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Kernel Methods, Pattern Analysis and Computational Biology (KEPACO)

The KEPACO group develops machine learning methods, models and tools for data science, in particular computational metabolomics. The methodological backbone of the group is formed by kernel methods and regularized learning. The group particularly focusses in learning with multiple and structured targets, multiple views and ensembles. Applications of interest include metabolomics, biomedicine, pharmacology and synthetic biology.

See overview of KEPACO research (in PDF)


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    Personnel and contact information

    The KEPACO group is located at the Department of Computer Science at the School of Science of Aalto University. We also belong to the Helsinki Institute for Information Technology.

    Contact information and how to get to CS department in Aalto University Otaniemi Campus


    Research projects

    • Biodesign - Virtual Laboratory for Enzyme Design, Jane and Aatos Erkko Foundation grant 2023-2027
    • MASF - Machine Learning for Systems Pharmacology. Academy of Finland grant 2021-2025
    • AIB - Artificial intelligence for interaction prediction in biomedicine, Academy of finland grant 2022-2024
    • MAGITICS - MAchine learning for diGItal diagnosTICS of antimicrobial resistance, JPI/Academy of Finland grant, 2020-2023

    Teaching 2021-23

    • CS-E4710 Machine Learning: Supervised Methods, Autumn 2022
    • CS-E4880 Machine Learning in Bioinformatics, Spring 2023


    Please find our software in GitHub page github.com/aalto-ics-kepaco.


    Selected and recent publications

    Visitors and Alumni

    Visitors to the group

    • 2023-24: Prof. Elena Casiraghi, Università degli Studi di Milano
    • 2023: Elina Francovic-Fontaine, PhD student, Laval University
    • 2023: Indumathi P, PhD student, IIT Madras
    • 2023: Golsar Fatemeh Abbasi, PhD student, University of Tehran
    • 2020: Prof. Cecile Capponi, Aix-Marseille Universite
    • 2019: Prof. Sahely Bhadra, IIT Palakkad, India, Dr. Kai Dührkop, Friedrich-Schiller University Jena
    • 2019: Dr. Luc Motte, Telecom Paris
    • 2018: Dr. Christina Leslie, Memorial Sloan Kettering Cancer Center, USA
    • 2017: Prof. Francois Laviolette, Laval University, Canada; Prof. Sebastian Boecker, Friedrich-Schiller University of Jena
    • 2016: Prof. Sebastian Boecker, Dr. Tim White, Marcus Ludwig, Kai Duehrkop, Friedrich-Schiller University Jena
    • 2015: Prof. Giorgio Valentini, Università degli Studi di Milano
    • 2013: Prof. Sebastian Boecker, Friedrich-Schiller University Jena


    • Dr. Taneli Pusa, post-doc, 2021-2024
    • Dr. Eric Bach, PhD 2023, now data scientist at Elisa (Linkedin)
    • Dr. Maryam Sabzevari, post-doc, 2018-2022, now at Nokia Bell Labs (Linkedin)
    • Dr. Viivi Uurtio, PhD 2020, now data scientist at Elisa (Linkedin)
    • Dr. Anna Cichonska, PhD 2018, moved to Nightingale Health (ResearchGate)
    • Dr. Celine Brouard, postdoc 2014-2018, moved to INRA Tolouse (ResearchGate)
    • Dr. Huibin Shen, PhD 2017, now at Amazon Berlin (LinkedIn)
    • Dr. Sahely Bhadra, post-doc, 2014-2016, now Assistant professor at IIT Palakkad (LinkedIn)
    • Dr. Elena Czeizler, research fellow, 2013-16, at Varian Medical Systems (LinkedIn )
    • Dr. Hongyu Su, PhD 2015, now at Nordea Bank (LinkedIn)
    • Dr. Jana Kludas, post-doc 2012-2015 (ResearchGate)
    • Dr. Jefrey Lijffijt, PhD 2013 (LinkedIn)
    • Dr. Markus Heinonen, PhD 2013, currently at CSB group, Aalto University (LinkedIn)
    • Dr. Esa Pitkänen, PhD 2010, currently at FIMM (LinkedIn)
    • Dr. Ari Rantanen, PhD 2006, currently at Tieto Corp (LinkedIn)

    Former students and interns

    • Ellimari Paunio, MSc 2023, currently at CSC - IT Center for Science
    • Luc Motte, PhD 2023, Telecom Paris
    • Amandine Grosfils, MSc 2021
    • Minna Oksanen, MSc 2021
    • Wen Xiang, intern 2020
    • Santeri Mentu, MSc 2020
    • Antoine Moulin, intern 2019
    • Bugra Aker Yilmaz, intern 2019
    • Jane Douat, intern 2019
    • Heli Julkunen, MSc 2019
    • Vilma Jägerroos, MSc 2019
    • Tolou Shadbahr, MSc 2019
    • Antoine Basse, intern 2018 (with Telecom ParisTech)
    • Fabio Colella, research assistant 2018
    • Parisa Mapar, MSc 2018 (LinkedIn)
    • Zheyang Shen, research assistant 2017
    • Anton Mattsson, intern 2017 (LinkedIn)
    • Linh Nguyen, MSc 2017 (LinkedIn)
    • Mohamed Jabri, MSc 2017 (LinkedIn)
    • Jinmin Lei, MSc 2016
    • Maja Ilievska, MSc 2016 (LinkedIn)
    • Nicole Althermeler, MSc 2016 (LinkedIn)
    • Iitu Kuittinen, MSc 2015 (LinkedIn)
    • Clemens Westrup, intern 2013-15 (LinkedIn)
    • Jian Hou, MSc 2014
    • Carlos Maycas Nadal, BSc 2014 (LinkedIn)
    • Fitsum Tamene, MSc 2013 (LinkedIn)
    • Yvonne Herrmann, MSc 2012 (LinkedIn)