K-Mer Counting Using Bloom Filters with an FPGA-Attached HMC

2017 ◽  
Author(s):  
Nathaniel Mcvicar ◽  
Chih-Ching Lin ◽  
Scott Hauck
Keyword(s):  
Bloom Filters

THE PROBLEM OF PROVIDING CACHE COHERENCE IN MULTIPROCESSOR SYSTEMS WITH MANY PROCESSORS

2018 ◽  
pp. 47-53
Author(s):  
B. Z. Shmeylin ◽  
E. A. Alekseeva
Keyword(s):  
Cache Coherence ◽  
Bloom Filters ◽  
Multiprocessor Systems ◽  
Cache Line ◽  
Maintenance Systems ◽  
Processor Caches ◽  
Conventional Systems ◽  
Additional Hardware

In this paper the tasks of managing the directory in coherence maintenance systems in multiprocessor systems with a large number of processors are solved. In microprocessor systems with a large number of processors (MSLP) the problem of maintaining the coherence of processor caches is significantly complicated. This is due to increased traffic on the memory buses and increased complexity of interprocessor communications. This problem is solved in various ways. In this paper, we propose the use of Bloom filters used to accelerate the determination of an element’s belonging to a certain array. In this article, such filters are used to establish the fact that the processor belongs to some subset of the processors and determine if the processor has a cache line in the set. In the paper, the processes of writing and reading information in the data shared between processors are discussed in detail, as well as the process of data replacement from private caches. The article also shows how the addresses of cache lines and processor numbers are removed from the Bloom filters. The system proposed in this paper allows significantly speeding up the implementation of operations to maintain cache coherence in the MSLP as compared to conventional systems. In terms of performance and additional hardware and software costs, the proposed system is not inferior to the most efficient of similar systems, but on some applications and significantly exceeds them.

Implementation of bloom filters in reconfigurable hardware for tracing network attacks

2006 ◽  
Vol 39 (21) ◽  
pp. 310-315
Author(s):  
Maciej Wołowiec ◽  
Jakub Botwicz ◽  
Piotr Sapiecha
Keyword(s):  
Reconfigurable Hardware ◽  
Bloom Filters ◽  
Network Attacks

Accelerating packet classification with counting bloom filters for virtual OpenFlow switching

2018 ◽  
Vol 15 (10) ◽  
pp. 117-128 ◽  
Author(s):  
Jinyuan Zhao ◽  
Zhigang Hu ◽  
Bing Xiong ◽  
Keqin Li
Keyword(s):  
Packet Classification ◽  
Bloom Filters ◽  
Counting Bloom Filters

scholarly journals Spaced Seed Data Structures forDe NovoAssembly

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Inanç Birol ◽  
Justin Chu ◽  
Hamid Mohamadi ◽  
Shaun D. Jackman ◽  
Karthika Raghavan ◽  
...  
Keyword(s):  
Data Structure ◽  
Data Structures ◽  
De Novo ◽  
Bloom Filters ◽  
De Bruijn Graph ◽  
Sequence Specificity ◽  
Sequencing Errors ◽  
Spaced Seeds ◽  
Read Error Correction ◽  
Seed Data

De novoassembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences. These data structures address memory and run time constraints imposed by longer reads. We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length. Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors. Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds. These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction.

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