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The present invention is directed to a method for inferring/estimating missing values in a data matrix d (q, r) having a plurality of rows and columns comprises the steps of organizing the columns of the data matrix d (q, r) into affinity folders of columns with similar data profile, organizing the rows of the data matrix d (q, r) into affinity folders of rows with similar data profile, forming a graph Q of augmented rows and a graph R of augmented columns by similarity or correlation of common entries; and expanding the data matrix d (q, r) in terms of an orthogonal basis of a graph QXR to infer/estimate the missing values in said data matrix d (q. r) on the diffusion geometry coordinates.