Samuel Kaski

Director, Finnish Centre of Excellence in Computational Inference Research COIN, Aalto University and University of Helsinki
Academy Professor (research professor), 2016-2020
Professor of Computer Science, Aalto University

Contact information   My research group   Publications   Teaching   CV   Jobs

• Statistical machine learning and probabilistic modeling, with applications in:
• Information visualization
• Data analysis, data science
• Computational biology and medicine, bioinformatics
• Brain signal analysis
• Information retrieval, proactive interfaces, user modeling

• Tuukka Ruotsalo, Giulio Jacucci, Petri Myllymäki, and Samuel Kaski. Interactive intent modeling: information discovery beyond search. Communications of the ACM, 58(1):86-92, 2015. dl.acm.com ...
• Arto Klami, Seppo Virtanen, Eemeli Leppäaho, and Samuel Kaski. Group factor analysis. IEEE Transactions on Neural Networks and Learning Systems, 26(9):2136-2147, 2015. [Link] [Code] [PDF] [Preprint]
• Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, and Samuel Kaski. Toward computational cumulative biology by combining models of biological datasets. PLOS ONE, 9(11):e113053, 2014. dx.doi.org
• James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, Nicholas J Wang, Mukesh Bansal, Muhammad Ammad ud din, Petteri Hintsanen, Suleiman A Khan, John-Patrick Mpindi, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, NCI DREAM Community, James J Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W Gray, and Gustavo Stolovitzky. A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology, 32:1202-1212, 2014. dx.doi.org ...
• Mehmet Gönen and Samuel Kaski. Kernelized Bayesian matrix factorization. IEEE Transactions on Pattern Analysis and Machine Intelligence, 36:2047-2060, 2014. dx.doi.org 10.1109/TPAMI.2014.2313125. Matlab and R implementations available at http://research.ics.aalto.fi/mi/software/kbmf/.
• Pekka Marttinen, Matti Pirinen, Antti-Pekka Sarin, Jussi Gillberg, Johannes Kettunen, Ida Surakka, Antti J. Kangas, Pasi Soininen, Paul O'Reilly, Marika Kaakinen, Mika Kähönen, Terho Lehtimäki, Mika Ala-Korpela, Olli T. Raitakari, Veikko Salomaa, Marjo-Riitta Järvelin, Samuli Ripatti, and Samuel Kaski. Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression. Bioinformatics, 30(14):2026–34, 2014. bioinformatics.oxfordjournals.org ...
• Antti Ajanki, Mark Billinghurst, Hannes Gamper, Toni Järvenpää, Melih Kandemir, Samuel Kaski, Markus Koskela, Mikko Kurimo, Jorma Laaksonen, Kai Puolamäki, Teemu Ruokolainen, and Timo Tossavainen. An augmented reality interface to contextual information. Virtual Reality, 15(2-3):161–173, 2011. PDF [See also: dx.doi.org ...]
• Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Oresic, and Samuel Kaski. Multivariate multi-way analysis of multi-source data. Bioinformatics, 26:i391–i398, 2010. (ISMB 2010). PDF
• Jarkko Venna, Jaakko Peltonen, Kristian Nybo, Helena Aidos, and Samuel Kaski. Information retrieval perspective to nonlinear dimensionality reduction for data visualization. Journal of Machine Learning Research, 11:451–490, 2010. jmlr.csail.mit.edu ...
• José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, and Samuel Kaski. Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics, 25:i145–i153, 2009. (ISMB/ECCB 2009). PDF (896 kB) [See also: bioinformatics.oxfordjournals.org ...]