A mapping estimation apparatus includes a mapping adjuster. The mapping adjuster estimates mappings which correlate a plurality of subset data items with respective parts of universal set data including union of the plurality of subset data items based on the plurality of subset data items and the universal set data. The mapping adjuster estimates a mode of selecting a plurality of codomain data items from the universal set data and modes of mappings applied to the plurality of subset data items so as to have a maximum probability that data items obtained by selecting a plurality of codomain data items of which a subset of union is the universal set data from the universal set data and applying the mappings to the plurality of subset data items as domains will be respectively the plurality of codomain data items.