Hierarchical decision tree induction in distributed genomic databases

Classification based on decision trees is one of the important problems in data mining and has applications in many fields. In recent years, database systems have become highly distributed, and distributed system paradigms, such as federated and peer-to-peer databases, are being adopted. In this paper, we consider the problem of inducing decision trees in a large distributed network of genomic databases. Our work is motivated by the existence of distributed databases in healthcare and in bioinformatics, and by the emergence of systems which automatically analyze these databases, and by the expectancy that these databases will soon contain large amounts of highly dimensional genomic data. Current decision tree algorithms require high communication bandwidth when executed on such data, which are large-scale distributed systems. We present an algorithm that sharply reduces the communication overhead by sending just a fraction of the statistical data. A fraction which is nevertheless sufficient to derive the exact same decision tree learned by a sequential learner on all the data-in the network. Extensive experiments using standard synthetic SNP data show that the algorithm utilizes the high dependency among attributes, typical to genomic data, to reduce communication overhead by up to 99 percent. Scalability tests show that the algorithm scales well with both the size of the data set, the dimensionality of the data, and the size of the distributed system.

1 Introduction

The analysis of large databases requires automation. Data mining tools have been shown to be useful for this task, in a variety of domains and architectures. It has recently been shown that data mining tools are extremely useful for the analysis of genomic data as well [1]. Since the number of genomic databases and the amount of data in them increases rapidly, there is a dire need for data mining tools designed specifically to target genomic data specifically.