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» Evolutionary algorithms and dynamic programming
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BCB
2010
156views Bioinformatics» more  BCB 2010»
14 years 11 months ago
Accelerating HMMER on GPUs by implementing hybrid data and task parallelism
Many biologically motivated problems are expressed as dynamic programming recurrences and are difficult to parallelize due to the intrinsic data dependencies in their algorithms. ...
Narayan Ganesan, Roger D. Chamberlain, Jeremy Buhl...
PLDI
2010
ACM
15 years 9 months ago
Adversarial memory for detecting destructive races
Multithreaded programs are notoriously prone to race conditions, a problem exacerbated by the widespread adoption of multi-core processors with complex memory models and cache coh...
Cormac Flanagan, Stephen N. Freund
BMCBI
2005
162views more  BMCBI 2005»
15 years 4 months ago
Accelerated probabilistic inference of RNA structure evolution
Background: Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary...
Ian Holmes
LATIN
1998
Springer
15 years 8 months ago
Fast Two-Dimensional Approximate Pattern Matching
We address the problem of approximate string matching in two dimensions, that is, to nd a pattern of size m m in a text of size n n with at most k errors (substitutions, insertions...
Ricardo A. Baeza-Yates, Gonzalo Navarro
KES
1998
Springer
15 years 8 months ago
Attractor systems and analog computation
Attractor systems are useful in neurodynamics,mainly in the modelingof associative memory. Thispaper presentsa complexity theory for continuous phase space dynamical systems with ...
Hava T. Siegelmann, Shmuel Fishman