Related papers: Achieving DNA Labeling Capacity with Minimum Label…
DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
A labeling scheme for nearest common ancestors assigns a distinct binary string, called the label, to every node of a tree, so that given the labels of two nodes (and no further information about the topology of the tree) we can compute the…
An ancestry labeling scheme assigns labels (bit strings) to the nodes of rooted trees such that ancestry queries between any two nodes in a tree can be answered merely by looking at their corresponding labels. The quality of an ancestry…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
A purely electrical sensing scheme is presented that determines the concentration of macromolecules in solution by measuring the capacitance between planar microelectrodes. Concentrations of DNA in the ng/mL range have been used in samples…
Answering exact shortest path distance queries is a fundamental task in graph theory. Despite a tremendous amount of research on the subject, there is still no satisfactory solution that can scale to billion-scale complex networks.…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
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…
Graph Neural Networks (GNNs) have achieved state-of-the-art results for semi-supervised node classification on graphs. Nevertheless, the challenge of how to effectively learn GNNs with very few labels is still under-explored. As one of the…
A recent study by one of the authors has demonstrated the importance of profile vectors in DNA-based data storage. We provide exact values and lower bounds on the number of profile vectors for finite values of alphabet size $q$, read length…
It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display…
Semi-supervised learning (SSL) has been extensively studied to improve the generalization ability of deep neural networks for visual recognition. To involve the unlabelled data, most existing SSL methods are based on common density-based…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
We consider the problem of topology recognition in wireless (radio) networks modeled as undirected graphs. Topology recognition is a fundamental task in which every node of the network has to output a map of the underlying graph i.e., an…
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…
Massively parallel DNA sequencing technologies are revolutionizing genomics research. Billions of short reads generated at low costs can be assembled for reconstructing the whole genomes. Unfortunately, the large memory footprint of the…
Entity recognition is a fundamental task in understanding document images. Traditional sequence labeling frameworks treat the entity types as class IDs and rely on extensive data and high-quality annotations to learn semantics which are…