Randomized algorithms
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Efficient approximation algorithms for the Hamming center problem
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
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A Polynominal Time Approximation Scheme for the Closest Substring Problem
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
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Information and Computation
Parameterized Intractability of Distinguishing Substring Selection
Theory of Computing Systems
On the Optimality of the Dimensionality Reduction Method
FOCS '06 Proceedings of the 47th Annual IEEE Symposium on Foundations of Computer Science
Ruling Out PTAS for Graph Min-Bisection, Dense k-Subgraph, and Bipartite Clique
SIAM Journal on Computing
Efficient Algorithms for the Closest String and Distinguishing String Selection Problems
FAW '09 Proceedings of the 3d International Workshop on Frontiers in Algorithmics
Closest Substring Problems with Small Distances
SIAM Journal on Computing
Detecting high log-densities: an O(n¼) approximation for densest k-subgraph
Proceedings of the forty-second ACM symposium on Theory of computing
Cycle detection and correction
ICALP'10 Proceedings of the 37th international colloquium conference on Automata, languages and programming
More Efficient Algorithms for Closest String and Substring Problems
SIAM Journal on Computing
Approximations and partial solutions for the consensus sequence problem
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
A three-string approach to the closest string problem
Journal of Computer and System Sciences
Efficient approximation schemes for geometric problems?
ESA'05 Proceedings of the 13th annual European conference on Algorithms
Slightly superexponential parameterized problems
Proceedings of the twenty-second annual ACM-SIAM symposium on Discrete Algorithms
Better inapproximability results for maxclique, chromatic number and min-3lin-deletion
ICALP'06 Proceedings of the 33rd international conference on Automata, Languages and Programming - Volume Part I
Parameterized Complexity and Approximation Algorithms
The Computer Journal
Hi-index | 5.23 |
Many problems in bioinformatics are about finding strings that approximately represent a collection of given strings. We look at more general problems where some input strings can be classified as outliers. The Close to Most Strings problem is, given a set S of the same-length strings, and a parameter d, find a string x that maximizes the number of ''non-outliers'' within Hamming distance d of x. We prove that this problem has no polynomial-time approximation scheme (PTAS) unless NP has randomized polynomial-time algorithms, correcting a decade-old erroneous proof made previously in the literature. The Most Strings with Few Bad Columns problem is to find a maximum-size subset of input strings so that the number of non-identical positions is at most k; we show it has no PTAS unless P=NP. We also observe Closest to k Strings has no efficient PTAS (EPTAS) unless a parameterized complexity hierarchy collapses. In sum, outliers help model problems associated with using biological data, but we show the problem of finding an approximate solution is computationally difficult.