EvoMiner: Frequent Subtree Mining in Phylogenetic Databases
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Computer Science—the theory, representation, processing, communication and use of information—is fundamentally transforming every aspect of human endeavor. The Department of Computer Science at Iowa State University advances computational and information sciences through; 1. educational and research programs within and beyond the university; 2. active engagement to help define national and international research, and 3. educational agendas, and sustained commitment to graduating leaders for academia, industry and government.
History
The Computer Science Department was officially established in 1969, with Robert Stewart serving as the founding Department Chair. Faculty were composed of joint appointments with Mathematics, Statistics, and Electrical Engineering. In 1969, the building which now houses the Computer Science department, then simply called the Computer Science building, was completed. Later it was named Atanasoff Hall. Throughout the 1980s to present, the department expanded and developed its teaching and research agendas to cover many areas of computing.
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1969-present
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- College of Liberal Arts and Sciences (parent college)
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Abstract
The problem of mining collections of trees to identify common patterns, called frequent subtrees (FSTs), arises often when trying to make sense of the results of phylogenetic analysis. FST mining generalizes the well-known maximum agreement subtree problem. Here we present EvoMiner, a new algorithm for mining frequent subtrees in collections of phylogenetic trees. EvoMiner is an Apriori-like level-wise method, which uses novel phylogeny-specific constant-time candidate generation scheme, an efficient fingerprinting-based technique for downward closure operation, and a lowest common ancestor based support counting step that requires neither costly subtree operations nor database traversal. As a result of these techniques, our algorithm achieves speed-ups of up to 100 times or more over phylominer, another algorithm for mining phylogenetic trees. EvoMiner can also work in vertical mining mode, to use less memory at the expense of speed.