Some embodiments provide a method for defining structure for an unstructured document that includes a number of primitive elements that are defined in terms of their position in the document. The method identifies a pairwise grouping of nearest primitive elements. The method sorts the pairwise primitive elements based on an order from the closest to the furthest pairs. The method stores a single value that identifies which of the pairwise primitive elements are sufficiently far apart to form a partition. The method uses the stored value to identify and analyze the partitions in order to define structural elements for the document.