Related papers: A fast divide-and-conquer algorithm for indexing h…
In this paper, a contrastive evaluation of massively parallel implementations of suffix tree and suffix array to accelerate genome sequence matching are proposed based on Intel Core i7 3770K quad-core and NVIDIA GeForce GTX680 GPU. Besides…
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…
Data intensive applications on clusters often require requests quickly be sent to the node managing the desired data. In many applications, one must look through a sorted tree structure to determine the responsible node for accessing or…
Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence…
The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
We propose a distributed computing framework, based on a divide and conquer strategy and hierarchical modeling, to accelerate posterior inference for high-dimensional Bayesian factor models. Our approach distributes the task of…
In this paper we present randomized algorithms for sorting and convex hull that achieves optimal performance (for speed-up and cache misses) on the multicore model with private cache model. Our algorithms are cache oblivious and generalize…
In this article, we advance divide-and-conquer strategies for solving the community detection problem in networks. We propose two algorithms which perform clustering on a number of small subgraphs and finally patches the results into a…
Motif discovery in DNA sequences is a challenging task in molecular biology. In computational motif discovery, Planted (l, d) motif finding is a widely studied problem and numerous algorithms are available to solve it. Both hardware and…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
Content-defined Chunking (CDC) algorithms dictate the overall space savings that deduplication systems achieve. However, due to their need to scan each file in its entirety, they are slow and often the main performance bottleneck within…
Data deduplication has gained wide acclaim as a mechanism to improve storage efficiency and conserve network bandwidth. Its most critical phase, data chunking, is responsible for the overall space savings achieved via the deduplication…
We present the Cuckoo Trie, a fast, memory-efficient ordered index structure. The Cuckoo Trie is designed to have memory-level parallelism -- which a modern out-of-order processor can exploit to execute DRAM accesses in parallel -- without…
Many popular machine learning models scale poorly when deployed on CPUs. In this paper we explore the reasons why and propose a simple, yet effective approach based on the well-known Divide-and-Conquer Principle to tackle this problem of…
FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…