An evaluation of the use of multidimensional scaling for understanding brain connectivity

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Abstract
A large amount of data is now available about the pattern of connections between brain regions. Computational methods are increasingly relevant for uncovering structure in such datasets. There has been recent interest in the use of non-metric multidimensional scaling (nmds) for such analysis, nmds produces a spatial representation of the ‘dissimilarities’ between a number of entities. Normally, it is applied to data matrices containing a large number of levels of dissimilarity, whereas for brain connectivity data there is a very small number. We address the suitability of nmds for this case. Systematic numerical studies are presented to evaluate the ability of this method to reconstruct known geometrical configurations from dissimilarity data possessing few levels. In this case there is a strong bias for nmds to produce annular configurations, whether or not such structure exists in the original data. For the case of a connectivity dataset derived from the primate cortical visual system, we demonstrate that great caution is needed in interpreting the resulting configuration. Application of an independent method that we developed also strongly suggests that the visual system nmds configuration is affected by an annular bias. We question the strength of support that an nmds analysis of the visual system data provides for the two streams view of visual processing.