Enlarged colour plots are provided in the Supplementary Material, which is available at http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/.

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We exploit the recent availability of a community reconstruction of the human metabolic network (‘Recon2’) to study how close in structural terms are marketed drugs to the nearest known metabolite(s) that Recon2 contains. While other encodings using different kinds of chemical fingerprints give greater differences, we find using the 166 Public MDL Molecular Access (MACCS) keys that 90 % of marketed drugs have a Tanimoto similarity of more than 0.5 to the (structurally) ‘nearest’ human metabolite. This suggests a ‘rule of 0.5’ mnemonic for assessing the metabolite-like properties that characterise successful, marketed drugs. Multiobjective clustering leads to a similar conclusion, while artificial (synthetic) structures are seen to be less human-metabolite-like. This ‘rule of 0.5’ may have considerable predictive value in chemical biology and drug discovery, and may represent a powerful filter for decision making processes.Electronic supplementary materialThe online version of this article (doi:10.1007/s11306-014-0733-z) contains supplementary material, which is available to authorized users.

Abstract-This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.

Ant-based clustering and sorting is a nature-inspired heuristic first introduced as a model for explaining two types of emergent behavior observed in real ant colonies. More recently, it has been applied in a data-mining context to perform both clustering and topographic mapping. Early work demonstrated some promising characteristics of the heuristic but did not extend to a rigorous investigation of its capabilities. We describe an improved version, called ATTA, incorporating adaptive, heterogeneous ants, a time-dependent transporting activity, and a method (for clustering applications) that transforms the spatial embedding produced by the algorithm into an explicit partitioning. ATTA is then subjected to the most rigorous experimental evaluation of an ant-based clustering and sorting algorithm undertaken to date: we compare its performance with standard techniques for clustering and topographic mapping using a set of analytical evaluation functions and a range of synthetic and real data collections. Our results demonstrate the ability of ant-based clustering and sorting to automatically identify the number of clusters inherent in a data collection, and to produce high quality solutions; indeed, we show that it is particularly robust for clusters of differing sizes and for overlapping clusters. The results obtained for topographic mapping are, however, disappointing. We provide evidence that the solutions generated by the ant algorithm are barely topolog y-preserving, and we explain in detail why results have -in spite of this -been misinterpreted (much more positively) in previous research.