Filters








14,234 Hits in 4.9 sec

Streaming Breakpoint Graph Analytics for Accelerating and Parallelizing the Computation of DCJ Median of Three Genomes

Zhaoming Yin, Jijun Tang, Stephen W. Schaeffer, David A. Bader
2013 Procedia Computer Science  
The problem of finding the median of three genomes is the key process in building the most parsimonious phylogenetic trees from genome rearrangement data.  ...  Last but not least, the introduction of a multi-thread shared memory parallel algorithm with two load balancing strategies bring in additional benefit by distributing search work efficiently among different  ...  With the introduction of heuristic, and parallel computing method, many real-size datasets can now be solved within a limit number of search nodes.  ... 
doi:10.1016/j.procs.2013.05.220 fatcat:z2sny3xyozdghp5pktobi4n4xq

Page 3749 of Mathematical Reviews Vol. , Issue 86h [page]

1986 Mathematical Reviews  
These counting problems are solved by ‘algebraic’ methods.” {For the entire collection see MR 86b:68001.} Gillett, Will D. (1-WASN) On binary tree encodements. Acta Inform. 21 (1984), no. 2, 183-192.  ...  We also solve the following well-known problem: Is there a class of deterministic automata for which the emptiness problem is decidable, but the equivalence problem is undecidable?”  ... 

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements

Marwa Al Arab, Matthias Bernt, Christian Höner zu Siederdissen, Kifah Tout, Peter F. Stadler
2017 Algorithms for Molecular Biology  
We show that this alignment problem can be solved by dynamic programming in cubic space and time.  ...  Conclusions: The partially local sequence alignment method is an effective way to investigate the mechanism of genomic rearrangement events.  ...  Furthermore parallel computing has been introduced to reduce the actual running time for large scale alignments [29] .  ... 
doi:10.1186/s13015-017-0113-0 pmid:28852417 pmcid:PMC5569537 fatcat:uiluxm5rxvc5zlidws6i4stwzq

Complexity of computations

Michael O. Rabin
1977 Communications of the ACM  
Scott for individual and joint contributions which not only have marked the course of theoretical computer science, but have set a standard of clarity and elegance for the entire field.  ...  Rabin and Scott's •959 paper, 'Finite Automata and Their Decision Problems,' has become a classic paper in formal language theory that still forms one of the best introductions to the area.  ...  Usually there are several possible algorithms for solving a problem such as evaluation of an algebraic expression, sorting a file, or parsing a string of symbols.  ... 
doi:10.1145/359810.359816 fatcat:jlj6n4wzlbgd7aq524lsmx2i5u

POY version 4: phylogenetic analysis using dynamic homologies

Andrés Varón, Le Sy Vinh, Ward C. Wheeler
2010 Cladistics  
We present POY version 4, an open source program for the phylogenetic analysis of morphological, prealigned sequence, unaligned sequence, and genomic data.  ...  POY allows phylogenetic inference when not only substitutions, but insertions, deletions, and rearrangement events are allowed (computed using the breakpoint or inversion distance).  ...  To solve this problem, POY 3 included ''controller'' processes, which could serve as intermediate relays, responsible for managing a smaller number of slaves (Janies and Wheeler, 2001) .  ... 
doi:10.1111/j.1096-0031.2009.00282.x pmid:34875752 fatcat:tky7efynibdbhhjshcfb7sya5e

Page 452 of Mathematical Reviews Vol. , Issue 89A [page]

1989 Mathematical Reviews  
(PL-WASW-I) A parallel bucket sort. Inform. Process. Lett. 27 (1988), no. 2, 57-61. Summary: “The problem of sorting integers on a parallel RAM is investigated.  ...  It is closer to optimality than any previously known deterministic al- gorithm that solves the stated restricted sorting problem in polylog time.” 89a:68034 68P10 68Q25 Ha, T. C.  ... 

Heuristics for semi-external depth first search on directed graphs

Jop F. Sibeyn, James Abello, Ulrich Meyer
2002 Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures - SPAA '02  
Computing the strong components of a directed graph is an essential operation for a basic structural analysis of it. This problem can be solved by twice running a depth-first search (DFS).  ...  In an external setting, in which all data can no longer be stored in the main memory, the DFS problem is unsolved so far.  ...  solve the problem for ever larger graphs [11, 13, 19] .  ... 
doi:10.1145/564913.564917 fatcat:r6hrsdzwfzd3jmks7vkepbrhye

Heuristics for semi-external depth first search on directed graphs

Jop F. Sibeyn, James Abello, Ulrich Meyer
2002 Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures - SPAA '02  
Computing the strong components of a directed graph is an essential operation for a basic structural analysis of it. This problem can be solved by twice running a depth-first search (DFS).  ...  In an external setting, in which all data can no longer be stored in the main memory, the DFS problem is unsolved so far.  ...  solve the problem for ever larger graphs [11, 13, 19] .  ... 
doi:10.1145/564870.564917 dblp:conf/spaa/SibeynAM02 fatcat:brpsuyhdpnhqpkr7njjh52q5ca

GPU-accelerated surgery simulation for opening a brain fissure

Kazuya Sase, Akira Fukuhara, Teppei Tsujita, Atsushi Konno
2015 ROBOMECH Journal  
This paper focuses on parallel algorithms for matrix assembly and matrix rearrangement related to FEM procedures by considering a sparse-matrix storage format. Finally, two simulations are conducted.  ...  These results show that the proposed method is effective in simulating dissection and retraction for opening a brain fissure. which permits unrestricted use, distribution, and reproduction in any medium  ...  for Challenging Exploratory Research (24650288), and the Grant-in-Aid for JSPS Fellows (15J01452).  ... 
doi:10.1186/s40648-015-0040-0 fatcat:uew2euhx3vg6hck7nilbrlnz6i

High Performance Pattern Matching on Heterogeneous Platform

Shima Soroushnia, Masoud Daneshtalab, Juha Plosila, Tapio Pahikkala, Pasi Liljeberg
2014 Journal of Integrative Bioinformatics  
SummaryPattern discovery is one of the fundamental tasks in bioinformatics and pattern recognition is a powerful technique for searching sequence patterns in the biological sequence databases.  ...  For this purpose, heterogeneous architectures can be a good choice due to their potential for high performance and energy efficiency.  ...  Fig.4 shows how data overlapping can solve the boundary problem.  ... 
doi:10.1515/jib-2014-253 fatcat:utiuj7bvlnbu5pcfuowadz2opa

High performance pattern matching on heterogeneous platform

Shima Soroushnia, Masoud Daneshtalab, Juha Plosila, Tapio Pahikkala, Pasi Liljeberg
2014 Journal of Integrative Bioinformatics  
Pattern discovery is one of the fundamental tasks in bioinformatics and pattern recognition is a powerful technique for searching sequence patterns in the biological sequence databases.  ...  For this purpose, heterogeneous architectures can be a good choice due to their potential for high performance and energy efficiency.  ...  Fig.4 shows how data overlapping can solve the boundary problem.  ... 
doi:10.2390/biecoll-jib-2014-253 pmid:25339087 fatcat:t6dlwxg42vdm3p4et3gwslzr7y

American Museum of Natural History

1989 Anthropology News  
branch rearrangement with tree fusing then TMP ← SPR(C) or TBR(C) depending on the rearrangement method selected end if Append TMP to BEST_TREES end if end for end for end for end for return BEST_TREES  ...  The most common resources are time (how many steps does it take to solve a problem) and space (how much memory does it take to solve a problem). congruence Agreement of data. Compare incongruence.  ...  are rearranged and evaluated for improvements in optimality.  ... 
doi:10.1111/an.1989.30.9.15.3 fatcat:urbhfqs5pvglno4w5rfea22aki

The American Museum of Natural History

1963 Nature  
branch rearrangement with tree fusing then TMP ← SPR(C) or TBR(C) depending on the rearrangement method selected end if Append TMP to BEST_TREES end if end for end for end for end for return BEST_TREES  ...  The most common resources are time (how many steps does it take to solve a problem) and space (how much memory does it take to solve a problem). congruence Agreement of data. Compare incongruence.  ...  are rearranged and evaluated for improvements in optimality.  ... 
doi:10.1038/1971155d0 fatcat:aer5t2kvlzdrdjygazckj3zyxu

THE AMERICAN MUSEUM OF NATURAL HISTORY

1909 Science  
branch rearrangement with tree fusing then TMP ← SPR(C) or TBR(C) depending on the rearrangement method selected end if Append TMP to BEST_TREES end if end for end for end for end for return BEST_TREES  ...  The most common resources are time (how many steps does it take to solve a problem) and space (how much memory does it take to solve a problem). congruence Agreement of data. Compare incongruence.  ...  are rearranged and evaluated for improvements in optimality.  ... 
doi:10.1126/science.29.738.289-a pmid:17743874 fatcat:yg25qbtsxfhgfcbebfvv6wzova

THE AMERICAN MUSEUM OF NATURAL HISTORY

1911 Science  
branch rearrangement with tree fusing then TMP ← SPR(C) or TBR(C) depending on the rearrangement method selected end if Append TMP to BEST_TREES end if end for end for end for end for return BEST_TREES  ...  The most common resources are time (how many steps does it take to solve a problem) and space (how much memory does it take to solve a problem). congruence Agreement of data. Compare incongruence.  ...  are rearranged and evaluated for improvements in optimality.  ... 
doi:10.1126/science.33.839.142 pmid:17731786 fatcat:rktmdddq3jblpniceihkfymqji
« Previous Showing results 1 — 15 out of 14,234 results