Related papers: SparseAssembler2: Sparse k-mer Graph for Memory Ef…
The growing demand for sparse tensor algebra (SpTA) in machine learning and big data has driven the development of various sparse tensor accelerators. However, most existing manually designed accelerators are limited to specific scenarios,…
General Sparse Matrix-Matrix Multiplication (SpGEMM) has attracted much attention from researchers in graph analyzing, scientific computing, and deep learning. Many optimization techniques have been developed for different applications and…
The string graph for a collection of next-generation reads is a lossless data representation that is fundamental for de novo assemblers based on the overlap-layout-consensus paradigm. In this paper, we explore a novel approach to compute…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Miller et al. \cite{MPVX15} devised a distributed\footnote{They actually showed a PRAM algorithm. The distributed algorithm with these properties is implicit in \cite{MPVX15}.} algorithm in the CONGEST model, that given a parameter $k =…
Transforming an input sequence into its constituent k-mers is a fundamental operation in computational genomics. To reduce storage costs associated with k-mer datasets, we introduce and formally analyze MCTR, a novel two-stage algorithm for…
Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. Since the sample sequence data typically harbors reads of variable lengths and different…
In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting…
Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of…
Deep learning-based cardiac segmentation has seen significant advancements over the years. Many studies have tackled the challenge of anatomically incorrect segmentation predictions by introducing auxiliary modules. These modules either…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Knowledge graph (KG) learning offers a powerful framework for generating new knowledge and making inferences. Training KG embedding can take a significantly long time, especially for larger datasets. Our analysis shows that the gradient…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
General sparse matrix-matrix multiplication (SpGEMM) is a fundamental building block for numerous applications such as algebraic multigrid method (AMG), breadth first search and shortest path problem. Compared to other sparse BLAS routines,…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still…
The problem of finding dense components of a graph is a widely explored area in data analysis, with diverse applications in fields and branches of study including community mining, spam detection, computer security and bioinformatics. This…