New applications of data mining, such as in biology, bioinformatics, or sociology, are faced with large datasets structured as graphs. We introduce a novel class of tree-shaped patterns called tree queries, and present algorithms for mining tree queries and tree-query associations in a large data graph. Novel about our class of patterns is that they can contain constants, and can contain existential nodes which are not counted when determining the number of occurrences of the pattern in the data graph. Our algorithms have a number of provable optimality properties, which are based on the theory of conjunctive database queries. We propose a practical, database-oriented implementation in SQL, and show that the approach works in practice through experiments on data about food webs, protein interactions, and citation analysis.
In recent years, the problem of association rule mining in transactional data has been well studied. We propose to extend the discovery of classical association rules to the discovery of association rules of conjunctive queries in arbitrary relational data, inspired by the WARMR algorithm, developed by Dehaspe and Toivonen, that discovers association rules over a limited set of conjunctive queries. Conjunctive query evaluation in relational databases is well understood, but still poses some great challenges when approached from a discovery viewpoint in which patterns are generated and evaluated with respect to some well defined search space and pruning operators. Within KDD, the discovery of frequent patterns has been studied in a variety of settings. In its simplest form, known from association rule mining, the task is to discover all frequent item sets, i.e., all combinations of items that are found in a sufficient number of examples. We present algorithms for relational association rule discovery that are well-suited for exploratory data mining. They offer the flexibility required to experiment with examples more complex than feature vectors and patterns more complex than item sets. Discovery of frequent patterns has been studied in a variety of data mining settings. In its simplest form, known from association rule mining, the task is to discover all frequent itemsets, i.e., all combinations of items that are found in a sufficient number of examples. The fundamental task of association rule and frequent set discovery has been extended in various directions, allowing more useful patterns to be discovered with special purpose algorithms. We present WARMR, a general purpose inductive logic programming algorithm that addresses frequent query discovery: a very general DATALOG formulation of the frequent pattern discovery problem. The motivation for this novel approach is twofold. First, exploratory data mining is well supported: WARMR offers the flexibility required to experiment with standard and in particular novel settings not supported by special purpose algorithms. Also, application prototypes based on WARMR can be used as benchmarks in the comparison and evaluation of new special purpose algorithms. Second, the unified representation gives insight to the blurred picture of the frequent pattern discovery domain. Within the DATALOG formulation a number of dimensions appear that relink diverged settings. We demonstrate the frequent query approach and its use on two applications, one in alarm analysis, and one in a chemical toxicology domain.