field. The 2D barcode PDF417 is presented as starting point. The adaptations…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
Many modern applications deal with multi-label data, such as functional categorizations of genes, image labeling and text categorization. Classification of such data with a large number of labels and latent dependencies among them is a…
A problem of index coding with side information was first considered by Y. Birk and T. Kol (IEEE INFOCOM, 1998). In the present work, a generalization of index coding scheme, where transmitted symbols are subject to errors, is studied.…
Label errors are a common issue in machine learning datasets, particularly for tasks such as Named Entity Recognition. Such label errors might hurt model training, affect evaluation results, and lead to an inaccurate assessment of model…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
Construction of capacity achieving deletion correcting codes has been a baffling challenge for decades. A recent breakthrough by Brakensiek $et~al$., alongside novel applications in DNA storage, have reignited the interest in this…
Semi-supervised semantic segmentation relieves the reliance on large-scale labeled data by leveraging unlabeled data. Recent semi-supervised semantic segmentation approaches mainly resort to pseudo-labeling methods to exploit unlabeled…
In this paper, we present a novel deep metric learning method to tackle the multi-label image classification problem. In order to better learn the correlations among images features, as well as labels, we attempt to explore a latent space,…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…
Error Detection and Correction Codes (ECCs) are often used in digital designs to protect data integrity. Especially in safety-critical systems such as automotive electronics, ECCs are widely used and the verification of such complex logic…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…