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A Soft Hierarchical Algorithm for the Clustering of Multiple Bioactive Chemical Compounds

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Bioinformatics Research and Development (BIRD 2007)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4414))

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Abstract

Most of the clustering methods used in the clustering of chemical structures such as Ward’s, Group Average, K- means and Jarvis-Patrick, are known as hard or crisp as they partition a dataset into strictly disjoint subsets; and thus are not suitable for the clustering of chemical structures exhibiting more than one activity. Although, fuzzy clustering algorithms such as fuzzy c-means provides an inherent mechanism for the clustering of overlapping structures (objects) but this potential of the fuzzy methods which comes from its fuzzy membership functions have not been utilized effectively. In this work a fuzzy hierarchical algorithm is developed which provides a mechanism not only to benefit from the fuzzy clustering process but also to get advantage of the multiple membership function of the fuzzy clustering. The algorithm divides each and every cluster, if its size is larger than a pre-determined threshold, into two sub clusters based on the membership values of each structure. A structure is assigned to one or both the clusters if its membership value is very high or very similar respectively. The performance of the algorithm is evaluated on two bench mark datasets and a large dataset of compound structures derived from MDL’s MDDR database. The results of the algorithm show significant improvement in comparison to a similar implementation of the hard c-means algorithm.

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Authors and Affiliations

  1. Faculty of Computer Science & Information Systems, Universiti Teknologi Malaysia, 81310 Skudai, Johor Darul Ta’zim, Malaysia

    Jehan Zeb Shah & Naomie bt Salim

Authors
  1. Jehan Zeb Shah
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  2. Naomie bt Salim
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Sepp Hochreiter Roland Wagner

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Shah, J.Z., Salim, N.b. (2007). A Soft Hierarchical Algorithm for the Clustering of Multiple Bioactive Chemical Compounds. In: Hochreiter, S., Wagner, R. (eds) Bioinformatics Research and Development. BIRD 2007. Lecture Notes in Computer Science(), vol 4414. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71233-6_12

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  • DOI: https://doi.org/10.1007/978-3-540-71233-6_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-71232-9

  • Online ISBN: 978-3-540-71233-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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