Clustering by compression

We present a new method for clustering based on compression. The method doesn't use subject-specific features or background knowledge, and works as follows: First, we determine a universal similarity distance, the normalized compression distance or NCD, computed from the lengths of compressed data files (singly and in pairwise concatenation). Second, we apply a hierarchical clustering method. The NCD is universal in that it is not restricted to a specific application area, and works across application area boundaries. A theoretical precursor, the normalized information distance, co-developed by one of the authors, is provably optimal but uses the non-computable notion of Kolmogorov complexity. We propose precise notions of similarity metric, normal compressor, and show that the NCD based on a normal compressor is a similarity metric that approximates universality. To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (binary tree) by a new quartet method and a fast heuristic to implement it. The method is implemented and available as public software, and is robust under choice of different compressors. To substantiate our claims of universality and robustness, we report evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors. In genomics we presented new evidence for major questions in Mammalian evolution, based on whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta hypothesis against the Theria hypothesis.Comment: LaTeX, 27 pages, 20 figure

Applying inspection to object-oriented software

The benefits of the object-oriented paradigmare widely cited. At the same time, inspection is deemed to be the most cost-effective means of detecting defects in software products. Why then, is there no published experience, let alone quantitative data, on the application of inspection to object-oriented systems? We describe the facilities of the object-oriented paradigm and the issues that these raise when inspecting object-oriented code. Several problems are caused by the disparity between the static code structure and its dynamic runtime behaviour. The large number of small methods in object-oriented systems can also cause problems. We then go on to describe three areas which may help mitigate problems found. Firstly, the use of various programming methods may assist in making object-oriented code easier to inspect. Secondly, improved program documentation can help the inspector understand the code which is under inspection. Finally, tool support can help the inspector to analyse the dynamic behaviour of the code. We conclude that while both the object-oriented paradigm and inspection provide excellent benefits on their own, combining the two may be a difficult exercise, requiring extensive support if it is to be successful