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Querying large read collections in main memory: a versatile data structure

Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, Eric Rivals
2011 BMC Bioinformatics  
Conclusions: Gk arrays constitute a versatile data structure that enables fast and more accurate read analysis in various contexts.  ...  Once constructed, the index structure is kept in main memory and is repeatedly accessed to answer queries like "given a k-mer, get the reads containing this k-mer (once/at least once)".  ...  Querying large read collections in main memory: a versatile data structure Philippe et al.  ... 
doi:10.1186/1471-2105-12-242 pmid:21682852 pmcid:PMC3163563 fatcat:7yx3jw7ybvdgpjsagzjglwlcgi

Relational Memory: Native In-Memory Accesses on Rows and Columns [article]

Shahin Roozkhosh, Denis Hoornaert, Ju Hyoung Mun, Tarikul Islam Papon, Ahmed Sanaullah, Ulrich Drepper, Renato Mancuso, Manos Athanassoulis
2022 arXiv   pre-print
Our approach, termed Relational Memory, relies on an FPGA- based accelerator that sits between the CPU and main memory and transparently transforms base data to any group of columns with minimal overhead  ...  Transforming rows to columns at runtime is expensive, hence, many analytical systems ingest data in row-first form and transform it in the background to columns to facilitate future analytical queries.  ...  ACKNOWLEDGEMENTS The material presented in this paper is based upon work supported by the National Science Foundation (  ... 
arXiv:2109.14349v2 fatcat:wh7g3ezf6jg2pd7zbd7727xmy4

Data Acquisition in Sensor Networks with Large Memories

D. Zeinalipour-Yazti, S. Neema, V. Kalogeraki, D. Gunopulos, W. Najjar
2005 21st International Conference on Data Engineering Workshops (ICDEW'05)  
In this paper we initiate a study on the deployment of large memories at sensor nodes.  ...  the sink could continuously gather the data in a centralized fashion, but this would become prohibitively expensive. 2  ...  Data can be buffered on the 32KB flash memory for reading and writing efficiently on the SD-Card. Data is transferred to the SDCard in blocks of 512 bytes at a maximum rate of 3 Mbps.  ... 
doi:10.1109/icde.2005.209 dblp:conf/icde/Zeinalipour-YaztiKGN05 fatcat:dvr2ilpv2zgipatkxvr7llgguq

Lightweight recoverable virtual memory

M. Satyanarayanan, Henry H. Mashburn, Puneet Kumar, David C. Steere, James J. Kistler
1993 ACM SIGOPS Operating Systems Review  
The data in Table II Fig. 5 . 5 This log record format of a typical log record read either way. .. .. . q .--"n. ..a ....a '.-....*. .. . z 40 .. .... . '... P..., a, q . . . ...9 . . ...*..  ...  They encapsulate all three of the basic transactional properties and provide data access via a query language interface.  ... 
doi:10.1145/173668.168631 fatcat:xl32xlkfrndwhlkwal2cmlihyu

Lightweight recoverable virtual memory

M. Satyanarayanan, Henry H. Mashburn, Puneet Kumar, David C. Steere, James J. Kistler
1994 ACM Transactions on Computer Systems  
The data in Table II Fig. 5 . 5 This log record format of a typical log record read either way. .. .. . q .--"n. ..a ....a '.-....*. .. . z 40 .. .... . '... P..., a, q . . . ...9 . . ...*..  ...  They encapsulate all three of the basic transactional properties and provide data access via a query language interface.  ... 
doi:10.1145/174613.174615 fatcat:rxmpdemslnd5roeo4hqoluv2mq

Lightweight recoverable virtual memory

M. Satyanarayanan, Henry H. Mashburn, Puneet Kumar, David C. Steere, James J. Kistler
1993 Proceedings of the fourteenth ACM symposium on Operating systems principles - SOSP '93  
The data in Table II Fig. 5 . 5 This log record format of a typical log record read either way. .. .. . q .--"n. ..a ....a '.-....*. .. . z 40 .. .... . '... P..., a, q . . . ...9 . . ...*..  ...  They encapsulate all three of the basic transactional properties and provide data access via a query language interface.  ... 
doi:10.1145/168619.168631 dblp:conf/sosp/SatyanarayananMKSK93 fatcat:br7dsj37iffnxaic7re7etpzke

Mosiqs: Persistent Memory Object Storage with Metadata Indexing and Querying for Scientific Computing

Awais Khan, Hyogi Sim, Sudharshan S. Vazhkudai, Youngjae Kim
2021 IEEE Access  
FIGURE 8 : 8 An example of versatile querying provided by MOSIQS. In particular, (a) and (b) shows a point query.  ...  TagIt [2] offers a file system integrated indexing and querying for a large collection of scientific files stored on a sharednothing distributed file system.  ...  He is also a Distinguished Scientist at ORNL and studies the fundamental underpinnings of supercomputers and data centers in many of the aforementioned areas.  ... 
doi:10.1109/access.2021.3087502 fatcat:vqaurh7hjjbbna6ei46e6mjlva

Key-Value Memory Networks for Directly Reading Documents [article]

Alexander Miller, Adam Fisch, Jesse Dodge, Amir-Hossein Karimi, Antoine Bordes, Jason Weston
2016 arXiv   pre-print
In this work we introduce a new method, Key-Value Memory Networks, that makes reading documents more viable by utilizing different encodings in the addressing and output stages of the memory read operation  ...  To compare using KBs, information extraction or Wikipedia documents directly in a single framework we construct an analysis tool, WikiMovies, a QA dataset that contains raw text alongside a preprocessed  ...  These models could be applied to storing and reading memories for other tasks as well, and future work should try them in other domains, such as in a full dialog setting.  ... 
arXiv:1606.03126v2 fatcat:emqrydo5gzdt3hqvmqi3unfhtq

Key-Value Memory Networks for Directly Reading Documents

Alexander Miller, Adam Fisch, Jesse Dodge, Amir-Hossein Karimi, Antoine Bordes, Jason Weston
2016 Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing  
In this work we introduce a new method, Key-Value Memory Networks, that makes reading documents more viable by utilizing different encodings in the addressing and output stages of the memory read operation  ...  To compare using KBs, information extraction or Wikipedia documents directly in a single framework we construct an analysis tool, WIKIMOVIES, a QA dataset that contains raw text alongside a preprocessed  ...  In this work, we introduce KV-MemNNs, a Memory Network model that operates a symbolic memory structured as (key, value) pairs.  ... 
doi:10.18653/v1/d16-1147 dblp:conf/emnlp/MillerFDKBW16 fatcat:drowuad6jzcovaemh6is3mkfiq

Fast In-Memory XPath Search over Compressed Text and Tree Indexes [article]

A. Arroyuelo, F. Claude, S. Maneth, V. Mäkinen, G. Navarro, K. Nguyen, J. Siren, N. Välimäki
2011 arXiv   pre-print
A large fraction of an XML document typically consists of text data. The XPath query language allows text search via the equal, contains, and starts-with predicates.  ...  The engine uses fast counting queries of the text index in order to dynamically determine whether to evaluate top-down or bottom-up with respect to the tree structure.  ...  We are grateful to Kunihiko Sadakane for making available to us his implementation of parentheses structure for succinct trees, and to Juha Karjalainen for composing the BioXML data.  ... 
arXiv:0907.2089v2 fatcat:zgureheimzbelicbnygo6epvjq

Fast in-memory XPath search using compressed indexes

Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Maakinen, Gonzalo Navarro, Kim Nguyen, Jouni Siren, Niko Valimaki
2010 2010 IEEE 26th International Conference on Data Engineering (ICDE 2010)  
We are grateful to Kunihiko Sadakane for making available to us his implementation of parentheses structure for succinct trees, and to Juha Karjalainen for composing the BioXML data.  ...  Compression of Complex Massive Data" (Number 08261).  ...  This is however not a problem for the use case we have targeted: a main memory query engine where the same large document is queried many times.  ... 
doi:10.1109/icde.2010.5447858 dblp:conf/icde/ArroyueloCMMNNSV10 fatcat:ztkg5utdardtti2kpue6kqsn2a

Data Processing and Information Classification—An In-Memory Approach

Milena Andrighetti, Giovanna Turvani, Giulia Santoro, Marco Vacca, Andrea Marchesin, Fabrizio Ottati, Massimo Ruo Roch, Mariagrazia Graziano, Maurizio Zamboni
2020 Sensors  
Memories are too slow, so microprocessors cannot fetch enough data from them, greatly limiting their performance. A solution is the Processing-In-Memory (PIM) approach.  ...  In this work we present an example of such a system, using as a case of study the Bitmap Indexing algorithm. Such algorithm is used to classify data coming from many sources in parallel.  ...  The Instruction Memory is used to collect the queries to execute.  ... 
doi:10.3390/s20061681 pmid:32197308 fatcat:r4olsv675redfcmuivslp3v4ay

Fast in-memory XPath search using compressed indexes

Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyễn, Jouni Sirén, Niko Välimäki
2013 Software, Practice & Experience  
On one hand, it represents the XML data in a compact indexed form, which allows it to handle larger collections in main memory while supporting powerful search and navigation operations over the text and  ...  We present a system for in-memory evaluation of XPath search queries, that is, queries with text and structure predicates, yet without advanced features such as backward axes, arithmetics, and joins.  ...  We are grateful to Kunihiko Sadakane for making available to us his implementation of parentheses structure for succinct trees, and to Juha Karjalainen for composing the BioXML data.  ... 
doi:10.1002/spe.2227 fatcat:s4zpsb4xajh43bdai3bfigkjzy

In-Memory Business Process Management

Soren Balko, Alistair Barros
2015 2015 IEEE 19th International Enterprise Distributed Object Computing Conference  
Significant research and development has been undertaken over several years concerning data management considerations of in-memory databases.  ...  In-memory databases have become a mainstay of enterprise computing offering significant performance and scalability boosts for online analytical and (to a lesser extent) transactional processing as well  ...  instructions of modern CPUs to rapidly process large amounts of data in main memory.  ... 
doi:10.1109/edoc.2015.21 dblp:conf/edoc/BalkoB15 fatcat:a5faarkbujhwjih2lrvibanzzu

Reclaiming Memory for Lock-Free Data Structures

Trevor Alexander Brown
2015 Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing - PODC '15  
Memory reclamation for sequential or lock-based data structures is typically easy. However, memory reclamation for lock-free data structures is a significant challenge.  ...  Our new scheme takes O(1) amortized steps per high-level operation on the lock-free data structure and O(1) steps in the worst case each time an object is removed from the data structure.  ...  (This is also a problem for data structures with lock-based updates and lockfree queries. The solutions presented hererin apply equally well to lock-based data structures with lock-free queries.)  ... 
doi:10.1145/2767386.2767436 dblp:conf/podc/Brown15 fatcat:fllpfktc6jakvhjxqzt6vldxzq
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