Laboratory of Computer and Information Science / Neural Networks Research Centre CIS Lab Helsinki University of Technology

Ilkka Huopaniemi

Ilkka Huopaniemi

Researcher, M.Sc. (Tech.)

Research

I work as a researcher in the Statistical Machine Learning And Bioinformatics group in the Transcendo project in which the overall objective of the project is to build a comprehensive modelling and biosimulation framework for studying human pathophysiology in silico, with the initial focus area of Diabetes.

My research interests are: data integration, translational modelling, multi-way analysis, Bayesian methods, metabolomics. I have a position in the FICS graduate school. I'm a board member (2009-2010, 2010-2011) in the Finnish Bioinformatics Society.

I am originally a physicist and I graduated in 2006 at the Department of Engineering Physics and Mathematics of HUT and moved to machine learning and bioinformatics.

Publications

Machine learning and bioinformatics

  • Laxman Yetukuri, Ilkka Huopaniemi, Artturi Koivuniemi, Marianna Maranghi, Anne Hiukka, Heli Nygren, Samuel Kaski, Marja-Riitta Taskinen, Ilpo Vattulainen, Matti Jauhiainene, Matej Orešič. 2011 High Density Lipoprotein Structural Changes and Drug Response in Lipidomic Profiles following the Long-Term Fenofibrate Therapy in the FIELD Substudy . PLoS ONE 6(8): e23589. (pdf)

  • Tommi Suvitaival, Ilkka Huopaniemi, Matej Orešič, and Samuel Kaski. Cross-species translation of multi-way biomarkers , In Timo Honkela et al., editors, Artificial Neural Networks and Machine Learning - ICANN 2011, volume 6791 of Lecture Notes in Computer Science, pages 209-216. Springer Berlin / Heidelberg, 2011

  • Ilkka Huopaniemi, Tommi Suvitaival, Matej Orešič, and Samuel Kaski. Graphical multi-way models , ECML PKDD 2010, 6321/2010, 538-553

  • Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Orešič, and Samuel Kaski. Multivariate multi-way analysis of multi-source data. Bioinformatics 2010 26: i391-i398 & ISMB 2010 (pdf)

  • Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Orešič, and Samuel Kaski. Multi-Way, Multi-View Learning. Talk in the NIPS 2009 workshop on Learning from Multiple Sources with Application to Robotics, December 12, Whistler, Canada. (pdf)

  • Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Orešič, and Samuel Kaski. Two-way analysis of high-dimensional collinear data. In Data Mining and Knowledge Discovery 19(2):261-276, 2009 (pdf)

    Journal publications in computational physics

    Dynamical scaling exponents for polymer translocation through a nanopore, K. Luo, S. Ollila, I. Huopaniemi, T. Ala-Nissila, P. Pomorski, M. Karttunen, S.-C. Ying and A. Bhattacharya, Phys. Rev. E 78, 050901 (2008),

    Polymer translocation through a nanopore under a pulling force, I. Huopaniemi, K. Luo, T. Ala-Nissila, and S.C. Ying, Phys. Rev. E 75, 061912 (2007).

    Langevin dynamics simulations of polymer translocation through nanopores, I. Huopaniemi, K. Luo, T. Ala-Nissila, and S.-C. Ying, J. Chem. Phys. 125, 124901 (2006)

    Polymer translocation through a nanopore under an applied external field, K. Luo, I. Huopaniemi, T. Ala-Nissila and S.-C. Ying, J. Chem. Phys. 124, 114704 (2006).

    Dynamics and kinetic roughening of interfaces in two-dimensional forced wetting, T. Laurila, C. Tong, I. Huopaniemi, S. Majaniemi, and T. Ala-Nissila, Eur. Phys. J. B 46, 553-561 (2005).

    Poster presentations

    Bioinformatics

    Leo Lahti, Olli-Pekka Huovilainen, Tommi Suvitaival, Ilkka Huopaniemi and Abhishek Tripathi, Probabilistic Tools for Dependency Modelling, ICML/MLOSS 2010

    MLSB 2009, poster presentation, 2-way analysis of high-dimensional metabolomics datasets

    ISMB/ECCB 2009, poster presentation, 2-way analysis of high-dimensional metabolomics datasets

    Brew 2008, Oral+paper presentation, Exploring cancer-related dependencies between several tissues

    Bioinformatics 2007, Poster presentation, Exploring cancer-related dependencies between several tissues

    Physics

    Physics days 2006, poster presentation, Langevin Dynamics Simulations of Polymer Translocation through Nanopores

    Physics days 2005, poster presentation, Dynamics of Interfaces and Kinetic Roughening in Forced Imbibition

    Teaching

    Course assistant at

    T-61.5050 High-Throughput Bioinformatics (2011)

    T-61.5050 High-Throughput Bioinformatics (2010)

    T-61.6070 Special course in bioinformatics I: Modeling of proteomics data (2008)

    Contact information

    Location
    Room A340
    Computer Science Building, 3rd floor
    Konemiehentie 2
    Mail
    Aalto University School of Science and Technology
    Department of Information and Computer Science
    P.O.Box 15400
    FIN-00076 Aalto, Finland
    FINLAND
    E-mail
    firstname.lastname at tkk.fi
    Homepage---Ilkka Huopaniemi
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