A Modified ACO-based Search Algorithm for Detecting Protein Functional Module From Protein Interaction Network
Recent high-throughput experiments have generated protein-protein interaction data on a genomic scale, yielding the complete protein-protein interaction network for several organisms. Various graph clustering algorithms have been applied to protein interaction networks for detecting protein func...
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| Format: | Conference or Workshop Item |
| Language: | English English |
| Published: |
2015
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| Online Access: | http://umpir.ump.edu.my/id/eprint/10699/1/A%20Modified%20ACO-based%20Search%20Algorithm%20for%20Detecting%20Protein%20Functional%20Module%20From%20Protein%20Interaction%20Network.pdf http://umpir.ump.edu.my/id/eprint/10699/7/fskkp-2015-jamaludin-Modified%20ACO.pdf |
| _version_ | 1825822503677722624 |
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| author | Jamaludin, Sallim Rozlina, Mohamed Roslina, Abd Hamid |
| author_facet | Jamaludin, Sallim Rozlina, Mohamed Roslina, Abd Hamid |
| author_sort | Jamaludin, Sallim |
| collection | UMP |
| description | Recent high-throughput experiments have generated
protein-protein interaction data on a genomic scale, yielding the
complete protein-protein interaction network for several
organisms. Various graph clustering algorithms have been
applied to protein interaction networks for detecting protein functional modules. Although the previous algorithms are scalable and robust, their accuracy is still limited because of the complex connectivity found in protein interaction networks. The Ant Colony Optimization (ACO) Algorithm has been adapted for
the protein functional module detection by modeling the problem as an optimization problem. The adapted ACO (ACO-PFMDA) has obtained feasible solution but not as magnificent as those reported in the literature. Some shortcomings were identified and addressed by proposing a Modified Ant Colony Optimization Algorithm (ACO-PFMDM), which introduces two new scheme for controlling the two main parameters of ACO to solve PFMDP. Experiments on one popular benchmark dataset namely "Saccharomyces cerevisiae" which taken from two popular databases DIP and MIPS has been performed. The experimental result have proved that ACO-PFMDM have improved the overall
performance of protein functional module detection. The search process of ACO-PFMDM has converged effectively compared to some state-of-art algorithms. Moreover, the proposed dynamic update of the heuristic parameters based on entropy has generated high quality tours and it can guide ants toward the effective solutions space in the initial search stages. |
| first_indexed | 2024-03-06T11:57:34Z |
| format | Conference or Workshop Item |
| id | UMPir10699 |
| institution | Universiti Malaysia Pahang |
| language | English English |
| last_indexed | 2024-03-06T11:57:34Z |
| publishDate | 2015 |
| record_format | dspace |
| spelling | UMPir106992018-03-12T03:04:11Z http://umpir.ump.edu.my/id/eprint/10699/ A Modified ACO-based Search Algorithm for Detecting Protein Functional Module From Protein Interaction Network Jamaludin, Sallim Rozlina, Mohamed Roslina, Abd Hamid QA76 Computer software Recent high-throughput experiments have generated protein-protein interaction data on a genomic scale, yielding the complete protein-protein interaction network for several organisms. Various graph clustering algorithms have been applied to protein interaction networks for detecting protein functional modules. Although the previous algorithms are scalable and robust, their accuracy is still limited because of the complex connectivity found in protein interaction networks. The Ant Colony Optimization (ACO) Algorithm has been adapted for the protein functional module detection by modeling the problem as an optimization problem. The adapted ACO (ACO-PFMDA) has obtained feasible solution but not as magnificent as those reported in the literature. Some shortcomings were identified and addressed by proposing a Modified Ant Colony Optimization Algorithm (ACO-PFMDM), which introduces two new scheme for controlling the two main parameters of ACO to solve PFMDP. Experiments on one popular benchmark dataset namely "Saccharomyces cerevisiae" which taken from two popular databases DIP and MIPS has been performed. The experimental result have proved that ACO-PFMDM have improved the overall performance of protein functional module detection. The search process of ACO-PFMDM has converged effectively compared to some state-of-art algorithms. Moreover, the proposed dynamic update of the heuristic parameters based on entropy has generated high quality tours and it can guide ants toward the effective solutions space in the initial search stages. 2015 Conference or Workshop Item PeerReviewed application/pdf en http://umpir.ump.edu.my/id/eprint/10699/1/A%20Modified%20ACO-based%20Search%20Algorithm%20for%20Detecting%20Protein%20Functional%20Module%20From%20Protein%20Interaction%20Network.pdf application/pdf en http://umpir.ump.edu.my/id/eprint/10699/7/fskkp-2015-jamaludin-Modified%20ACO.pdf Jamaludin, Sallim and Rozlina, Mohamed and Roslina, Abd Hamid (2015) A Modified ACO-based Search Algorithm for Detecting Protein Functional Module From Protein Interaction Network. In: International Conference on Computer, Communication and Information Sciences, and Engineering (ICCCISE 2015) , 26-27 Jan 2015 , Jeddah, Saudi Arabia. . (Unpublished) (Unpublished) |
| spellingShingle | QA76 Computer software Jamaludin, Sallim Rozlina, Mohamed Roslina, Abd Hamid A Modified ACO-based Search Algorithm for Detecting Protein Functional Module From Protein Interaction Network |
| title | A Modified ACO-based Search Algorithm for Detecting Protein Functional Module From Protein Interaction Network |
| title_full | A Modified ACO-based Search Algorithm for Detecting Protein Functional Module From Protein Interaction Network |
| title_fullStr | A Modified ACO-based Search Algorithm for Detecting Protein Functional Module From Protein Interaction Network |
| title_full_unstemmed | A Modified ACO-based Search Algorithm for Detecting Protein Functional Module From Protein Interaction Network |
| title_short | A Modified ACO-based Search Algorithm for Detecting Protein Functional Module From Protein Interaction Network |
| title_sort | modified aco based search algorithm for detecting protein functional module from protein interaction network |
| topic | QA76 Computer software |
| url | http://umpir.ump.edu.my/id/eprint/10699/1/A%20Modified%20ACO-based%20Search%20Algorithm%20for%20Detecting%20Protein%20Functional%20Module%20From%20Protein%20Interaction%20Network.pdf http://umpir.ump.edu.my/id/eprint/10699/7/fskkp-2015-jamaludin-Modified%20ACO.pdf |
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