Several data analysis tools such as (kernel) canonical correlation analysis and various multi-view learning methods require paired observations in two data sets. We study the problem of inferring such pairing for data sets with no known one-to-one pairing. The pairing is found by an iterative algorithm that alternates between searching for feature representations that reveal statistical dependencies between the data sets, and finding the best pairs for the samples. The method is applied on pairing probe sets of two different microarray platforms.

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All authors belong to Helsinki Institute for Information Technology HIIT and Adaptive Informatics Research Centre. The work was partly supported by PASCAL2, EU Network of Excellence, and by a grant from University of Helsinki's Research Funds