Related papers: Lock-free de Bruijn graph

Finding dense substructures in a graph is a fundamental graph mining operation, with applications in bioinformatics, social networks, and visualization to name a few. Yet most standard formulations of this problem (like clique, quasiclique,…

Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture…

Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…

We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…

With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the…

Graph Neural Networks (GNNs) have emerged as a promising tool to handle data exhibiting an irregular structure. However, most GNN architectures perform well on homophilic datasets, where the labels of neighboring nodes are likely to be the…

In this paper we propose an online approximate k-nn graph building algorithm, which is able to quickly update a k-nn graph using a flow of data points. One very important step of the algorithm consists in using the current distributed graph…

Building a library of concurrent data structures is an essential way to simplify the difficult task of developing concurrent software. Lock-free data structures, in which processes can help one another to complete operations, offer the…

We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB…

The future of main memory appears to lie in the direction of new technologies that provide strong capacity-to-performance ratios, but have write operations that are much more expensive than reads in terms of latency, bandwidth, and energy.…

DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…

The advent of Graph Neural Networks (GNNs) has revolutionized the field of machine learning, offering a novel paradigm for learning on graph-structured data. Unlike traditional neural networks, GNNs are capable of capturing complex…

Semi-supervised learning (SSL) is effectively used for numerous classification problems, thanks to its ability to make use of abundant unlabeled data. The main assumption of various SSL algorithms is that the nearby points on the data…

In this paper, we propose an efficient concurrent wait-free algorithm to construct an unbounded directed graph for shared memory architecture. To the best of our knowledge that this is the first wait-free algorithm for an unbounded directed…

Single particle, cryogenic electron microscopy (cryo-EM) experiments now routinely produce high-resolution data for large proteins and their complexes. Building an atomic model into a cryo-EM density map is challenging, particularly when no…

Graph Convolutional Networks (GCNs) are extensively utilized for deep learning on graphs. The large data sizes of graphs and their vertex features make scalable training algorithms and distributed memory systems necessary. Since the…

This paper presents a new and practical approach to lock-free locks based on helping, which allows the user to write code using fine-grained locks, but run it in a lock-free manner. Although lock-free locks have been suggested in the past,…

This work is motivated by the necessity to automate the discovery of structure in vast and evergrowing collection of relational data commonly represented as graphs, for example genomic networks. A novel algorithm, dubbed Graphitour, for…