Related papers: A universal DNA computing model for solving NP-har…
In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formalizations of the tag set design problem, and show that these…
In recent years there have been multiple successful attempts tackling document processing problems separately by designing task specific hand-tuned strategies. We argue that the diversity of historical document processing tasks prohibits to…
The 0/1 knapsack problem is weakly NP-hard in that there exist pseudo-polynomial time algorithms based on dynamic programming that can solve it exactly. There are also the core branch and bound algorithms that can solve large randomly…
Graph Convolutional Networks (GCN) is a pioneering model for graph-based semi-supervised learning. However, GCN does not perform well on sparsely-labeled graphs. Its two-layer version cannot effectively propagate the label information to…
The network embedding problem that maps nodes in a graph to vectors in Euclidean space can be very useful for addressing several important tasks on a graph. Recently, graph neural networks (GNNs) have been proposed for solving such a…
Graph similarity search is among the most important graph-based applications, e.g. finding the chemical compounds that are most similar to a query compound. Graph similarity computation, such as Graph Edit Distance (GED) and Maximum Common…
In this work, we investigate the diffusive optical tomography (DOT) problem in the case that limited boundary measurements are available. Motivated by the direct sampling method (DSM), we develop a deep direct sampling method (DDSM) to…
Deep Learning models have transformed various domains, including the healthcare sector, particularly biomedical image classification by learning intricate features and enabling accurate diagnostics pertaining to complex diseases. Recent…
Guided depth super-resolution (GDSR) is an essential topic in multi-modal image processing, which reconstructs high-resolution (HR) depth maps from low-resolution ones collected with suboptimal conditions with the help of HR RGB images of…
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…
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…
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…
We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e., DNA…
Deep neural networks have demonstrated highly competitive performance in super-resolution (SR) for natural images by learning mappings from low-resolution (LR) to high-resolution (HR) images. However, hyperspectral super-resolution remains…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
As a fundamental topic in graph mining, Densest Subgraph Discovery (DSD) has found a wide spectrum of real applications. Several DSD algorithms, including exact and approximation algorithms, have been proposed in the literature. However,…
Deep neural networks (DNN) have been used successfully in many scientific problems for their high prediction accuracy, but their application to genetic studies remains challenging due to their poor interpretability. In this paper, we…
In this paper we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where a data set is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
In a variety of geoscientific applications scientists often need to image properties of the Earth's interior in order to understand the heterogeneity and processes taking place within the Earth. Seismic tomography is one such method which…