Jukka Corander, Professor of Statistics, University of Helsinki and University of Oslo
Learning of Ultra High-Dimensional Potts Models for Bacterial Population Genomics
Abstract: The potential for genome-wide modeling of epistasis has recently surfaced given the possibility of sequencing densely sampled populations and the emerging families of statistical interaction models. Direct coupling analysis (DCA) has earlier been shown to yield valuable predictions for single protein structures, and has recently been extended to genome-wide analysis of bacteria, identifying novel interactions in the co-evolution between resistance, virulence and core genome elements. However, earlier computational DCA methods have not been scalable to enable model fitting simultaneously to 10000-100000 polymorphisms, representing the amount of core genomic variation observed in analyses of many bacterial species. Here we introduce a novel inference method (SuperDCA) which employs a new scoring principle, efficient parallelization, optimization and filtering on phylogenetic information to achieve scalability for up to 100000 polymorphisms. Using two large population samples of Streptococcus pneumoniae, we demonstrate the ability of SuperDCA to make additional significant biological findings about this major human pathogen. We also show that our method can uncover signals of selection that are not detectable by genome-wide association analysis, even though our analysis does not require phenotypic measurements. SuperDCA thus holds considerable potential in building understanding about numerous organisms at a systems biological level.
Machine Learning Coffee seminars are weekly seminars held jointly by the Aalto University and the University of Helsinki. The seminars aim to gather people from different fields of science with interest in machine learning. Talks will begin at 9:15 am and porridge and coffee will be served from 9:00 am.
Next talks:
Nov 20, Otaniemi: Perttu Hämäläinen "Towards Intelligent Exergames"
Nov 27, Kumpula: Erik Aurell
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