Related papers: Error-Correcting Codes for Labeled DNA Sequences
In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA…
Although the sequence-to-sequence (encoder-decoder) model is considered the state-of-the-art in deep learning sequence models, there is little research into using this model for recovering missing sensor data. The key challenge is that the…
Mislabeled examples are a common issue in real-world data, particularly for tasks like token classification where many labels must be chosen on a fine-grained basis. Here we consider the task of finding sentences that contain label errors…
Due to the redundant nature of DNA synthesis and sequencing technologies, a basic model for a DNA storage system is a multi-draw "shuffling-sampling" channel. In this model, a random number of noisy copies of each sequence is observed at…
The labor-intensive annotation process of semantic segmentation datasets is often prone to errors, since humans struggle to label every pixel correctly. We study algorithms to automatically detect such annotation errors, in particular…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
Burst errors involving simultaneous insertions, deletions, and substitutions occur in practical scenarios, including DNA data storage and document synchronization, motivating developments of channel codes that can correct such errors. In…
When digital data are transmitted over a noisy channel, it is important to have a mechanism allowing recovery against a limited number of errors. Normally, a user string of 0's and 1's, called bits, is encoded by adding a number of…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
DNA sequencing allows for the determination of the genetic code of an organism, and therefore is an indispensable tool that has applications in Medicine, Life Sciences, Evolutionary Biology, Food Sciences and Technology, and Agriculture. In…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
We investigate the design challenges of constructing effective and efficient neural sequence labeling systems, by reproducing twelve neural sequence labeling models, which include most of the state-of-the-art structures, and conduct a…
Labeling datasets for supervised object detection is a dull and time-consuming task. Errors can be easily introduced during annotation and overlooked during review, yielding inaccurate benchmarks and performance degradation of deep neural…
Tokens serve as the basic units of representation in DNA language models (DNALMs), yet their design remains underexplored. Unlike natural language, DNA lacks inherent token boundaries or predefined compositional rules, making tokenization a…
Three-dimensional (3D) printing's accessibility enables rapid manufacturing but also poses security risks, such as the unauthorized production of untraceable firearms and prohibited items. To ensure traceability and accountability,…
In recent years, deep neural network is widely used in machine learning. The multi-class classification problem is a class of important problem in machine learning. However, in order to solve those types of multi-class classification…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…