20062020

Research output per year

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Personal profile

Artistic and research interests

I am interested in developing principled machine learning methods, models and tools for computational and data science. My methods toolbox is primarily built on regularised learning, kernels and sparsity, as well as efficient convex/non-convex optimisation methods. My favourite topics include learning with multiple and structured targets, multiple views and ensembles. Applications of interest include metabolomics, biomedicine, pharmacology and synthetic biology.

Keywords

  • Algorithms
  • Metabolomics
  • Graph and network data
  • Structured prediction
  • Kernel methods
  • Machine learning

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Research Output

Bayesian metabolic flux analysis reveals intracellular flux couplings

Heinonen, M., Osmala, M., Mannerström, H., Wallenius, J., Kaski, S., Rousu, J. & Lähdesmäki, H., 15 Jul 2019, In : Bioinformatics. 35, 14, p. i548-i557 btz315.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
  • 86 Downloads (Pure)

    Improved Small Molecule Identification through Learning Combinations of Kernel Regression Models

    Brouard, C., Basse, A., d'Alche-Buc, F. & Rousu, J., Aug 2019, In : METABOLITES. 9, 8, 14 p., 160.

    Research output: Contribution to journalArticleScientificpeer-review

    Open Access
    File
    1 Citation (Scopus)
    117 Downloads (Pure)

    Large-Scale Sparse Kernel Canonical Correlation Analysis

    Uurtio, V., Bhadra, S. & Rousu, J., 2019, 36th International Conference on Machine Learning, ICML 2019. p. 6383-6391 9 p. (Proceedings of Machine Learning Research; vol. 97).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

    Open Access
    File
  • 7 Downloads (Pure)

    SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

    Dührkop, K., Fleischauer, M., Ludwig, M., Aksenov, A. A., Melnik, A. V., Meusel, M., Dorrestein, P. C., Rousu, J. & Böcker, S., 1 Apr 2019, In : Nature Methods. 16, 4, p. 299-302 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

    Open Access
    File
  • 58 Citations (Scopus)
    312 Downloads (Pure)

    Analysis of fluxomic experiments with principal metabolic flux mode analysis

    Bhadra, S. & Rousu, J., 1 Jan 2018, Methods in Molecular Biology. Mamitsuka, H. (ed.). p. 141-161 21 p. (Methods in Molecular Biology; vol. 1807).

    Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

  • Projects

    Machine learning for digItal diagnostics of antimicrobial resistance

    Rousu, J., Huusari, R. & Xiang, W.

    01/01/202031/12/2022

    Project: Academy of Finland: Other research funding

    Machine Learning for Computational Metabolomics

    Rousu, J., Bach, E., Brouard, C., Sabzevari, M. & Huusari, R.

    01/09/201731/08/2021

    Project: Academy of Finland: Other research funding

    AI4SynBio: Artificial Intelligence for SynBio Powerhouse

    Rousu, J. & Sabzevari, M.

    01/07/201831/12/2019

    Project: Other external funding: Other public funding

    Tensor Learning for Biomedicine

    Rousu, J., Mapar, P., Uurtio, V., Shadbahr, T., Sabzevari, M. & Julkunen, H.

    01/01/201831/12/2019

    Project: Academy of Finland: Other research funding

    Data-Driven Support for Digital Health

    Rousu, J. & Rinta-Koski, O.

    01/01/201631/12/2017

    Project: Academy of Finland: Other research funding

    Prizes

  • PhD thesis award

    Juho Rousu (Supervisor) & Huibin Shen (Recipient), 11 May 2018

    Prize: Award or honor granted for a specific work

  • Second place in Critical Assesment of Metabolite Identification (CASMI) contest 2016

    Juho Rousu (Recipient), Kai Duehrkop (Recipient), Sebastian Böcker (Recipient), Huibin Shen (Recipient) & Marvin Meusel (Recipient), 6 May 2016

    Prize: Invitation or ranking in competition

  • Semi-Finalist in Helsinki Challenge competition

    Juho Rousu (Recipient), 2017

    Prize: Invitation or ranking in competition

    Winner in Critical Assesment of Metabolite Identification (CASMI) contest 2016

    Juho Rousu (Recipient), Celine Brouard (Recipient), Huibin Shen (Recipient), Sebastian Böcker (Recipient) & Kai Duehrkop (Recipient), 6 May 2016

    Prize: Invitation or ranking in competition

  • Activities

    Sparse Non-linear Canonical Correlation Analysis

    Juho Rousu (Speaker)
    2 May 2019

    Activity: Talk or presentation typesPublic or invited talk

    University of Glasgow

    Juho Rousu (Visiting researcher)
    8 Apr 201920 Jun 2019

    Activity: Visiting an external institution typesVisit abroad

    Machine Learning for Small Molecules

    Juho Rousu (Speaker)
    15 Mar 2019

    Activity: Talk or presentation typesPublic or invited talk

    Machine Learning for Small Molecules

    Juho Rousu (Speaker)
    1 Feb 2019

    Activity: Talk or presentation typesPublic or invited talk

    Predicting multi-view and structured data with kernel methods

    Juho Rousu (Speaker)
    1 May 2019

    Activity: Talk or presentation typesPublic or invited talk

    Press / Media

    Principal Metabolic Flux Mode Analysis

    Juho Rousu

    06/02/2018

    1 item of Media coverage

    Press/Media: Media appearance

    UEF researchers compete in semi-finals of Helsinki Challenge

    Juho Rousu

    19/01/2017

    1 item of Media coverage

    Press/Media: Media appearance

    Big Data can help leukemia patients and prematurely born babies

    Juho Rousu

    16/01/2016

    1 item of Media coverage

    Press/Media: Media appearance

    Search engine for more accurate and fast recognition of metabolites

    Juho Rousu

    01/10/2015

    2 items of Media coverage

    Press/Media: Media appearance