SMART: unique splitting-while-merging framework for gene clustering.
Successful clustering algorithms are highly dependent on parameter settings. The clustering performance degrades significantly unless parameters are properly set, and yet, it is difficult to set these parameters a priori. To address this issue, in this paper, we propose a unique splitting-while-merg...
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0094141&type=printable |
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| author | Rui Fa David J Roberts Asoke K Nandi |
| author_facet | Rui Fa David J Roberts Asoke K Nandi |
| author_sort | Rui Fa |
| collection | DOAJ |
| description | Successful clustering algorithms are highly dependent on parameter settings. The clustering performance degrades significantly unless parameters are properly set, and yet, it is difficult to set these parameters a priori. To address this issue, in this paper, we propose a unique splitting-while-merging clustering framework, named "splitting merging awareness tactics" (SMART), which does not require any a priori knowledge of either the number of clusters or even the possible range of this number. Unlike existing self-splitting algorithms, which over-cluster the dataset to a large number of clusters and then merge some similar clusters, our framework has the ability to split and merge clusters automatically during the process and produces the the most reliable clustering results, by intrinsically integrating many clustering techniques and tasks. The SMART framework is implemented with two distinct clustering paradigms in two algorithms: competitive learning and finite mixture model. Nevertheless, within the proposed SMART framework, many other algorithms can be derived for different clustering paradigms. The minimum message length algorithm is integrated into the framework as the clustering selection criterion. The usefulness of the SMART framework and its algorithms is tested in demonstration datasets and simulated gene expression datasets. Moreover, two real microarray gene expression datasets are studied using this approach. Based on the performance of many metrics, all numerical results show that SMART is superior to compared existing self-splitting algorithms and traditional algorithms. Three main properties of the proposed SMART framework are summarized as: (1) needing no parameters dependent on the respective dataset or a priori knowledge about the datasets, (2) extendible to many different applications, (3) offering superior performance compared with counterpart algorithms. |
| format | Article |
| id | doaj-art-e54cba2b9a174311b903dcbc5604308d |
| institution | OA Journals |
| issn | 1932-6203 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-e54cba2b9a174311b903dcbc5604308d2025-08-20T02:34:10ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0194e9414110.1371/journal.pone.0094141SMART: unique splitting-while-merging framework for gene clustering.Rui FaDavid J RobertsAsoke K NandiSuccessful clustering algorithms are highly dependent on parameter settings. The clustering performance degrades significantly unless parameters are properly set, and yet, it is difficult to set these parameters a priori. To address this issue, in this paper, we propose a unique splitting-while-merging clustering framework, named "splitting merging awareness tactics" (SMART), which does not require any a priori knowledge of either the number of clusters or even the possible range of this number. Unlike existing self-splitting algorithms, which over-cluster the dataset to a large number of clusters and then merge some similar clusters, our framework has the ability to split and merge clusters automatically during the process and produces the the most reliable clustering results, by intrinsically integrating many clustering techniques and tasks. The SMART framework is implemented with two distinct clustering paradigms in two algorithms: competitive learning and finite mixture model. Nevertheless, within the proposed SMART framework, many other algorithms can be derived for different clustering paradigms. The minimum message length algorithm is integrated into the framework as the clustering selection criterion. The usefulness of the SMART framework and its algorithms is tested in demonstration datasets and simulated gene expression datasets. Moreover, two real microarray gene expression datasets are studied using this approach. Based on the performance of many metrics, all numerical results show that SMART is superior to compared existing self-splitting algorithms and traditional algorithms. Three main properties of the proposed SMART framework are summarized as: (1) needing no parameters dependent on the respective dataset or a priori knowledge about the datasets, (2) extendible to many different applications, (3) offering superior performance compared with counterpart algorithms.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0094141&type=printable |
| spellingShingle | Rui Fa David J Roberts Asoke K Nandi SMART: unique splitting-while-merging framework for gene clustering. PLoS ONE |
| title | SMART: unique splitting-while-merging framework for gene clustering. |
| title_full | SMART: unique splitting-while-merging framework for gene clustering. |
| title_fullStr | SMART: unique splitting-while-merging framework for gene clustering. |
| title_full_unstemmed | SMART: unique splitting-while-merging framework for gene clustering. |
| title_short | SMART: unique splitting-while-merging framework for gene clustering. |
| title_sort | smart unique splitting while merging framework for gene clustering |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0094141&type=printable |
| work_keys_str_mv | AT ruifa smartuniquesplittingwhilemergingframeworkforgeneclustering AT davidjroberts smartuniquesplittingwhilemergingframeworkforgeneclustering AT asokeknandi smartuniquesplittingwhilemergingframeworkforgeneclustering |