Laboratory of Computer and Information Science / Neural Networks Research Centre CIS Lab Helsinki University of Technology
[an error occurred while processing this directive]

Jarkko Salojärvi

I am currently doing bioinformatics research at University of Helsinki at the plant stress research group and at Willem de Vos research group at Veterinary Microbiology and Epidemiology.

Until August 2009, I was a lecturing researcher (pro tem) at the Statistical Machine Learning and Bioinformatics research group in the Department of Information and Computer Science of Helsinki University of Technology.
Part of the duties as lecturer was being the academic coordinator (on behalf of TKK) of the Master's Degree Programme in Bioinformatics (MBI), jointly organized with University of Helsinki. Questions regarding those topics can be directed to my successor, Fabien Hoti. The MBI programme forms a part of the new Erasmus Mundus Master's Course in Systems Biology (euSYSBIO), a joint programme with KTH at Stockholm and IST at Lisbon.

My earlier research projects include the Proactive Information Retrieval by Adaptive Models of Users' Attention and Interests (PRIMA), and WEBSOM.

Jarkko Salojarvi

Teaching

Lecturer (Aalto; 2009,2010): T-61.5050: High-throughput bioinformatics.

Lecturer (UH; 2010): Transcriptomics and Resequencing.

Co-lecturer (UH; 2008,2009) at: 525021 Advanced Computer Methods for Biologists.

Seminar course (Aalto/TKK, 2008): T-61.6080: High-throughput sequencing and its applications.


List of publications

M. Wrzaczek, M. Brosche, J. Salojärvi, S. Kangasjärvi, N. Idänheimo, S. Mersmann, S. Robatzek, S. Karpinski, B. Karpinska and J. Kangasjärvi.
Dual transcriptional regulation of the CRK/DUF26 group of Receptor-like protein kinases by ozone and plant hormones in Arabidopsis.
Accepted to BMC Plant Biology.

P. Jaspers, K. Overmyer, M. Wrzaczek, J. P. Vainonen, T. Blomster, J. Salojärvi, R. A. Reddy and J. Kangasjärvi.
The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants.
Accepted to BMC Genomics.

T. Vahisalu, I. Puzorjova, M. Brosche, E. Valk, M. Lepiku, H. Moldau, P. Pechter, Y-S Wang, O. Lindgren, J. Salojärvi, M. Loog, J. Kangasjärvi and H. Kollist
Ozone-triggered rapid stomatal response involves production of reactive oxygen species and is controlled by SLAC1 and OST1.
Accepted to The Plant Journal.

Pinja Jaspers, Tiina Blomster, Mikael Brosché, Jarkko Salojärvi, Reetta Ahlfors, Julia Vainonen, Ramesha Reddy, Richard Immink, Gerco Angenent, Franziska Turck, Kirk Overmyer, and Jaakko Kangasjärvi
Unequally Redundant RCD1 and SRO1 Mediate Stress and Developmental Responses and Interact with Transcription Factors.
The Plant Journal.60(2):268-279, 2009.

Jarkko Salojärvi.
Inferring Relevance from Eye Movements with Wrong Models.
PhD Thesis, Helsinki University of Technology, Faculty of Information and Natural Sciences, 2008.

Jaana Simola, Jarkko Salojärvi, and Ilpo Kojo.
Using Hidden Markov Model to Uncover Processing States from Eye Movements in Information Search Tasks.
Cognitive Systems Research,9:237-251, 2008.
(DOI).

Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski.
On Discriminative Joint Density Modeling.
In: Gama, Camacho, Brazdil, Jorge, Torgo (eds.): Machine Learning: ECML 2005.
(Proceedings of 16th European Conference on Machine Learning),
Lecture Notes in Artificial Intelligence 3270, pages 341-352. Springer-Verlag, Berlin, Germany. 2005.
(abstract,pdf,DOI).

Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski.
Expectation Maximization Algorithms for Conditional Likelihoods.
In: De Raedt and Wrobel (eds.): Proceedings of the 22nd International Conference on Machine Learning (ICML 2005),
pages 753-760. ACM press, New York, USA. 2005.
(abstract,pdf).

Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski.
Implicit Relevance Feedback from Eye Movements.
In: Duch, Kacprzyk, Oja, Zadrozny (eds.): Artificial Neural Networks: Biological Inspirations - ICANN 2005.
Proceedings, Part I. Lecture Notes in Computer Science 3696, pages 513 - 518. Springer-Verlag, Berlin, Germany. 2005.
(abstract,pdf,DOI).

Kai Puolamäki, Jarkko Salojärvi, Eerika Savia, Jaana Simola, and Samuel Kaski.
Combining Eye Movements and Collaborative Filtering for Proactive Information Retrieval.
In: Marchionini, Moffat, Tait, Baeza-Yates, Ziviani (eds.):
SIGIR 2005: Proceedings of the 28th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval.
pages 146-153. ACM press, New York, USA. 2005.
(abstract,pdf,DOI).

Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski.
Relevance Feedback from Eye Movements for Proactive Information Retrieval.
In: Workshop on Processing Sensory Information for Proactive Systems (PSIPS 2004), Oulu Finland, June 14-15, 2004.
(abstract,pdf).

Jarkko Salojärvi, Ilpo Kojo, Jaana Simola and Samuel Kaski.
Can Relevance Be Inferred from Eye Movements in Information Retrieval?
In Proceedings of the Workshop on Self-Organizing Maps (WSOM'03), Hibikino, Japan, 11-14 September 2003, pages 261-266.
(abstract,pdf).

Jarkko Salojärvi, Samuel Kaski and Janne Sinkkonen.
Discriminative Clustering in Fisher Metrics.
In: O. Kaynak, E. Alpaydin, E. Oja, L. Xu, (eds.): Artificial Neural Networks and Neural Information Processing - Supplementary proceedings ICANN/ICONIP 2003, Istanbul, Turkey, June 2003, pages 161-164.
(abstract,ps).

Jarkko Salojärvi and Samuel Kaski.
Mixture Density from Autonomous Experts.
International Journal of Knowledge-Based Intelligent Engineering Systems, 6:48-55, 2002.
(abstract,ps).

Samuel Kaski and Jarkko Salojärvi.
Generative Mixture Modeling by Autonomous Estimators.
In: N. Baba, L. C. Jain and R. J. Howlett, (eds.): Knowledge-Based Intelligent Information Engineering Systems & Allied Technologies,
Proceedings of KES'2001, 1:250-254, IOS Press, Amsterdam, 2001.

Teuvo Kohonen, Samuel Kaski, Krista Lagus, Jarkko Salojärvi, Jukka Honkela, Vesa Paatero, and Antti Saarela.
Self Organization of a Massive Document Collection.
IEEE Transactions on Neural Networks, 11:574-585, 2000.

Teuvo Kohonen, Samuel Kaski, Krista Lagus, Jarkko Salojärvi, Jukka Honkela, Vesa Paatero, and Antti Saarela.
Self Organization of a Massive Text Document Collection.
In: Erkki Oja and Samuel Kaski, editors, Kohonen Maps, pages 171-182. Elsevier, Amsterdam, 1999.

Teuvo Kohonen, Samuel Kaski, Harri Lappalainen, and Jarkko Salojärvi.
The Adaptive-Subspace Self-Organizing Map (ASSOM).
In: Proceedings of WSOM'97, Workshop on Self-Organizing Maps, Espoo, Finland,June 4-6,
pages 191-196. Helsinki University of Technology, Neural Networks Research Centre, Espoo, Finland, 1997.

H. Alles, A. V. Babkin, P.J. Hakonen, J. P. Ruutu, J. T. Salojärvi, and J. P. Saramäki.
Spreading of superfluid 4He on MgF2.
Journal of Low Temperature Physics 102(1):21-29, 1996.

Non-refereed publications:

Jarkko Salojärvi, Kai Puolamäki, Eerika Savia, and Samuel Kaski.
Inference with Discriminative Posterior.
Manuscript, 2008. (pdf available at arXiv).

Jarkko Salojärvi, Kai Puolamäki, Jaana Simola, Lauri Kovanen, Ilpo Kojo, and Samuel Kaski.
Inferring Relevance from Eye Movements: Feature Extraction.
Tech. Rep. A82, Helsinki University of Technology, Publications in Computer and Information Science, Espoo, Finland, 2005.
(abstract,pdf).

Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski.
Relevance Feedback from Eye Movements for Proactive Information Retrieval.
Tech. Rep. A73, Helsinki University of Technology, Publications in Computer and Information Science, Espoo, Finland, 2003.
(a poster presented at Machine Learning Meets the User Interface (MLUI'03) workshop at NIPS'03, tech.rep. published in PSIPS 2004).

Jarkko Salojärvi. Implementation of New Efficient Document Encoding Methods in the WEBSOM.
Master's Thesis. April 26th, 1998.


I have also helped to organize this Pascal NoE challenge and the associated workshop:



CV
Email: jarkko.salojarvi'at'cis.hut.fi



Last modified 26.9.2008
[an error occurred while processing this directive]