11/10/2014
Written by
Nathan Russell, Industrial Engineering senior, received the 2014 Gianturco Family Foundation Scholarship to attend the Individualizing Medicine Conference at Mayo Clinic, where he presented his collaborative research, titled: “Feature Interaction Detection with Random Forest in a High Dimensional Microbiome Setting.”
The Individualizing Medicine Conference was held from October 6-8 at Mayo Clinic in Rochester, Minn. The 2014 Conference was titled “From Promise to Practice” and concentrated on the idea of converting personalized medicine into practice. The event featured speakers, case studies, and sessions including a poster session where Russell’s collaborative research was presented.
The research is based on data received from new methods of sequencing technology. The focus of their efforts is to: “1) apply and refine analytical approaches for the selection and ranking of features from genetic, microbial, mass spectrometry and other relevant data, and 2) to develop interactive visualization methods that put these results in a biological context allowing the researcher to study the data effectively.”
They present the Extended Random Forest (ERF) approach to better deal with the challenges of biomarker discovery and data driven hypothesis generation that arise in ‘P>>N’ data sets. The ERF algorithm can be used with mixed data types and is described as a computationally intensive approach that estimates feature importance from an ensemble of classification or regression trees and then estimates the network structure of relevant features. Their research also presents how to best display and interpret the results from the Random Forest method.
“We developed a workflow of machine learning techniques and visualization tools to aid researchers in extracting insight from data that arise in multi-omics biology,” Russell said. He was responsible for developing computational tools for knowledge discovery and prediction from ‘P >> N’ data sets, and did this as a member of the Visual Analytics team at the National Center for Supercomputing Applications (NSCA).
“NCSA and the Mayo Illinois Alliance have been incredibly supportive of my ambitions and I consider myself very fortunate,” Russell said. The research was completed by a number of collaborators coming from NSCA and the Institute for Genomic Biology at University of Illinois at Urbana- Champaign, the Cancer Center at University of Illinois College of Medicine in Chicago, the Department of Urology at Northwestern University Feinberg School of Medicine in Chicago, and the Department of Medical Microbiology at Southern Illinois University in Springfield.
“We have many great collaborators and funding sources that made our work possible,” Russell said. “I am grateful to work alongside so many dedicated and talented scientists and engineers.”
The Mayo-Illinois Alliance for Technology Based Healthcare was formed in 2010 to provide educational, research, and entrepreneurial opportunities. The Gianturco Family Foundation Scholarship is offered by the Mayo-Illinois Alliance in memory of Dr. Cesare Gianturco, who was born in Italy in 1905 and was a radiologist who came to America to be a Fellow at Mayo Clinic from 1930-34. He taught at the University of Illinois, was a co-founder of Carle Hospital Clinic, and held numerous patents.
Russell described the conference as a great learning opportunity. “I gained exposure to a wide spectrum of challenges in both biomedical research and clinical applications,” he said. “I was humbled by the expertise and dedication of so many in attendance, as well as invigorated to tackle the great challenges ahead in health care. I plan to continue my research at the crossroads of computational analytics and biomedical research.”
Funding for the visual analytics portion of this project provided by ARI and NCSA at the University of Illinois at Urbana-Champaign.