A system for clustering a plurality of documents having input and output space data is disclosed that uses both input and output space criteria. The system can aggregate documents into clusters based on input and/or output space similarity measures, and then refine the clusters based on further input and/or output space similarity measures. Aggregation of documents into clusters can include forming a hierarchical tree based on the input and/or output space similarity measures where the hierarchical tree has a root node, branching into intermediate nodes, and branching into leaf nodes covering individual documents, where the hierarchical tree includes a leaf node for each document of the plurality of documents. The system can include forming a forest of sub-trees of the hierarchical tree based on cluster criteria. Textual and numeric similarity measures can be used depending on the type and distribution of data in the input and output spaces.