Quest for Quakes

QuakeFinder, an R&D project within Stellar Solutions Inc., has collected a decades worth of data along major faultlines using specialized sensors. The goal of this 2015 NASA challenge was to characterize pre-earthquake electromagnetic signals and develop a forecasting algorithm capable... Read more about Quest for Quakes

Dental Image Recognition System

In collaboration with Charite-Berlin Hospital, we are studying the drivers of variability in doctor performance when diagnosing ailments in dental x-ray images, and how multiple human-labelings of the same data can yield more reliable diagnoses of ailments. These studies aim to provide new insights on improving clinical care and... Read more about Dental Image Recognition System

Karim R. Lakhani, Andrew Hill, Po-Ru Loh, Ragu B. Bharadwaj, Pascal Pons, Jingbo Shang, Eva C. Guinan, Iain Kilty, and Scott Jelinsky. 2017. “Stepwise Distributed Open Innovation Contests for Software Development: Acceleration of Genome-Wide Association Analysis.” GigaScience, 6, 5, Pp. 1-10. Publisher's VersionAbstract

BACKGROUND: The association of differing genotypes with disease-related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low-cost genotyping and sequencing has made collecting large-scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies is being used to capture numerous new and complex phenotypic descriptors. As a result, genotype and phenotype datasets have grown exponentially. Genome-wide association studies associate genotypes and phenotypes using methods such as logistic regression. As existing tools for association analysis limit the efficiency by which value can be extracted from increasing volumes of data, there is a pressing need for new software tools that can accelerate association analyses on large genotype-phenotype datasets.

RESULTS: Using open innovation (OI) and contest-based crowdsourcing, the logistic regression analysis in a leading, community-standard genetics software package (PLINK 1.07) was substantially accelerated. OI allowed us to do this in <6 months by providing rapid access to highly skilled programmers with specialized, difficult-to-find skill sets. Through a crowd-based contest a combination of computational, numeric, and algorithmic approaches was identified that accelerated the logistic regression in PLINK 1.07 by 18- to 45-fold. Combining contest-derived logistic regression code with coarse-grained parallelization, multithreading, and associated changes to data initialization code further developed through distributed innovation, we achieved an end-to-end speedup of 591-fold for a data set size of 6678 subjects by 645 863 variants, compared to PLINK 1.07's logistic regression. This represents a reduction in run time from 4.8 hours to 29 seconds. Accelerated logistic regression code developed in this project has been incorporated into the PLINK2 project.

CONCLUSIONS: Using iterative competition-based OI, we have developed a new, faster implementation of logistic regression for genome-wide association studies analysis. We present lessons learned and recommendations on running a successful OI process for bioinformatics.