Related papers: High-Performance Sorting-Based k-mer Counting in D…
Datacenters are increasingly becoming heterogeneous, and are starting to include specialized hardware for networking, video processing, and especially deep learning. To leverage the heterogeneous compute capability of modern datacenters, we…
Polyspectral estimation is a problem of great importance in the analysis of nonlinear time series that has applications in biomedical signal processing, communications, geophysics, image, radar, sonar and speech processing, etc. Higher…
We consider the scenario of $n$ sensor nodes observing streams of data. The nodes are connected to a central server whose task it is to compute some function over all data items observed by the nodes. In our case, there exists a total order…
To reduce training time of large-scale DNNs, scientists have started to explore parallelization strategies like data-parallelism, model-parallelism, and hybrid-parallelism. While data-parallelism has been extensively studied and developed,…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity…
There has been surprisingly little work on algorithms for sorting strings on distributed-memory parallel machines. We develop efficient algorithms for this problem based on the multi-way merging principle. These algorithms inspect only…
In this paper, we present the design of a sample sort algorithm for manycore GPUs. Despite being one of the most efficient comparison-based sorting algorithms for distributed memory architectures its performance on GPUs was previously…
This paper describes a new QR factorization algorithm which is especially designed for massively parallel platforms combining parallel distributed multi-core nodes. These platforms make the present and the foreseeable future of…
Hash tables are used in a plethora of applications, including database operations, DNA sequencing, string searching, and many more. As such, there are many parallelized hash tables targeting multicore, distributed, and accelerator-based…
Quantum computing is a promising paradigm based on quantum theory for performing fast computations. Quantum algorithms are expected to surpass their classical counterparts in terms of computational complexity for certain tasks, including…
Investigating molecular heterogeneity provides insights about tumor origin and metabolomics. The increasing amount of data gathered makes manual analyses infeasible - therefore, automated unsupervised learning approaches are utilized for…
This paper provides a comprehensive survey of data structures for representing k-mer sets, which are fundamental in high-throughput sequencing analysis. It categorizes the methods into two main strategies: those using fingerprinting and…
De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…
Sorting algorithms are the deciding factor for the performance of common operations such as removal of duplicates or database sort-merge joins. This work focuses on 32-bit integer keys, optionally paired with a 32-bit value. We present a…
This paper introduces a novel K-means clustering algorithm, an advancement on the conventional Big-means methodology. The proposed method efficiently integrates parallel processing, stochastic sampling, and competitive optimization to…
Balanced hypergraph partitioning is a classical NP-hard optimization problem with applications in various domains such as VLSI design, simulating quantum circuits, optimizing data placement in distributed databases or minimizing…
Sorting is one of the most fundamental problems in the field of computer science. With the rapid development of manycore processors, it shows great importance to design efficient parallel sort algorithm on manycore architecture. This paper…
With increasing complexity of hardwares, systems with different memory nodes are ubiquitous in High Performance Computing (HPC). It is paramount to develop strategies to overlap the data transfers between memory nodes with computations in…
Sliding window sums are widely used in bioinformatics applications, including sequence assembly, k-mer generation, hashing and compression. New vector algorithms which utilize the advanced vector extension (AVX) instructions available on…