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Undergraduate Projects in the Application of Artificial Intelligence
to Chemistry. II Self-organizing Maps

Hugh Cartwright

Physical and Theoretical Chemistry Laboratory
Oxford University, South Parks Road, Oxford OX1 3QZ, England

hugh.cartwright@chem.ox.ac.uk

Published in The Chemical Educator, 2000, 5, 196-206.


Abstract

It is often necessary in science to identify samples which have features in common. For example, one might wish to find those NMR spectra in a large database which have similar patterns of resonances, or identify samples amongst a large number of specimens of river water which analysis shows have similar biochemical oxygen demand, heavy metals concentration, organochlorine content and so on.

The determination of relationships among samples is a task to which Artificial Intelligence is increasingly being applied. In this paper we investigate the Self-Organizing Map (SOM), whose role is to perform just this kind of task; in other words, to cluster data samples so as to reveal the relationships that exist among them. The self-organizing map is a method which, unusually, combines a mathematical foundation with an intuitive interpretation.

We will describe how a simple SOM operates, what kinds of data may be analysed using one, and how a computer program to run a SOM can be written by anyone - whether student or teacher - with modest programming skills. Portions of sample source code are included in this paper, and program listings for the examples which are discussed can be downloaded from the web site given at the end of the paper, which also can be used to see the maps in operation.