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The 13th International Conference on Knowledge Discovery and Data Mining

Dynamic hybrid clustering of bioinformatics by incorporating text mining and citation analysis

author: Frizo Janssens, Katholieke Universiteit Leuven

Description

To unravel the concept structure and dynamics of the bioinformatics field, we analyze a set of 7401 publications from the Web of Science and MEDLINE databases, publication years 1981–2004. For delineating this complex, interdisciplinary field, a novel bibliometric retrieval strategy is used. Given that the performance of unsupervised clustering and classification of scientific publications is significantly improved by deeply merging textual contents with the structure of the citation graph, we proceed with a hybrid clustering method based on Fisher’s inverse chi-square. The optimal number of clusters is determined by a compound semiautomatic strategy comprising a combination of  istancebased and stability-based methods. We also investigate the relationship between number of Latent Semantic Indexing factors, number of clusters, and clustering performance. The HITS and PageRank algorithms are used to determine representative publications in each cluster. Next, we develop a methodology for dynamic hybrid clustering of evolving bibliographic data sets. The same clustering methodology is applied to consecutive periods defined by time windows on the set, and in a subsequent phase chains are formed by matching and tracking clusters through time. Term networks for the eleven resulting cluster chains present the cognitive structure of the field. Finally, we provide a view on how much attention the bioinformatics community has devoted to the different subfields through time.

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Slides
0:03 Dynamic Hybrid Clustering of Bioinformatics by Incorporating Text Mining and Citation Analysis
0:21 Overview of the presentation
0:53 General context
1:42 Agglomerative hierarchical clustering
2:46 Indexing in Vector Space Model
3:37 Bibliometrics and network analysis
4:29 Hybrid (integrated) clustering
4:49 Hybrid clustering: intermediate integration
6:18 Weighted linear combination (linco)
7:20 Fisher’s inverse chi-square method (1)
7:42 Fisher’s inverse chi-square method (2)
8:53 Fisher’s inverse chi-square method (3)
9:26 Conclusions from previous research
10:21 Dynamic hybrid mapping of bioinformatics
10:53 Number of clusters and LSI factors
12:39 Number of clusters: stability diagram
13:02 Number of clusters: link-based Silhouette values
13:15 Dendrogram
13:41 slide 19
15:21 slide 20
16:10 Dynamics
17:11 Dynamic term networks
17:21 Conclusions (1)
18:05 Conclusions (2)

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