Knowledge representation and data mining for biological imaging

Wamiq M. Ahmed*

Purdue University Cytometry Laboratories, Bindley Bioscience Center, 1203 W. State Street, West Lafayette, IN 47907, USA. wahmed@flowcyt.cyto.purdue.edu

Proc LSS Comput Syst Bioinform Conf. August, 2008. Vol. 7, p. 311-314. Full-Text PDF

*To whom correspondence should be addressed.

Biological and pharmaceutical research relies heavily on microscopically imaging cell populations for understanding their structure and function. Much work has been done on automated analysis of biological images, but image analysis tools are generally focused only on extracting quantitative information for validating a particular hypothesis. Images contain much more information than is normally required for testing individual hypotheses. The lack of symbolic knowledge representation schemes for representing semantic image information and the absence of knowledge mining tools are the biggest obstacles in utilizing the full information content of these images. In this paper we first present a graph- based scheme for integrated representation of semantic biological knowledge contained in cellular images acquired in spatial, spectral, and temporal dimensions. We then present a spatio-temporal knowledge mining framework for extracting non-trivial and previously unknown association rules from image data sets. This mechanism can change the role of biological imaging from a tool used to validate hypotheses to one used for automatically generating new hypotheses. Results for an apoptosis screen are also presented.