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» Isometries and Computability Structures
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210
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PLDI
2010
ACM
15 years 12 months ago
Finding low-utility data structures
Many opportunities for easy, big-win, program optimizations are missed by compilers. This is especially true in highly layered Java applications. Often at the heart of these misse...
Guoqing Xu, Nick Mitchell, Matthew Arnold, Atanas ...
208
Voted
JCB
2008
106views more  JCB 2008»
15 years 6 months ago
Statistics of Random Protein Superpositions: p-Values for Pairwise Structure Alignment
Quantification of statistical significance is essential for the interpretation of protein structural similarity. To address this, a random model for protein structure comparison w...
James O. Wrabl, Nick V. Grishin
232
Voted
BMCBI
2002
108views more  BMCBI 2002»
15 years 6 months ago
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algo...
Sean R. Eddy
AI
1999
Springer
15 years 6 months ago
Coalition Structure Generation with Worst Case Guarantees
Coalition formation is a key topic in multiagent systems. One may prefer a coalition structure that maximizes the sum of the values of the coalitions, but often the number of coal...
Tuomas Sandholm, Kate Larson, Martin Andersson, On...
BMCBI
2011
15 years 1 months ago
Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars
Background: The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state...
Zsuzsanna Sukosd, Bjarne Knudsen, Morten Vaerum, J...