Related papers: Extreme-Scale De Novo Genome Assembly
High-throughput cDNA sequencing (RNA-seq) is a very powerful technique to quantify gene expression in an unbiased way. The Crustacean family is among the groups of organisms sparsely represented in current genomic databases. Here we present…
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…
Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the…
Nucleus decompositions have been shown to be a useful tool for finding dense subgraphs. The coreness value of a clique represents its density based on the number of other cliques it is adjacent to. One useful output of nucleus decomposition…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
We introduce harmonization, an ensembling method that combines several "noisy" decoders to generate highly accurate decoding predictions. Harmonized ensembles of MWPM-based decoders achieve lower logical error rates than their individual…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
Recent semantic segmentation methods exploit encoder-decoder architectures to produce the desired pixel-wise segmentation prediction. The last layer of the decoders is typically a bilinear upsampling procedure to recover the final…
RNA-seq allows detection and precise quantification of transcripts, provides comprehensive understanding of exon/intron boundaries, aids discovery of alternatively spliced isoforms and fusion transcripts along with measurement of…
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…
High precision atomic data is indispensable for experiments involving studies of fundamental interactions, astrophysics, atomic clocks, plasma science, and others. We develop new parallel atomic structure codes and explore the difficulties…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
Brain-inspired hyperdimensional (HD) computing models neural activity patterns of the very size of the brain's circuits with points of a hyperdimensional space, that is, with hypervectors. Hypervectors are $D$-dimensional (pseudo)random…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Optimally hybrid numerical solvers were constructed for massively parallel generalized eigenvalue problem (GEP).The strong scaling benchmark was carried out on the K computer and other supercomputers for electronic structure calculation…
Convolutional Neural Networks (CNNs) have demonstrated their superiority in image classification, and evolutionary computation (EC) methods have recently been surging to automatically design the architectures of CNNs to save the tedious…
Upcoming many core processors are expected to employ a distributed memory architecture similar to currently available supercomputers, but parallel pattern mining algorithms amenable to the architecture are not comprehensively studied. We…
Motivation: As cancer researchers have come to appreciate the importance of intratumor heterogeneity, much attention has focused on the challenges of accurately profiling heterogeneity in individual patients. Experimental technologies for…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Hyperspectral imaging has attracted significant attention to identify spectral signatures for image classification and automated pattern recognition in computer vision. State-of-the-art implementations of snapshot hyperspectral imaging rely…