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A survey of modern high-performance switching techniques

H. Ahmadi, W.E. Denzel
1989 IEEE Journal on Selected Areas in Communications  
"Efficient implementation of the Warm-up algorithm for the construction of length-restricted prefix codes," Proceedings of the ALENEX, Baltimore, Maryland and in vol. 1619, Lecture Notes in Computer Science  ...  "Warm-up algorithm: A lagrangean construction of length restricted huffman codes," Monografias em Ciencia da Computacao, no. 15, January 1996. [60] R.L. Mildiu and E.S. Laber.  ... 
doi:10.1109/49.44557 fatcat:hvvcuntbv5hyfo2ztudkhdylie

Twenty (or so) Questions: D-ary Length-Bounded Prefix Coding [article]

Michael B. Baer
2007 arXiv   pre-print
Efficient optimal prefix coding has long been accomplished via the Huffman algorithm. However, there is still room for improvement and exploration regarding variants of the Huffman problem.  ...  Length-limited Huffman coding, useful for many practical applications, is one such variant, for which codes are restricted to the set of codes in which none of the n codewords is longer than a given length  ...  ACKNOWLEDGMENTS The author wishes to thank Zhen Zhang for first bringing a related problem to his attention and David Morgenthaler for constructive discussions on this topic.  ... 
arXiv:cs/0602085v4 fatcat:hiftrhbsbvgyniso5t5re4rgv4

Kleenex: compiling nondeterministic transducers to deterministic streaming transducers

Bjørn Bugge Grathwohl, Fritz Henglein, Ulrik Terp Rasmussen, Kristoffer Aalund Søholm, Sebastian Paaske Tørholm
2016 Proceedings of the 43rd Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages - POPL 2016  
We present and illustrate Kleenex, a language for expressing general nondeterministic finite transducers, and its novel compilation to streaming string transducers with essentially optimal streaming behavior  ...  In use cases it achieves consistently high throughput rates around the 1 Gbps range on stock hardware, performing well, especially in complex use cases, in comparison to both specialized and related tools  ...  The order of authors is insignificant; please list all authors-or none-when citing this paper.  ... 
doi:10.1145/2837614.2837647 dblp:conf/popl/GrathwohlHRST16 fatcat:e5nzqgpisban5lk44oi5hqcjty

Kleenex: compiling nondeterministic transducers to deterministic streaming transducers

Bjørn Bugge Grathwohl, Fritz Henglein, Ulrik Terp Rasmussen, Kristoffer Aalund Søholm, Sebastian Paaske Tørholm
2016 SIGPLAN notices  
We present and illustrate Kleenex, a language for expressing general nondeterministic finite transducers, and its novel compilation to streaming string transducers with essentially optimal streaming behavior  ...  In use cases it achieves consistently high throughput rates around the 1 Gbps range on stock hardware, performing well, especially in complex use cases, in comparison to both specialized and related tools  ...  The order of authors is insignificant; please list all authors-or none-when citing this paper.  ... 
doi:10.1145/2914770.2837647 fatcat:awp6t3efmva6xg5dlewzclsp6e

Database indexing for large DNA and protein sequence collections

Ela Hunt, Malcolm P. Atkinson, Robert W. Irving
2002 The VLDB journal  
We detail the requirements for further database and algorithmic research to support efficient use of large suffix indexes in biological applications.  ...  For a range of query lengths and error bounds the suffix tree reduces the size of the unoptimised O(mn) dynamic programming calculation required in the evaluation of string similarity, and the gain from  ...  We would like to acknowledge the contribution of the members of the PJama team at Glasgow and SUN Labs. We thank the anonymous referees, Paolo Ferragina, and Ricardo Baeza-Yates for their comments.  ... 
doi:10.1007/s007780200064 fatcat:jupeurrbfrdunf4lvkumm2zuge

Ball-Larus path profiling across multiple loop iterations

Daniele Cono D'Elia, Camil Demetrescu
2013 Proceedings of the 2013 ACM SIGPLAN international conference on Object oriented programming systems languages & applications - OOPSLA '13  
Previous results, based on rather complex algorithms, have attempted to circumvent this limitation at the price of significant performance losses even for a small number of iterations.  ...  Identifying the hottest paths in the control flow graph of a routine can direct optimizations to portions of the code where most resources are consumed.  ...  A warm acknowledgment goes to Irene Finocchi for her contributions to the design of the approach presented in this paper and for her help in setting up our experimental package for the OOPSLA 2013 artifact  ... 
doi:10.1145/2509136.2509521 dblp:conf/oopsla/DEliaD13 fatcat:q7oqiz6tpbgibpmpbz3cyjjc2u

Phrasal Rank-Encoding: Exploiting Phrase Redundancy and Translational Relations for Phrase Table Compression

Marcin Junczys-Dowmunt
2012 Prague Bulletin of Mathematical Linguistics  
Using this and other methods for space reduction in a new binary phrase table implementation, a size reduction by an order of magnitude is achieved when comparing to the Moses on-disk phrase table implementation  ...  A combination of PR-Enc with Huffman coding allows to reduce the size of an aggressively compressed phrase table by another 39 percent.  ...  Acknowledgements Part of this research was carried out at and funded by the World Intellectual Property Organization (WIPO) in Geneva.  ... 
doi:10.2478/v10108-012-0009-6 fatcat:spiup3y2rjfwzme37whklamtdy

Efficient Construction of (Distributed) Verifiable Random Functions [chapter]

Yevgeniy Dodis
2002 Lecture Notes in Computer Science  
We give the first simple and efficient construction of verifiable random functions (VRFs).  ...  The efficiency of our VRF construction is only slightly worse than that of a regular PRF construction of Naor and Reingold [16] .  ...  I would also like to thank Dan Boneh and Don Coppersmith for their preliminary (positive) evaluation of the sf-DDH assumption. Finally, I would like to thank Anna Lysyanskaya for inspiring this work.  ... 
doi:10.1007/3-540-36288-6_1 fatcat:iwd5lok2lzgsbdui6pzlb2y2d4

Stream Processing using Grammars and Regular Expressions [article]

Ulrik Terp Rasmussen
2017 arXiv   pre-print
The algorithm is based on a bottom-up tabulation algorithm reformulated using least fixed points and evaluated using an instance of the chaotic iteration scheme by Cousot and Cousot.  ...  The second algorithm is a single-pass and optimally streaming algorithm which outputs as much of the parse tree as is semantically possible based on the input prefix read so far, and resorts to buffering  ...  For all (i, j) ∈ Index:  ... 
arXiv:1704.08820v1 fatcat:twr3ysgyzzg3nap22n6xvepp5i

Tagged Deterministic Finite Automata with Lookahead [article]

Ulya Trofimovich
2019 arXiv   pre-print
The main goal of this work is application of TDFA to lexer generators that optimize for speed of the generated code.  ...  All discussed algorithms are implemented in the open source lexer generator RE2C.  ...  And many thanks to all the good people who cheered me up during this work. :)  ... 
arXiv:1907.08837v1 fatcat:gnlgj5jx3vhkfguyzrgkg2gc6q

Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units

Michael P. Howard, Joshua A. Anderson, Arash Nikoubashman, Sharon C. Glotzer, Athanassios Z. Panagiotopoulos
2016 Computer Physics Communications  
We compare this to a GPU implementation of the current state-of-the-art CPU algorithm based on stenciled cell lists.  ...  LBVHs outperformed the stenciled cell lists for systems with moderate or large size disparity and dilute or semidilute fractions of large particles, conditions typical of colloidal systems.  ...  We performed 1,000 warm-up steps to determine optimal kernel launch parameters for each algorithm, and then profiled the time required to construct the neighbor list during 10,000 simulation steps.  ... 
doi:10.1016/j.cpc.2016.02.003 fatcat:watajxsutjf4rpaspxrpsekmwy

Dictionary-Based Compression for Long Time-Series Similarity

Willis Lang, Michael Morse, Jignesh M. Patel
2010 IEEE Transactions on Knowledge and Data Engineering  
We also develop heuristics to automatically identify suitable parameters for our method, thus removing the task of parameter tuning found in other existing methods.  ...  We show that off-the-shelf compressors do not fair well for computing time-series similarity.  ...  ACKNOWLEDGEMENTS We would like to thank the reviewers of this paper for their constructive comments on a previous version of this manuscript.  ... 
doi:10.1109/tkde.2009.201 fatcat:q5y3wktlnbhsda7zpl4wzozpua

Fast Compressed Tries through Path Decompositions [article]

Roberto Grossi, Giuseppe Ottaviano
2011 arXiv   pre-print
Tries are popular data structures for storing a set of strings, where common prefixes are represented by common root-to-node paths.  ...  For (1), we obtain data structures that outperform other state-of-the-art compressed dictionaries in space efficiency, while obtaining predictable query times that are competitive with data structures  ...  Acknowledgments We would like to thank the authors of [10] for kindly providing the source code for their algorithms.  ... 
arXiv:1111.5220v2 fatcat:ulc4fk2z2bau5dv2lxaekyxrku

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers

Daniel Liu
2019 PeerJ  
There are many tools for solving the problem of deduplicating reads based on their finding reads with the same alignment coordinates and UMIs.  ...  We implement our data structures and optimizations in a tool called UMICollapse, which is able to deduplicate over one million unique UMIs of length 9 at a single alignment position in around 26 s, using  ...  The best time for each dataset is bolded. Empty cells indicate algorithms that took longer than 10 min total to run one warm-up trial and three actual trials.  ... 
doi:10.7717/peerj.8275 pmid:31871845 pmcid:PMC6921982 fatcat:mra73difbndctmk5roisphi3hm

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers [article]

Daniel Liu
2019 bioRxiv   pre-print
We implement our data structures and optimizations in a tool called UMICollapse, which is able to deduplicate over one million unique UMIs of length 9 at a single alignment position in around 26 seconds  ...  Although there are many tools for solving the problem of deduplicating reads based on their finding reads with the same alignment coordinates and UMIs, many tools either cannot handle substitution errors  ...  This is used by later versions of UMI-tools [5] to speed up the construction of its networks for UMI deduplication.  ... 
doi:10.1101/648683 fatcat:clz6nlfjtjbfxmbx5xqq7iraeq
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