Search results for "minhash"
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MetaCache-GPU: Ultra-Fast Metagenomic Classification
2021
The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is commonly facilitated by constructing index data structures which allow for efficient querying of substrings. Recent metagenomic classification pipelines annotate reads with taxonomic labels by analyzing their $k$-mer histograms with respect to a reference genome database. CPU-based index construction is often performed in a preprocessing phase due to the relatively high cost of building irregular data structures such as hash maps. However, the rapidly growi…
Large Scale Knowledge Matching with Balanced Efficiency-Effectiveness Using LSH Forest
2017
Evolving Knowledge Ecosystems were proposed to approach the Big Data challenge, following the hypothesis that knowledge evolves in a way similar to biological systems. Therefore, the inner working of the knowledge ecosystem can be spotted from natural evolution. An evolving knowledge ecosystem consists of Knowledge Organisms, which form a representation of the knowledge, and the environment in which they reside. The environment consists of contexts, which are composed of so-called knowledge tokens. These tokens are ontological fragments extracted from information tokens, in turn, which originate from the streams of information flowing into the ecosystem. In this article we investigate the u…