Research Output per year
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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Network
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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 journal › Article › Scientific › peer-review
Open Access
File
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 journal › Article › Scientific › peer-review
Open Access
File
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 proceeding › Conference contribution › Scientific › peer-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 journal › Article › Scientific › peer-review
Open Access
File
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 proceeding › Chapter › Scientific › peer-review
Projects
Machine learning for digItal diagnostics of antimicrobial resistance
Rousu, J., Huusari, R. & Xiang, W.
01/01/2020 → 31/12/2022
Project: Academy of Finland: Other research funding
Machine Learning for Computational Metabolomics
Rousu, J., Bach, E., Brouard, C., Sabzevari, M. & Huusari, R.
01/09/2017 → 31/08/2021
Project: Academy of Finland: Other research funding
AI4SynBio: Artificial Intelligence for SynBio Powerhouse
01/07/2018 → 31/12/2019
Project: Other external funding: Other public funding
Tensor Learning for Biomedicine
Rousu, J., Mapar, P., Uurtio, V., Shadbahr, T., Sabzevari, M. & Julkunen, H.
01/01/2018 → 31/12/2019
Project: Academy of Finland: Other research funding
Data-Driven Support for Digital Health
Rousu, J. & Rinta-Koski, O.
01/01/2016 → 31/12/2017
Project: Academy of Finland: Other research funding
Datasets
CamOptimus
Cankorur-Cetinkaya, A. (Contributor), Apollo - University of Cambridge Repository , 1 Jan 2016
DOI: 10.17863/cam.10257, https://www.repository.cam.ac.uk/handle/1810/265930
Dataset
Critical Assessment of Small Molecule Identification 2016: automated methods
Schymanski, E. L. (Contributor), 1 Jan 2017
DOI: 10.6084/m9.figshare.c.3727522.v1, https://figshare.com/collections/Critical_Assessment_of_Small_Molecule_Identification_2016_automated_methods/3727522/1
Dataset
Data Used In "Fast Metabolite Identification With Input Output Kernel Regression"
Brouard, C. (Contributor), 1 Jan 2017
DOI: 10.5281/zenodo.804241, https://zenodo.org/record/804241
Dataset
Data Used In "Fast Metabolite Identification With Input Output Kernel Regression"
Brouard, C. (Contributor), 1 Jan 2017
DOI: 10.5281/zenodo.804240, https://zenodo.org/record/804240
Dataset
Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy
Honeyborne, I. (Contributor), 1 Jan 2016
DOI: 10.6084/m9.figshare.c.3628568.v1, https://figshare.com/collections/Profiling_persistent_tubercule_bacilli_from_patient_sputa_during_therapy_predicts_early_drug_efficacy/3628568/1
Dataset
Prizes
Best paper award, International Conference on Bioinformatics Models, Methods and Algorithms, Valencia, Spain
Juho Rousu (Recipient), 2010
Prize: Award or honor granted for a specific work
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 types › Public or invited talk
University of Glasgow
Juho Rousu (Visiting researcher)8 Apr 2019 → 20 Jun 2019
Activity: Visiting an external institution types › Visit abroad
Machine Learning for Small Molecules
Juho Rousu (Speaker)15 Mar 2019
Activity: Talk or presentation types › Public or invited talk
Machine Learning for Small Molecules
Juho Rousu (Speaker)1 Feb 2019
Activity: Talk or presentation types › Public or invited talk
Predicting multi-view and structured data with kernel methods
Juho Rousu (Speaker)1 May 2019
Activity: Talk or presentation types › Public or invited talk
Press / Media
Principal Metabolic Flux Mode Analysis
06/02/2018
1 item of Media coverage
Press/Media: Media appearance
UEF researchers compete in semi-finals of Helsinki Challenge
19/01/2017
1 item of Media coverage
Press/Media: Media appearance
Big Data can help leukemia patients and prematurely born babies
16/01/2016
1 item of Media coverage
Press/Media: Media appearance
Search engine for more accurate and fast recognition of metabolites
01/10/2015
2 items of Media coverage
Press/Media: Media appearance