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Compression of nucleotide databases for fast searching

Hugh Williams, Justin Zobel
1997 Bioinformatics  
Results: We present a purpose-built direct coding scheme for fast retrieval and compression of genomic nucleotide data.  ...  The scheme is lossless, readily integrated with sequence search tools, and does not require a model.  ...  Acknowledgements We are grateful to Alistair Moffat for his implementation of canonical Huffman coding.  ... 
doi:10.1093/bioinformatics/13.5.549 fatcat:r7huv4zeyfb5xdz2bl3yauqsxq

ZIP-IO: Architecture for application-specific compression of Big Data

Sang Woo Jun, Kermin E. Fleming, Michael Adler, Joel Emer
2012 2012 International Conference on Field-Programmable Technology  
To address this issue, we investigate ZIP-IO, a framework for FPGA-accelerated compression.  ...  Compression is an effective way to deal with many of these large data sets, and application-specific compression algorithms have become popular in problems with large working sets.  ...  Existing compression architectures typically employ general-purpose compression schemes [25] , which do a poor job of compressing generic data.  ... 
doi:10.1109/fpt.2012.6412159 dblp:conf/fpt/JunFAE12 fatcat:wi4mvrk4yravrftd6fobkwlgme

Document Compaction for Efficient Query Biased Snippet Generation [chapter]

Yohannes Tsegay, Simon J. Puglisi, Andrew Turpin, Justin Zobel
2009 Lecture Notes in Computer Science  
For efficiency, search engines operating on large collections need to cache snippets for common queries, and to cache documents to allow fast generation of snippets for uncached queries.  ...  In particular, we argue against further improvements to document compression, and argue for schemes that prune documents based on the a priori likelihood that a sentence will be used as part of a snippet  ...  [14] introduced a compression scheme that was practical for large collections, and worked well in their experiments. But is it worth investing effort in improving such a compression scheme?  ... 
doi:10.1007/978-3-642-00958-7_45 fatcat:l57ewhdi3vfbfkrhokfg3jcn3m

A Reliable Data Compression Scheme in Sensor-Cloud Systems Based on Edge Computing

Shaofei Lu, Qinhua Xia, Xiaolin Tang, Xuyang Zhang, Yingping Lu, Jingke She
2021 IEEE Access  
algorithm, a new data hybrid compression scheme is proposed based on data purpose.  ...  In terms of data usage, the equipment operating status and sensor monitoring data collected by IoT devices generally have two purposes in actual application scenarios.  ... 
doi:10.1109/access.2021.3068753 fatcat:345jtssezvd6bpxt53ustolrk4

A Multimedia Data Compression Scheme for Disaster Prevention in Wireless Multimedia Sensor Networks

Jun-Ho Park, Jong-Tae Lim, Jae-Soo Yoo, Yong-Sun Oh, Sang-Hoon Oh, Byung-Won Min, Sun-Gyu Park, Hwang-Woo Noh, Yukuo Hayashida
2015 International Journal of Contents  
However, the multimedia streams generate a very large amount of data.  ...  Recent years have seen a significant increase in demand for multimedia data over wireless sensor networks for monitoring applications that utilize sensor nodes to collect multimedia data, including sound  ...  For the purpose of performance improvement in the wireless multimedia sensor networks, the multimedia data compression schemes have been actively in progress as a representative study.  ... 
doi:10.5392/ijoc.2015.11.2.031 fatcat:6b4a44r7zrglxejjkxksnj33ga

Compressing Integers for Fast File Access

H. E. Williams
1999 Computer journal  
In this paper we show experimentally that, for large or small collections, storing integers in a compressed format reduces the time required for either sequential stream access or random access.  ...  Integers are the basis of indexes used to resolve queries, for example, in large internet search systems and numeric data forms a large part of most databases.  ...  ACKNOWLEDGEMENTS We thank Agnes Apostolou, Neil Christie, Neil Sharman, and Lachlan Wainwright for making available their satellite, contour, and temperature data.  ... 
doi:10.1093/comjnl/42.3.193 fatcat:g7j4e7iumrak3o6vt3jl3m2j2q

Fast generation of result snippets in web search

Andrew Turpin, Yohannes Tsegay, David Hawking, Hugh E. Williams
2007 Proceedings of the 30th annual international ACM SIGIR conference on Research and development in information retrieval - SIGIR '07  
We begin by proposing and analysing a document compression method that reduces snippet generation time by 58% over a baseline using the zlib compression library.  ...  These experiments reveal that finding documents on secondary storage dominates the total cost of generating snippets, and so caching documents in RAM is essential for a fast snippet generation process.  ...  Thanks to Nick Lester and Justin Zobel for valuable discussions.  ... 
doi:10.1145/1277741.1277766 dblp:conf/sigir/TurpinTHW07 fatcat:zhmevpbsxjbdpebfogv5mzuoge

An Empirical Evaluation of XML Compression Tools [chapter]

Sherif Sakr
2009 Lecture Notes in Computer Science  
The study reports the behavior of nine XML compressors using a large corpus of XML documents which covers the different natures and scales of XML documents.  ...  Finally, we provide some guidelines and recommendations which are useful for helping developers and users for making an effective decision for selecting the most suitable XML compression tool for their  ...  XMLPPM is considered as an adaptation of the general purpose P rediction by P artial M atching compression scheme (PPM) [21] .  ... 
doi:10.1007/978-3-642-04205-8_6 fatcat:hdbcrz7uxjewhbxnzd6bwiwgh4

Lightweight Data Compression in Wireless Sensor Networks Using Huffman Coding

Henry Ponti Medeiros, Marcos Costa Maciel, Richard Demo Souza, Marcelo Eduardo Pellenz
2014 International Journal of Distributed Sensor Networks  
This paper presents a lightweight data compression method for wireless sensor networks monitoring environmental parameters with low resolution sensors.  ...  for wireless sensor networks.  ...  However, WSNs are generally deployed with the purpose of monitoring a particular phenomenon of interest [12] .  ... 
doi:10.1155/2014/672921 fatcat:afm2mh5ejzb7lcufyijk5j62qy

LZ4m: A fast compression algorithm for in-memory data

Se-Jun Kwon, Sang-Hoon Kim, Hyeong-Jun Kim, Jin-Soo Kim
2017 2017 IEEE International Conference on Consumer Electronics (ICCE)  
Compressing in-memory data is a cost-effective solution for dealing with the memory demand from data-intensive applications.  ...  This paper proposes a fast data compression algorithm for in-memory data that improves performance by utilizing the characteristics frequently observed from in-memory data.  ...  CONCLUSION We optimized a popular general-purpose compression algorithm by utilizing the inherent characteristics of in-memory data.  ... 
doi:10.1109/icce.2017.7889380 dblp:conf/iccel/KwonKKK17 fatcat:yu2dasanazdcpfzoggfy7xl6wi

Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files

Muhammad Nazmus Sakib, Jijun Tang, W. Jim Zheng, Chin-Tser Huang, Leonardo Mariño-Ramírez
2011 PLoS ONE  
In this paper, we present SAMZIP, a specialized encoding scheme, for sequence alignment data in SAM (Sequence Alignment/Map) format, which improves the compression ratio of existing compression tools available  ...  One way to improve the transmission time of large files is to apply a maximum lossless compression on them.  ...  Introduction One of the primary tasks in bioinformatics research is to collect and analyze large volume of genomic sequencing data.  ... 
doi:10.1371/journal.pone.0028251 pmid:22164252 pmcid:PMC3229529 fatcat:hbjh4srutjhyni6pcmaj65xfdu

XML compression techniques: A survey and comparison

Sherif Sakr
2009 Journal of computer and system sciences (Print)  
We report the behavior of nine XML compressors using a large corpus of XML documents which covers the different natures and scales of XML documents.  ...  Several XML compression techniques has been introduced to deal with these problems. In this paper, we provide a complete survey over the state-of-the-art of XML compression techniques.  ...  Hence, a straightforward logical approach for compressing XML documents is to use the traditional general purpose text compression tools.  ... 
doi:10.1016/j.jcss.2009.01.004 fatcat:dvluugsp5vajhaols2fftuc23a

An Experimental Investigation of XML Compression Tools [article]

Sherif Sakr
2008 arXiv   pre-print
The study reports the behavior of nine XML compressors using a large corpus of XML documents which covers the different natures and scales of XML documents.  ...  Finally, we provide some guidelines and recommen- dations which are useful for helping developers and users for making an effective decision for selecting the most suitable XML compression tool for their  ...  XMLPPM is considered as an adaptation of the general purpose P rediction by P artial M atching compression scheme (PPM) [23] .  ... 
arXiv:0806.0075v1 fatcat:ktibyclo2bed7hkfrekoycwsoa

Portable trace compression through instruction interpretation

Svilen Kanev, Robert Cohn
2011 (IEEE ISPASS) IEEE INTERNATIONAL SYMPOSIUM ON PERFORMANCE ANALYSIS OF SYSTEMS AND SOFTWARE  
The compression scheme exploits the general similarity between compression and prediction. A simplified functional simulator is used to predict instruction effects in a repeatable manner.  ...  In this paper we present Zcompr -a compression scheme that allows practical usage of full-state traces that are billions of instructions long.  ...  Finally, a general-purpose compressor compresses the output of the interpretation-based compressor.  ... 
doi:10.1109/ispass.2011.5762720 dblp:conf/ispass/KanevC11 fatcat:4mgsolbhibbqbisim4vzwt7x54

A Collaborative Data Collection Scheme Based on Optimal Clustering for Wireless Sensor Networks

Guorui Li, Haobo Chen, Sancheng Peng, Xinguang Li, Cong Wang, Shui Yu, Pengfei Yin
2018 Sensors  
By comparing it o the existing compression-based and non-compression-based data collection schemes, the average reductions of energy consumption are 17.9% and 67.9%, respectively.  ...  Different from existing data collection models in WSNs, we propose a collaborative data collection scheme based on optimal clustering to collect the sensed data in an energy-efficient and load-balanced  ...  A number of sensor localization algorithms for WSNs can be used for this purpose [32] .  ... 
doi:10.3390/s18082487 pmid:30071592 fatcat:55t6lgzdxbgkliuvv7vg24vrvu
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