Main Article Content
Abstract
This study examined graph clustering as a combinatorial optimization problem and evaluated the computational complexity of related algorithms. The main objective of this research was to analyze the relationship between multi-cluster objectives and modularity-based goals and to identify the limitations of modularity in graph clustering. This qualitative review study employed mathematical analyses and tests with various algorithms. The findings showed that graph clustering, due to its exponential search space, is an NP-hard problem, and modularity, despite its widespread use, suffers from a resolution limit and cannot accurately detect small-scale clusters. The results also highlighted the superiority of multi-cluster objectives in identifying more subtle structures. By confirming previous findings and offering new insights, this research provided a deeper understanding of optimization and graph clustering and suggested pathways to enhance existing algorithms.
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References
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- Bagon, S., & Galun, M. (2011). Large scale correlation clustering optimization. arXiv preprint. Retrieved from https://arxiv.org/abs/1112.2903
- Bansal, N., Blum, A., & Chawla, S. (2014). Correlation clustering. Machine Learining, 56, 89-113. Retrieved from https://link.springer.com/article/10.1023/b:mach.0000033116.57574.95
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- Ben-Dor, A., Shamir, R., & Yakhini, Z. (1999). Clustering gene expression patterns. Journal of computational biology, 281-297. https://doi.org/https://doi.org/10.1089/106652799318274
- Bhaskara, A., Daruki, S., & Venkatasubramanian, S. (2018). Sublinear algorithms for MAXCUT and correlation clustering. In Proceeding International Conference on Automata, Logic and Programming. Retrieved from https://arxiv.org/abs/1802.06992
- Bhattacharya, A., & De, R. K. (2008). Divisive correlation clustering algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles. Bioinformatics, 1359-1366. https://doi.org/10.1093/bioinformatics/btn133.
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- Buskirk, G., Fan, C., & Raichel, B. (2018). Metric violation distance: Hardness and approximation. In Proceeding of the 29th Annual ACM-SIAm Symposium on Discrete Algorithms, 196-209. Retrieved from https://epubs.siam.org/doi/abs/10.1137/1.9781611975031.14
- Charikar, M., Gupta, N., & Schwartz, R. (2017). Local guarantees in graph cuts and clustering. In International Conference on Integer Programming and Combinatorial Optimization, 136-147. Retrieved from https://link.springer.com/chapter/10.1007/978-3-319-59250-3_12
- Chawla, S., Makarychev, K., Schramm, T., & Yaroslavtsev, G. (2015). Near optimal lp rounding algorithm for correlationclustering on complete and complete k-partite graphs. In Proceedings of the 47th Annual ACM on symposium on Theory of COmputing, 219-228. Retrieved from https://dl.acm.org/doi/abs/10.1145/2746539.2746604
- Chierichetti, F., Dalvi, N., & Kumar, R. (2014). Correlation clustering in mapreduce. In Proceeding of the 20th ACM SIGKDD international conference on knowledge discovery and data mining, 641-650. Retrieved from https://dl.acm.org/doi/abs/10.1145/2623330.2623743
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- Chung, F. (1997). Spectral Graph Theory. American Mathematical Society.
- Coleman, T., Saunderson, J., & Wirth, A. (2008). A local-seach 2-approximation for 2 correlation-clustering. Springer Berlin Heidelberg, 308-319. Retrieved from https://link.springer.com/chapter/10.1007/978-3-540-87744-8_26
- Damaschke, P. (2009). Bounded-Degree Techniques Accelerate Some Parameterized Graph Algorithms. Springer Berlin Heidelberg, 98-109. https://doi.org/10.1007/978-3-642-11269-0 8.
- Dau, P. L., Puleo, G., & Milenkovic, O. (2017). Motif clustering and overlapping clustering for social network analysis. In IEEE INFOCOM 2017 - IEEE Conference on Computer Communications, 1-9. https://doi.org/10.1109/INFOCOM.2017.8056956.
- Delvenne, J., Yaliraki, S., & Barahona, M. (2010). Stability of graph communities across thime scales. Proceedings of the National Academy of Sciences, 12755-12760. Retrieved from https://www.pnas.org/doi/abs/10.1073/pnas.0903215107
- Demain, E., Dinh, T., LI, X., & Thai, M. (2015). Network clustering via maximizing modularity: Approximation algorithms and theoretical limits. In Proceeding of the 2015 IEEE International Xonference on Data Mining, 101-110. https://doi.org/10.1016/j.tcs.2006.05.008.
- Fan, C. (2009). A local graph partitioning algorithm using heat kernel pagerank. Algorithms and Models for the Web-Graph, 62-75. https://doi.org/10.1007/PL00012580.
- Fortuato, S., & Hric, D. (2016). Community dtection in networks: A user guide. Physics Reports. https://doi.org/10.1016/j.physrep.2009.11.002.
- Fukunaga, T. (2018). Lp-based pivoting algorithm for higher-order correlation clustering. Springer Ingernational Publishing. Retrieved from https://link.springer.com/article/10.1007/s10878-018-0354-y
- Gao, Y., Hare, D., & Nastos, J. (2013). The cluster deletion problem for cographs. Discrete Mathematics, 2763-2771. Retrieved from https://www.mdpi.com/2504-2289/7/2/70
- Gleich, D. F., Veldt, N., & Wirth, A. (2018). Correlation Clustering Generalized. In 29th International Symposium on Algorithms and Computatiion, 44. https://doi.org/10.4230/LIPIcs.ISAAC.2018.44.
- Hou, J. P., Emad, A., Puleo, G. J., Ma, J., & Milenkovic, O. (2016). A new correlation clustering method for cancer mutation analysis. Bioinformatics, 3717-3728. https://doi.org/10.1093/bioinformatics/btw546.
- Kim, S., Nowozin, S., Kohli, P., & Yoo, C. (2011). Higher-order correlation clustering for image segmentation. Advances in Neural Information Processing Systems, 24, 1530-1538. Retrieved from http://papers.nips.cc/paper/4406-higher-order-correlation-clustering-for-image-segmentation.pdf.
- Kloumann, I. M., Ugander, J., & Kleinberg, J. (2017). Block models and personalized pagerank. Proceedings of the National Academy of Sciences, 33-38. https://doi.org/10.1073/pnas.1611275114.
- Lange, J.-H., Karrenbauer, A., & Andres, B. (2018). Partial optimality and fast lower bounds for weighted correlation clustering. Proceedings of the 35th International Conference on Machine Learning, 2898-2907. Retrieved from proceedings.mlr.press/v80/lange18a.html.
- Lu, L. F. (2002). Connected components in random graphs with given expected degree sequences. Annuals of Combinatorics, 125-145. https://doi.org/10.1090/cbms/092.
- Neewman, M. (2016). Equivalence between modularity optimization and maximum likelihood methods for community detection. physics, 94-100. https://doi.org/10.1103/PhysRevE.94.052315.
- Newman, M. E. (2013). Community detection and graph partitioning. Europhysics Letters, 103-105. Retrieved from stacks.iop.org/0295-5075/103/i=2/a=28003.
- Pan, X., Papiliopoulos, D., Oymak, S., Recht, B., Ramchandran, K., & Jordan, M. (2015). Parallel correlation clustering on big graphs. Advances in Neural Information Processing systems, 82-90. Retrieved from papers.nips.cc/paper/5814-parallel-correlation-clustering-on-big-graphs.pdf.
- Puleo, G. J., & Milenkovic, O. (2018). Correlation clustering and biclustering with locally bounded errors. IEEE Transactions on Information Theory, 4105-4119. https://doi.org/10.1109/TIT.2018.2819696.
- Puleo, G., & Milenkovic, O. (2015). Correlation clustering with constrained cluster sizes and extended Weights bounds. SIAM Journal on Optimization, 1857-1872. https://doi.org/10.1137/140994198.
- Schulz, C., Bayer, S. K., Hess, C., Steiger, C., Teichmann, M., Jacob, J., . . . Hayrapetyan, S. (2016). Graph partitioning and graph clustering in theory and practice. Lecture notes at Institute for Theoretical Informatics Karlsruhe Institute of Technology. Retrieved from https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=98ec106b2757cfcaa27673765b58f9a14a580e6e
- Sharma, P., & Singh, M. (2016). Multi chromatics balls with relaxed criterion to detect larger communities in social networks. Smart Trends in Information Technology and Computer Communication, 196-203. Retrieved from https://link.springer.com/chapter/10.1007/978-981-10-3433-6_24
- Swoboda, P., & Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem. In 2017 IEEE Conference on Computer Vision and Pattern Recognition, 4990-4999. https://doi.org/10.1109/CVPR.2017.530.
- Veldt, N., Gleich, D., & Wirth, A. (2018). A correlation clustering framework for community detection. In Proceeding of the 2018 WWW Conference, 439-448. https://doi.org/10.1145/3178876.3186110.
- Veldt, N., Wirth, A. I., & Gleich, D. F. (2017). Correlation clustrering with low-rank matrices. In Proceedings og the 26th International Conference on World Wide Web, 1025-1034. https://doi.org/10.1145/3038912.3052586.
- Wang, D., Fountoulakis, K., Henzinger, M., Mahoney, M. W., & Rao, S. (2017). Capacity releasing diffusion for speed and locality. Proceedings of the 34th International Conference on Machine Learning, 3598-3607. Retrieved from proceedings.mlr.press/v70/wang17b.html.
- Wang, Y., Huang, H., Feng, C., & Liu, Z. (2015). Community detection based on minimum-cut partitioning. Web-Age Information Management, 57-69. Retrieved from https://link.springer.com/chapter/10.1007/978-3-319-21042-1_5
- Wirth, A., Veldt, N., Gleich, D., & Saunderson, J. (2018a). A projection method for metric-constrained optimization. arXiv preprint arXiv. Retrieved from https://arxiv.org/abs/1806.01678
- Yang, J., & Leskovec, J. (2015). Defining and evaluationg network communities based on ground-truth. Knowledge and Information Systems, 181-213. https://doi.org/10.1007/s10115-013-0693-z.
- Yu, L., & Ding, C. (2010). Network community discovery: Solving modularity clustering via normalized cut. In Proceeding of the Eighth Workshop on Mining and Learning with Graphs, 34-36. https://doi.org/10.1145/1830252.1830257.
- Zhou, H., Li, J., Zhang, F., & Cui, Y. (2017). A graph clustering method for commuinty detection in complex network. Physica A: Statistical Mechanics and its Applications, 551-562. https://doi.org/10.1016/j.physa.2016.11.015.
References
Abbe, E. (2018). Community detection and stochastic block models: Recent developments. Journal of Machine Learning Research, 18(177), 1-86. Retrieved from http://jmlr.org/papers/v18/16-480.html
Ahn, K. J., Cormode, G., Guha, S., McGregor, A., & Wirth, A. (2015). Correlation clustering in data streams. In Proceedings of the 32nd International Conference on International Conference on Machine Learning, 37, 2237-2246. Retrieved from http://dl.acm.org/citation.cfm?id=3045118.3045356.
Anava, Y., Avigdor-Elgrabli, N., & Gamzu, I. (2015). Improved theoretical and practical guarantees for chromatic correlation clustering. In Proceedings of the 24th International Conference on World Wide Web, WWW, 15, 55-65. https://doi.org/10.1145/2736277.2741629
Andersen, R., Chung, F., & Lang, K. (2006). Local graph partitioning using PageRank Vectors. InProcedddings of the 47th Annual IEEE Symposium on Foundations of Computer Science. Retrieved from http://www.math.ucsd.edu/~fan/wp/localpartition.pdf.
Arora, S., Rao, S., & Vaziani, U. (2009). Expander flows, geometric embeddings and graph partitioning. Journal of the ACM (JACM), 56(2). Retrieved from https://dl.acm.org/doi/abs/10.1145/1502793.1502794
Asteris, M., Kryillidis, A., Papailiopoulos, D., & Dimakis, A. G. (2016). Bipartite correlation clustering: Maximizing agreements. In Proceeding of the 19th International Conference on Artificial Intelligence and Statistics (AISTATS), 51. Retrieved from http://proceedings.mlr.press/v51/asteris16.html
Bader, D. A., Meyerhenke, H., Sanders, P., & Wagner, D. (2013). Graph partitioning and graph clustering (Vol. 588). American Mathematical Socity.
Bagon, S., & Galun, M. (2011). Large scale correlation clustering optimization. arXiv preprint. Retrieved from https://arxiv.org/abs/1112.2903
Bansal, N., Blum, A., & Chawla, S. (2014). Correlation clustering. Machine Learining, 56, 89-113. Retrieved from https://link.springer.com/article/10.1023/b:mach.0000033116.57574.95
Beier, T., Hamprecht, F. A., & Kappes, J. H. (2015). Fusion moves for correlation clustering. In Proceeding of the IEEE Conference on Computer Vision and Pattern Recognition, 3507-3516. Retrieved from http://openaccess.thecvf.com/content_cvpr_2015/html/Beier_Fusion_Moves_for_2015_CVPR_paper.html
Beier, T., Kroeger, T., Kappes, J. H., Kthe, U., & Hamprecht, F. A. (2014). Cut, glue, amp; cut: A fast, approximate solver for multicut partitioning. In 2014 IEEE Conference on Computer Vision and Pattern Recongnition, 73-80. https://doi.org/10.1109/CVPR.2014.17
Ben-Dor, A., Shamir, R., & Yakhini, Z. (1999). Clustering gene expression patterns. Journal of computational biology, 281-297. https://doi.org/https://doi.org/10.1089/106652799318274
Bhaskara, A., Daruki, S., & Venkatasubramanian, S. (2018). Sublinear algorithms for MAXCUT and correlation clustering. In Proceeding International Conference on Automata, Logic and Programming. Retrieved from https://arxiv.org/abs/1802.06992
Bhattacharya, A., & De, R. K. (2008). Divisive correlation clustering algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles. Bioinformatics, 1359-1366. https://doi.org/10.1093/bioinformatics/btn133.
Bocker, S., & Baumbach, J. (2013). Cluster editing. Springer Berlin Heidelberg, 33-44. Retrieved from https://link.springer.com/chapter/10.1007/978-3-642-39053-1_5
Bolla, M. (2011). Penalized versions of the newman-girvan modularity and their relation to normalized cuts and k-means clustering. phys. https://doi.org/10.1103/PhysRevE.84.
Bonchi, F., Gionis, A., Gullo, F., Tsourakakis, C. E., & Ukkonen, A. (2015). Chromatic correlation clustering. ACM Trans, 1-34. https://doi.org/10.1145/2728170.
Bonomo, F., Duran, G., Napoli, A., & Valencia-Pabon, M. (2015b). Complexity of the cluster deletion problem on subclasses of chordal graphs. Theoretical Computer Science, 59-69. Retrieved from https://www.sciencedirect.com/science/article/pii/S0304397515005800
Boonomo, F., Duran, G., Napoli, A., & Valencia-Pabon, M. (2015a). A one-to-one correspondence between potential solution of the cluster deletion problem and the minimum sum coloring problem, and its application to p4-sparse graphs. Information Processing Letters, 600-603. Retrieved from https://lipn.fr/~valenciapabon/papers/cluster-del-chordal-v7.pdf
Buskirk, G., Fan, C., & Raichel, B. (2018). Metric violation distance: Hardness and approximation. In Proceeding of the 29th Annual ACM-SIAm Symposium on Discrete Algorithms, 196-209. Retrieved from https://epubs.siam.org/doi/abs/10.1137/1.9781611975031.14
Charikar, M., Gupta, N., & Schwartz, R. (2017). Local guarantees in graph cuts and clustering. In International Conference on Integer Programming and Combinatorial Optimization, 136-147. Retrieved from https://link.springer.com/chapter/10.1007/978-3-319-59250-3_12
Chawla, S., Makarychev, K., Schramm, T., & Yaroslavtsev, G. (2015). Near optimal lp rounding algorithm for correlationclustering on complete and complete k-partite graphs. In Proceedings of the 47th Annual ACM on symposium on Theory of COmputing, 219-228. Retrieved from https://dl.acm.org/doi/abs/10.1145/2746539.2746604
Chierichetti, F., Dalvi, N., & Kumar, R. (2014). Correlation clustering in mapreduce. In Proceeding of the 20th ACM SIGKDD international conference on knowledge discovery and data mining, 641-650. Retrieved from https://dl.acm.org/doi/abs/10.1145/2623330.2623743
Christian, S. (2013). High Quality Graph Partitioning. PhD thesis, Karlsruhe Institute of Technology. Retrieved from https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=bb7389d0d8d4f8935e23b763c032eab20316b026
Chung, F. (1997). Spectral Graph Theory. American Mathematical Society.
Coleman, T., Saunderson, J., & Wirth, A. (2008). A local-seach 2-approximation for 2 correlation-clustering. Springer Berlin Heidelberg, 308-319. Retrieved from https://link.springer.com/chapter/10.1007/978-3-540-87744-8_26
Damaschke, P. (2009). Bounded-Degree Techniques Accelerate Some Parameterized Graph Algorithms. Springer Berlin Heidelberg, 98-109. https://doi.org/10.1007/978-3-642-11269-0 8.
Dau, P. L., Puleo, G., & Milenkovic, O. (2017). Motif clustering and overlapping clustering for social network analysis. In IEEE INFOCOM 2017 - IEEE Conference on Computer Communications, 1-9. https://doi.org/10.1109/INFOCOM.2017.8056956.
Delvenne, J., Yaliraki, S., & Barahona, M. (2010). Stability of graph communities across thime scales. Proceedings of the National Academy of Sciences, 12755-12760. Retrieved from https://www.pnas.org/doi/abs/10.1073/pnas.0903215107
Demain, E., Dinh, T., LI, X., & Thai, M. (2015). Network clustering via maximizing modularity: Approximation algorithms and theoretical limits. In Proceeding of the 2015 IEEE International Xonference on Data Mining, 101-110. https://doi.org/10.1016/j.tcs.2006.05.008.
Fan, C. (2009). A local graph partitioning algorithm using heat kernel pagerank. Algorithms and Models for the Web-Graph, 62-75. https://doi.org/10.1007/PL00012580.
Fortuato, S., & Hric, D. (2016). Community dtection in networks: A user guide. Physics Reports. https://doi.org/10.1016/j.physrep.2009.11.002.
Fukunaga, T. (2018). Lp-based pivoting algorithm for higher-order correlation clustering. Springer Ingernational Publishing. Retrieved from https://link.springer.com/article/10.1007/s10878-018-0354-y
Gao, Y., Hare, D., & Nastos, J. (2013). The cluster deletion problem for cographs. Discrete Mathematics, 2763-2771. Retrieved from https://www.mdpi.com/2504-2289/7/2/70
Gleich, D. F., Veldt, N., & Wirth, A. (2018). Correlation Clustering Generalized. In 29th International Symposium on Algorithms and Computatiion, 44. https://doi.org/10.4230/LIPIcs.ISAAC.2018.44.
Hou, J. P., Emad, A., Puleo, G. J., Ma, J., & Milenkovic, O. (2016). A new correlation clustering method for cancer mutation analysis. Bioinformatics, 3717-3728. https://doi.org/10.1093/bioinformatics/btw546.
Kim, S., Nowozin, S., Kohli, P., & Yoo, C. (2011). Higher-order correlation clustering for image segmentation. Advances in Neural Information Processing Systems, 24, 1530-1538. Retrieved from http://papers.nips.cc/paper/4406-higher-order-correlation-clustering-for-image-segmentation.pdf.
Kloumann, I. M., Ugander, J., & Kleinberg, J. (2017). Block models and personalized pagerank. Proceedings of the National Academy of Sciences, 33-38. https://doi.org/10.1073/pnas.1611275114.
Lange, J.-H., Karrenbauer, A., & Andres, B. (2018). Partial optimality and fast lower bounds for weighted correlation clustering. Proceedings of the 35th International Conference on Machine Learning, 2898-2907. Retrieved from proceedings.mlr.press/v80/lange18a.html.
Lu, L. F. (2002). Connected components in random graphs with given expected degree sequences. Annuals of Combinatorics, 125-145. https://doi.org/10.1090/cbms/092.
Neewman, M. (2016). Equivalence between modularity optimization and maximum likelihood methods for community detection. physics, 94-100. https://doi.org/10.1103/PhysRevE.94.052315.
Newman, M. E. (2013). Community detection and graph partitioning. Europhysics Letters, 103-105. Retrieved from stacks.iop.org/0295-5075/103/i=2/a=28003.
Pan, X., Papiliopoulos, D., Oymak, S., Recht, B., Ramchandran, K., & Jordan, M. (2015). Parallel correlation clustering on big graphs. Advances in Neural Information Processing systems, 82-90. Retrieved from papers.nips.cc/paper/5814-parallel-correlation-clustering-on-big-graphs.pdf.
Puleo, G. J., & Milenkovic, O. (2018). Correlation clustering and biclustering with locally bounded errors. IEEE Transactions on Information Theory, 4105-4119. https://doi.org/10.1109/TIT.2018.2819696.
Puleo, G., & Milenkovic, O. (2015). Correlation clustering with constrained cluster sizes and extended Weights bounds. SIAM Journal on Optimization, 1857-1872. https://doi.org/10.1137/140994198.
Schulz, C., Bayer, S. K., Hess, C., Steiger, C., Teichmann, M., Jacob, J., . . . Hayrapetyan, S. (2016). Graph partitioning and graph clustering in theory and practice. Lecture notes at Institute for Theoretical Informatics Karlsruhe Institute of Technology. Retrieved from https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=98ec106b2757cfcaa27673765b58f9a14a580e6e
Sharma, P., & Singh, M. (2016). Multi chromatics balls with relaxed criterion to detect larger communities in social networks. Smart Trends in Information Technology and Computer Communication, 196-203. Retrieved from https://link.springer.com/chapter/10.1007/978-981-10-3433-6_24
Swoboda, P., & Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem. In 2017 IEEE Conference on Computer Vision and Pattern Recognition, 4990-4999. https://doi.org/10.1109/CVPR.2017.530.
Veldt, N., Gleich, D., & Wirth, A. (2018). A correlation clustering framework for community detection. In Proceeding of the 2018 WWW Conference, 439-448. https://doi.org/10.1145/3178876.3186110.
Veldt, N., Wirth, A. I., & Gleich, D. F. (2017). Correlation clustrering with low-rank matrices. In Proceedings og the 26th International Conference on World Wide Web, 1025-1034. https://doi.org/10.1145/3038912.3052586.
Wang, D., Fountoulakis, K., Henzinger, M., Mahoney, M. W., & Rao, S. (2017). Capacity releasing diffusion for speed and locality. Proceedings of the 34th International Conference on Machine Learning, 3598-3607. Retrieved from proceedings.mlr.press/v70/wang17b.html.
Wang, Y., Huang, H., Feng, C., & Liu, Z. (2015). Community detection based on minimum-cut partitioning. Web-Age Information Management, 57-69. Retrieved from https://link.springer.com/chapter/10.1007/978-3-319-21042-1_5
Wirth, A., Veldt, N., Gleich, D., & Saunderson, J. (2018a). A projection method for metric-constrained optimization. arXiv preprint arXiv. Retrieved from https://arxiv.org/abs/1806.01678
Yang, J., & Leskovec, J. (2015). Defining and evaluationg network communities based on ground-truth. Knowledge and Information Systems, 181-213. https://doi.org/10.1007/s10115-013-0693-z.
Yu, L., & Ding, C. (2010). Network community discovery: Solving modularity clustering via normalized cut. In Proceeding of the Eighth Workshop on Mining and Learning with Graphs, 34-36. https://doi.org/10.1145/1830252.1830257.
Zhou, H., Li, J., Zhang, F., & Cui, Y. (2017). A graph clustering method for commuinty detection in complex network. Physica A: Statistical Mechanics and its Applications, 551-562. https://doi.org/10.1016/j.physa.2016.11.015.