Algorithms in combinatorial geometry
Algorithms in combinatorial geometry
On the complexity of learning strings and sequences
COLT '91 Proceedings of the fourth annual workshop on Computational learning theory
Finding similar regions in many strings
STOC '99 Proceedings of the thirty-first annual ACM symposium on Theory of computing
Distinguishing string selection problems
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
On approximation algorithms for local multiple alignment
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
On the Complexity of Deriving Score Functions from Examples for Problems in Molecular Biology
ICALP '98 Proceedings of the 25th International Colloquium on Automata, Languages and Programming
Inferring a Union of Halfspaces from Examples
COCOON '02 Proceedings of the 8th Annual International Conference on Computing and Combinatorics
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PSSMs (Position-Specific Score Matrices) have been applied to various problems in Bioinformatics. We study the following problem: given positive examples (sequences) and negative examples (sequences), finda PSSM which correctly discriminates between positive and negative examples. We prove that this problem is solvedin polynomial time if the size of a PSSM is bounded by a constant. On the other hand, we prove that this problem is NP-hard if the size is not bounded. We also prove similar results on deriving a mixture of PSSMs.