Interview with Robert Techentin, Mayo Foundation on the usage of Cray XMT for Clinical Research

Robert (Bob) Techentin is Principal Software Engineer in the Special Purpose Processor Development Group at Mayo Foundation (Rochester, Minnesota). Robert is one of the first users of the new Cray XMT supercomputer specially designed to analyze large amounts of data.

The Mayo Clinic is a large clinical practice for medicine and is specialized on medical research and medical education. The new Cray XMT is being used to tackle different kinds of biomedical and bioinformatic problems that have been very challenging using traditional computer architectures.

In one research project Bob is going to work with the electronic medical records on a million of patients with millions of events. The researchers assume that there are secrets buried in the information that is very challenging to extract using traditional data mining techniques. One example is the discovery that weight loss drug Fen-phen can lead to heart valve damage. The relationship has accidentally been discovered by a Mayo clinic data analyst. A supercomputer could have helped researcher find earlier such a relationship.

There are other interesting and very valuable insights in the medical data that can not be mined out using a traditional relational data base management system. The Cray XMT is very good at graph analytics and can be used to find patterns that are very difficult to discover otherwise. The algorithms and the necessary data structures are being developed together with Cray and the Pacific Northwest National Laboratory. The first results of this common effort are expected in about one year from now.

At Mayo the Cray XMT is also being used to look at different ways to assemble the genomic sequences from the sequence data and to analyze the differences between individuals and the species references. Another possible application is free form text analysis. The clinic has a lot of free form text that is recorded as part of medical records that can be analyzed using the XMT to draw new conclusions.

CSCS is also deploying one of the first Cray XMT worldwide that is made available to research from different scientific fields.