An improved lower bound on approximation algorithms for the Closest Substring problem
The Closest Substring problem (the CSP problem) is a basic NP-hard problem in the study of computational biology. It is known that the problem has polynomial time approximation schemes. In this paper, we prove that unless the Exponential Time Hypothesis fails, the CSP problem has no polynomial time...
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| Vydáno v: | Information processing letters Ročník 107; číslo 1; s. 24 - 28 |
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| Médium: | Journal Article |
| Jazyk: | angličtina |
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Amsterdam
Elsevier B.V
30.06.2008
Elsevier Science Elsevier Sequoia S.A |
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| ISSN: | 0020-0190, 1872-6119 |
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| Abstract | The Closest Substring problem (the CSP problem) is a basic NP-hard problem in the study of computational biology. It is known that the problem has polynomial time approximation schemes. In this paper, we prove that unless the Exponential Time Hypothesis fails, the CSP problem has no polynomial time approximation schemes of running time
f
(
1
/
ε
)
n
o
(
1
/
ε
)
for any function
f. This essentially excludes the possibility that the CSP problem has a practical polynomial time approximation scheme even for moderate values of the error bound
ε. As a consequence, it is unlikely that the study of approximation schemes for the CSP problem in the literature would lead to practical approximation algorithms for the problem for small error bound
ε. |
|---|---|
| AbstractList | The Closest Substring problem (the CSP problem) is a basic NP-hard problem in the study of computational biology. It is known that the problem has polynomial time approximation schemes. In this paper, the authors prove that unless the Exponential Time Hypothesis fails, the CSP problem has no polynomial time approximation schemes of running time ... for any function f. This essentially excludes the possibility that the CSP problem has a practical polynomial time approximation scheme even for moderate values of the error bound ... As a consequence, it is unlikely that the study of approximation schemes for the CSP problem in the literature would lead to practical approximation algorithms for the problem for small error bound ... (ProQuest: ... denotes formulae/symbols omitted.) The Closest Substring problem (the CSP problem) is a basic NP-hard problem in the study of computational biology. It is known that the problem has polynomial time approximation schemes. In this paper, we prove that unless the Exponential Time Hypothesis fails, the CSP problem has no polynomial time approximation schemes of running time f ( 1 / ε ) n o ( 1 / ε ) for any function f. This essentially excludes the possibility that the CSP problem has a practical polynomial time approximation scheme even for moderate values of the error bound ε. As a consequence, it is unlikely that the study of approximation schemes for the CSP problem in the literature would lead to practical approximation algorithms for the problem for small error bound ε. |
| Author | Chen, Jianer Huang, Min Wang, Jianxin |
| Author_xml | – sequence: 1 givenname: Jianxin surname: Wang fullname: Wang, Jianxin email: jxwang@mail.csu.edu.cn organization: School of Information Science and Engineering, Central South University, Changsha 410083, The People's Republic of China – sequence: 2 givenname: Jianer surname: Chen fullname: Chen, Jianer organization: School of Information Science and Engineering, Central South University, Changsha 410083, The People's Republic of China – sequence: 3 givenname: Min surname: Huang fullname: Huang, Min organization: School of Information Science and Engineering, Central South University, Changsha 410083, The People's Republic of China |
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| Cites_doi | 10.1007/s11390-005-0003-7 10.1145/506147.506150 10.1016/j.jcss.2006.04.007 10.1109/SFCS.2005.70 10.1016/S0890-5401(03)00057-9 10.1007/3-540-45123-4_10 10.1007/s00224-004-1185-z 10.1007/s10878-006-7137-6 10.1007/s00493-006-0011-4 10.1016/0022-0000(91)90023-X 10.1006/jcss.2001.1774 |
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| Keywords | Closest substring problem Lower bound Approximation algorithms Analysis of algorithms Computational biology Polynomial Error estimation Computer theory Polynomial approximation Biology Approximation algorithm Hypothesis Polynomial time NP hard problem Information processing Algorithm analysis |
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| References | Fellows, Gramm, Niedermeier (bib006) 2006; 26 D. Marx, The closest substring problem with small distances, in: Proc. 46th Annual IEEE Symp. Foundations of Computer Science (FOCS 2005), 2005, pp. 63–72 Chen (bib001) 2005; 20 Gramm, Guo, Niedermeier (bib007) 2006; 39 Downey, Fellows (bib004) 1999 Li, Ma, Wang (bib010) 2002; 49 B. Ma, A polynomial time approximation scheme for the closest substring problem, in: Proc. 11th Annual Symposium on Combinatorial Pattern Matching, 2000, pp. 99–107 Papadimitriou, Yannakakis (bib013) 1991; 43 Chen, Huang, Kanj, Xia (bib003) 2006; 11 Chen, Huang, Kanj, Xia (bib002) 2006; 72 Impagliazzo, Paturi, Zane (bib008) 2001; 63 Fellows, Gramm, Niedermeier (bib005) 2002; vol. 2285 Kevin Lanctot, Li, Ma, Wang, Zhang (bib009) 2003; 185 Downey (10.1016/j.ipl.2007.12.005_bib004) 1999 Gramm (10.1016/j.ipl.2007.12.005_bib007) 2006; 39 10.1016/j.ipl.2007.12.005_bib011 10.1016/j.ipl.2007.12.005_bib012 Chen (10.1016/j.ipl.2007.12.005_bib002) 2006; 72 Impagliazzo (10.1016/j.ipl.2007.12.005_bib008) 2001; 63 Li (10.1016/j.ipl.2007.12.005_bib010) 2002; 49 Fellows (10.1016/j.ipl.2007.12.005_bib006) 2006; 26 Kevin Lanctot (10.1016/j.ipl.2007.12.005_bib009) 2003; 185 Chen (10.1016/j.ipl.2007.12.005_bib003) 2006; 11 Fellows (10.1016/j.ipl.2007.12.005_bib005) 2002; vol. 2285 Papadimitriou (10.1016/j.ipl.2007.12.005_bib013) 1991; 43 Chen (10.1016/j.ipl.2007.12.005_bib001) 2005; 20 |
| References_xml | – volume: 20 start-page: 18 year: 2005 end-page: 37 ident: bib001 article-title: Parameterized computation and complexity: A new approach dealing with NP-hardness publication-title: Journal of Computer Science and Technology – volume: 185 start-page: 42 year: 2003 end-page: 55 ident: bib009 article-title: Distinguishing string selection problems publication-title: Information and Computation – volume: 43 start-page: 425 year: 1991 end-page: 440 ident: bib013 article-title: Optimization, approximation, and complexity classes publication-title: Journal of Computer and System Sciences – volume: 72 start-page: 1346 year: 2006 end-page: 1367 ident: bib002 article-title: Strong computational lower bounds via parameterized complexity publication-title: Journal of Computer and System Sciences – volume: 49 start-page: 157 year: 2002 end-page: 171 ident: bib010 article-title: On the closest string and substring problems publication-title: Journal of the ACM – volume: 26 start-page: 141 year: 2006 end-page: 167 ident: bib006 article-title: On the parameterized intractability of motif search problems publication-title: Combinatorica – reference: D. Marx, The closest substring problem with small distances, in: Proc. 46th Annual IEEE Symp. Foundations of Computer Science (FOCS 2005), 2005, pp. 63–72 – volume: 11 start-page: 231 year: 2006 end-page: 247 ident: bib003 article-title: On the computational hardness based on linear FPT-reductions publication-title: Journal of Combinatorial Optimization – volume: vol. 2285 start-page: 262 year: 2002 end-page: 273 ident: bib005 article-title: On the parameterized intractability of Closest Substring and related problems publication-title: STACS 2002 – volume: 39 start-page: 545 year: 2006 end-page: 560 ident: bib007 article-title: Parameterized intractability of distinguished substring selection publication-title: Theory of Computing Systems – year: 1999 ident: bib004 article-title: Parameterized Complexity – reference: B. Ma, A polynomial time approximation scheme for the closest substring problem, in: Proc. 11th Annual Symposium on Combinatorial Pattern Matching, 2000, pp. 99–107 – volume: 63 start-page: 512 year: 2001 end-page: 530 ident: bib008 article-title: Which problems have strongly exponential complexity? publication-title: Journal of Computer and System Sciences – volume: 20 start-page: 18 year: 2005 ident: 10.1016/j.ipl.2007.12.005_bib001 article-title: Parameterized computation and complexity: A new approach dealing with NP-hardness publication-title: Journal of Computer Science and Technology doi: 10.1007/s11390-005-0003-7 – volume: 49 start-page: 157 year: 2002 ident: 10.1016/j.ipl.2007.12.005_bib010 article-title: On the closest string and substring problems publication-title: Journal of the ACM doi: 10.1145/506147.506150 – volume: 72 start-page: 1346 year: 2006 ident: 10.1016/j.ipl.2007.12.005_bib002 article-title: Strong computational lower bounds via parameterized complexity publication-title: Journal of Computer and System Sciences doi: 10.1016/j.jcss.2006.04.007 – ident: 10.1016/j.ipl.2007.12.005_bib012 doi: 10.1109/SFCS.2005.70 – volume: 185 start-page: 42 year: 2003 ident: 10.1016/j.ipl.2007.12.005_bib009 article-title: Distinguishing string selection problems publication-title: Information and Computation doi: 10.1016/S0890-5401(03)00057-9 – year: 1999 ident: 10.1016/j.ipl.2007.12.005_bib004 – ident: 10.1016/j.ipl.2007.12.005_bib011 doi: 10.1007/3-540-45123-4_10 – volume: 39 start-page: 545 year: 2006 ident: 10.1016/j.ipl.2007.12.005_bib007 article-title: Parameterized intractability of distinguished substring selection publication-title: Theory of Computing Systems doi: 10.1007/s00224-004-1185-z – volume: 11 start-page: 231 year: 2006 ident: 10.1016/j.ipl.2007.12.005_bib003 article-title: On the computational hardness based on linear FPT-reductions publication-title: Journal of Combinatorial Optimization doi: 10.1007/s10878-006-7137-6 – volume: 26 start-page: 141 year: 2006 ident: 10.1016/j.ipl.2007.12.005_bib006 article-title: On the parameterized intractability of motif search problems publication-title: Combinatorica doi: 10.1007/s00493-006-0011-4 – volume: vol. 2285 start-page: 262 year: 2002 ident: 10.1016/j.ipl.2007.12.005_bib005 article-title: On the parameterized intractability of Closest Substring and related problems – volume: 43 start-page: 425 year: 1991 ident: 10.1016/j.ipl.2007.12.005_bib013 article-title: Optimization, approximation, and complexity classes publication-title: Journal of Computer and System Sciences doi: 10.1016/0022-0000(91)90023-X – volume: 63 start-page: 512 year: 2001 ident: 10.1016/j.ipl.2007.12.005_bib008 article-title: Which problems have strongly exponential complexity? publication-title: Journal of Computer and System Sciences doi: 10.1006/jcss.2001.1774 |
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| Snippet | The Closest Substring problem (the CSP problem) is a basic NP-hard problem in the study of computational biology. It is known that the problem has polynomial... |
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| SubjectTerms | Algorithmics. Computability. Computer arithmetics Algorithms Analysis of algorithms Applied sciences Approximation Approximation algorithms Approximations and expansions Closest substring problem Computational biology Computer science; control theory; systems Errors Exact sciences and technology Lower bound Mathematical analysis Mathematics Miscellaneous Sciences and techniques of general use Studies Theoretical computing |
| Title | An improved lower bound on approximation algorithms for the Closest Substring problem |
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