Comparing Hierarchical Data in External Memory

Abstract

We present an external-memory algorithm for computing a minimum-cost edit script between two rooted, ordered, labeled trees. The I/O, RAM, and CPU costs of our algorithm are, respectively, 4 7 5, 6, and 1 5, where and are the input tree sizes, is the block size,, and . This algorithm can make effective use of surplus RAM capacity to quadratically reduce I/O cost. We extend to trees the commonly used mapping from sequence comparison problems to shortest-path problems in edit graphs.