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Neighborhood algorithms may take a considerable percentage of computer time in discrete element methods (DEM). While the sort-and-sweep algorithm is ideal in some ways, as it only deal with particles whose relative positions change in one…

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…

Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…

Supercomputers are equipped with an increasingly large number of cores to use computational power as a way of solving problems that are otherwise intractable. Unfortunately, getting serial algorithms to run in parallel to take advantage of…

We design and implement parallel prefix sum (scan) algorithms using Ascend AI accelerators. Ascend accelerators feature specialized computing units: the cube units for efficient matrix multiplication and the vector units for optimized…

Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene…

This work introduces two techniques for the design and analysis of branching algorithms, illustrated through the case study of the Vertex Cover problem. First, we present a method for automatically generating branching rules through a…

We present an algorithm for classification tasks on big data. Experiments conducted as part of this study indicate that the algorithm can be as accurate as ensemble methods such as random forests or gradient boosted trees. Unlike ensemble…

This paper introduces a search algorithm for index structures based on a B+ tree, specifically optimized for execution on a field-programmable gate array (FPGA). Our implementation efficiently traverses and reuses tree nodes by processing a…

This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…

This paper describes in detail the bitonic sort algorithm,and implements the bitonic sort algorithm based on cuda architecture.At the same time,we conduct two effective optimization of implementation details according to the characteristics…

The performance of today's in-memory indexes is bottlenecked by the memory latency/bandwidth wall. Processing-in-memory (PIM) is an emerging approach that potentially mitigates this bottleneck, by enabling low-latency memory access whose…

Accurate segmentation of 3-D cell nuclei in microscopy images is essential for the study of nuclear organization, gene expression, and cell morphodynamics. Current image segmentation methods are challenged by the complexity and variability…

Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…

Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing…

Rapid sequencing of individual human genome is prerequisite to genomic medicine, where diseases will be prevented by preemptive cures. Quantum-mechanical tunneling through single-stranded DNA in a solid-state nanopore has been proposed for…

We develop methods for accelerating metric similarity search that are effective on modern hardware. Our algorithms factor into easily parallelizable components, making them simple to deploy and efficient on multicore CPUs and GPUs. Despite…

Similarity search approaches based on graph walks have recently attained outstanding speed-accuracy trade-offs, taking aside the memory requirements. In this paper, we revisit these approaches by considering, additionally, the memory…

Protein motifs are conserved fragments occurred frequently in protein sequences. They have significant functions, such as active site of an enzyme. Search and clustering protein sequence motifs are computational intensive. Most existing…

The present work attempts to integrate the independent efforts in the fast N-body community to create the fastest N-body library for many-core and heterogenous architectures. Focus is placed on low accuracy optimizations, in response to the…