Abstract

Several recent studies suggest that negative frequency-dependent selection (NFDS) acting through accessory genome loci is a strong force influencing the population evolution of major human bacterial pathogens. Such models can be fitted using likelihood- free inference for simulator-based statistical models, for example using the ELFI software (elfi.ai). Here we review some of these results and combine them with machine learning to introduce a practical method for optimizing vaccines by jointly using data from genomic population surveys and epidemiological studies. The results may lead to largely improved workflows to design new vaccines.

Bio

Jukka Corander is a professor at the Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Norway, also a professor at the Department of Mathematics and Statistics, University of Helsinki, Finland, and an honorary faculty member at the Wellcome Sanger Institute, Cambridge, UK. He has won two ERC grants, an ERC StG (2009-2014) from the mathematics and statistics panel and an ERC AdG (2017-2022) from the infection and immunity panel. He has published nearly 250 scientific peer-reviewed articles and his main research interests are microbial evolution and transmission modeling, statistical machine learning, population genomics, and inference algorithms. The statistical methods introduced by his research group have led to numerous discoveries on the evolution, resistance, virulence, and transmission of pathogenic bacteria and viruses.

Machine Learning Coffee seminars are weekly seminars organized by Finnish Center for Artificial Intelligence (FCAI) and are 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. Seminars will be held weekly on Mondays at 9:00-10:00. The location alternates between Aalto University and the University of Helsinki. At Aalto University, talks will be held in Konemiehentie 2, seminar room T5 and at the University of Helsinki in Kumpula, seminar room Exactum D122 (Gustaf Hällströmin katu 2b), unless otherwise noted. Talks will begin at 9:15 and coffee will be served from 9:00.