Date(s) - 17/04/2019
12:00 pm - 2:00 pm
School of Computing Science
We are delighted to welcome SICSA DVF Professor Juho Rousu, Professor of Computing Science at Aalto University, Finland to the the University of Glasgow to give a talk on Small Molecule Identification through Machine Learning: CSI:FingerID and beyond on Wednesday 17th April 2019.
Identification of small molecules from biological samples remains a major bottleneck in understanding the inner workings of biological cells and their environment. Machine learning on data from large public databases of tandem mass spectrometric data has transformed this field in recent years, with tools like CSI:FingerID, and CSI:IOKR demonstrating a step-change improvement in identification rates compared to previous approaches. In this presentation, I will give an overview of the technology inside these tools and review some recent developments in making use of additional information sources for improving the identification rates, in particular learning to predict the order of molecules eluting from liquid-chromatographic system.
Bach, E., Szedmak, S., Brouard, C., Böcker, S. and Rousu, J., 2018. Liquid-chromatography retention order prediction for metabolite identification. Bioinformatics, 34(17), pp.i875-i883.
Brouard, C., Bach, E., Böcker, S. and Rousu, J., 2017, November. Magnitude-preserving ranking for structured outputs. In Asian Conference on Machine Learning (pp. 407-422).
Brouard, C., Shen, H., Dührkop, K., d’Alché-Buc, F., Böcker, S. and Rousu, J., 2016. Fast metabolite identification with input output kernel regression. Bioinformatics, 32(12), pp.i28-i36.
Dührkop, K., Fleischauer, M., Ludwig, M., Aksenov, A.A., Melnik, A.V., Meusel, M., Dorrestein, P.C., Rousu, J. and Böcker, S., 2019. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nature Methods 16, pp- 299-302
Dührkop, K., Shen, H., Meusel, M., Rousu, J. and Böcker, S., 2015. Searching molecular structure databases with tandem mass spectra using CSI: FingerID. Proceedings of the National Academy of Sciences, 112(41), pp.12580-12585
Professor Rousu’s Short Bio:
Juho Rousu is a Professor of Computer Science at Aalto University, Finland. Rousu obtained his PhD in 2001 form University of Helsinki, while working at VTT Technical Centre of Finland. In 2003-2005 he was a Marie Curie Fellow at Royal Holloway University of London. In 2005-2011 he held Lecturer and Professor positions at University of Helsinki, before moving to Aalto University in 2012 where he leads a research group on Kernel Methods, Pattern Analysis and Computational Metabolomics (KEPACO). Rousu’s main research interest is in learning with multiple and structured targets, multiple views and ensembles, with methodological emphasis in regularised learning, kernels and sparsity, as well as efficient convex/non-convex optimisation methods. His applications of interest include metabolomics, biomedicine, pharmacology and synthetic biology