Publications by Samuel Kaski

to appear

247Dorota Głowacka, Tuukka Ruotsalo, Ksenia Konyushkova, Kumaripaba Athukorala, Samuel Kaski, and Giulio Jacucci. Directing exploratory search: Reinforcement learning from user interactions with keywords. In Proceedings of IUI'13, International Conference on Intelligent User Interfaces, to appear.
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2012

246José Caldas, Nils Gehlenborg, Eeva Kettunen, Ali Faisal, Mikko Rönty, Andrew G. Nicholson, Sakari Knuutila, Alvis Brazma, and Samuel Kaski. Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. Bioinformatics, 28(2):246–253, 2012. Supplementary data and source code are available from http://www.ebi.ac.uk/fg/research/rex.
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245Jukka Corander, Tero Aittokallio, Samuli Ripatti, and Samuel Kaski. The rocky road to personalized medicine: computational and statistical challenges. Personalized Medicine, 9(2):109–114, 2012.
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244Ali Faisal, Jussi Gillberg, Jaakko Peltonen, Gayle Leen, and Samuel Kaski. Sparse nonparametric topic model for transfer learning. In Proceedings of 20th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, pages 269–274, 2012.
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243Suleiman A. Khan, Ali Faisal, John Patrick Mpindi, Juuso A. Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli P. Kallioniemi, Krister Wennerberg, and Samuel Kaski. Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs. BMC Bioinformatics, 13(112), 2012.
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242Miika Koskinen, Jaakko Viinikanoja, Mikko Kurimo, Arto Klami, Samuel Kaski, and Riitta Hari. Identifying fragments of natural speech from the listener's MEG signals. Human Brain Mapping, -(-):–, 2012.
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241Gayle Leen, Jaakko Peltonen, and Samuel Kaski. Focused multi-task learning in a Gaussian process framework. Machine Learning, 89(1-2):157–182, 2012.
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240Jaakko Peltonen, Tapani Raiko, and Samuel Kaski, editors. Neurocomputing, Special Issue on Machine Learning for Signal Processing 2010, 80:1-128, -, 2012. -.
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239Seppo Virtanen, Arto Klami, Suleiman A. Khan, and Samuel Kaski. Bayesian group factor analysis. In Neil Lawrence and Mark Girolami, editors, Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, volume 22 of JMLR W&CP, pages 1269–1277. JMLR, 2012.
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2011

238Antti Ajanki and Samuel Kaski. Probabilistic proactive timeline browser. In Timo Honkela, Wlodzislaw Duch, Mark A. Girolami, and Samuel Kaski, editors, Proceedings of the 21st International Conference on Artificial Neural Networks (ICANN), Part II, Lecture Notes in Computer Science, pages 357–364, Berlin, 2011. Springer.
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237Antti 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.
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236José Caldas and Samuel Kaski. Hierarchical generative biclustering for microRNA expression analysis. Journal of Computational Biology, 18:251–261, 2011.
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235Ali Faisal, Riku Louhimo, Leo Lahti, Sampsa Hautaniemi, and Samuel Kaski. Biomarker discovery via dependency analysis of multi-view functional genomics data. In NIPS 2011 workshop "From Statistical Genetics to Predictive Models in Personalized Medicine", 2011. Extended abstract.
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234Riku Louhimo, Viljami Aittomäki, Ali Faisal, Marko Laakso, Ping Chen, Kristian Ovaska, Erkka Valo, Leo Lahti, Vladimir Rogojin, Samuel Kaski, and Sampsa Hautaniemi. Systematic use of computational methods allows stratifying treatment responders in glioblastoma multiforme. In Proceedings of CAMDA 2011 conference, Critical Assessment of Massive Data Analysis, 2011. Source code available at http://csbi.ltdk.helsinki.fi/camda/.
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233Timo Honkela, Wlodzislaw Duch, Mark Girolami, and Samuel Kaski, editors. Artificial Neural Networks and Machine Learning Research - ICANN 2011, Part I, Berlin, 2011. Springer.
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232Timo Honkela, Wlodzislaw Duch, Mark Girolami, and Samuel Kaski, editors. Artificial Neural Networks and Machine Learning Research - ICANN 2011, Part II, Berlin, 2011. Springer.
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231Samuel Kaski and Jaakko Peltonen. Dimensionality reduction for data visualization. IEEE Signal Processing Magazine, 28(2):100–104, 2011.
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230Arto Klami, Pavan Ramkumar, Seppo Virtanen, Lauri Parkkonen, Riitta Hari, and Samuel Kaski. ICANN/PASCAL2 challenge: MEG mind reading – overview and results. In Arto Klami, editor, Proceedings of ICANN/PASCAL2 Challenge: MEG Mind Reading, Aalto University Publication series SCIENCE + TECHNOLOGY 29/2011, pages 3–19, Espoo, 2011.
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229Leo Lahti, Laura L. Elo, Tero Aittokallio, and Samuel Kaski. Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8:217–225, 2011.
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228Gayle Leen, Jaakko Peltonen, and Samuel Kaski. Focused multi-task learning using Gaussian processes. In Dimitrios Gunopulos, Thomas Hofmann, Donato Malerba, and Michalis Vazirgiannis, editors, Machine Learning and Knowledge Discovery in Databases (Proceedings of ECML PKDD 2011), Part II, pages 310–325. Springer Berlin / Heidelberg, 2011. Best Paper Award in Machine Learning.
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227Jaakko Peltonen and Samuel Kaski. Generative modeling for maximizing precision and recall in information visualization. In Geoffrey Gordon, David Dunson, and Miroslav Dudik, editors, Proceedings of the Fourteenth International Conference on Artificial Intelligence and Statistics, volume 15 of JMLR W&CP, pages 597–587. JMLR, 2011.
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226Tommi Suvitaival, Ilkka Huopaniemi, Matej Orešic, and Samuel Kaski. Cross-species translation of multi-way biomarkers. In Timo Honkela, Wlodzislaw Duch, Mark Girolami, and Samuel Kaski, editors, Proceedings of the 21st International Conference on Artificial Neural Networks (ICANN), Part I, volume 6791 of Lecture Notes in Computer Science, pages 209–216. Springer, 2011.
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225Tommi Suvitaival, Ilkka Huopaniemi, Matej Orešic, and Samuel Kaski. Detecting similar high-dimensional responses to experimental factors between human and model organism. In NIPS 2011 workshop "From Statistical Genetics to Predictive Models in Personalized Medicine", 2011. Extended abstract.
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224Marko Sysi-Aho, Andrey Ermolov, Peddinti V. Gopalacharyulu, Abhishek Tripathi, Tuulikki Seppänen-Laakso, Johanna Maukonen, Ismo Mattila, Suvi T. Ruohonen, Laura Vähätalo, Laxman Yetukuri, Taina Härkönen, Erno Lindfors, Janne Nikkilä, Jorma Ilonen, Olli Simell, Maria Saarela, Mikael Knip, Samuel Kaski, Eriika Savontaus, and Matej Orešic. Metabolic regulation in progression to autoimmune diabetes. PLoS Computational Biology, 7:e1002257, 2011.
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223Seppo Virtanen, Arto Klami, and Samuel Kaski. Bayesian CCA via group sparsity. In Lise Getoor and Tobias Scheffer, editors, Proceedings of the 28th International Conference on Machine Learning (ICML-11), ICML '11, pages 457–464, New York, NY, 2011. ACM. Implementation in R available at http://research.ics.tkk.fi/mi/software/gsCCA/.
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222S.V.N. Vishwanathan, Samuel Kaski, Jennifer Neville, and Stefan Wrobel, editors. Machine Learning, Special Issue on Learning and Mining with Graphs, 82(2), 2011.
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221Abhishek Tripathi, Arto Klami, Matej Orešic, and Samuel Kaski. Matching samples of multiple views. Data Mining and Knowledge Discovery, 23:300–321, 2011.
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220Laxman Yetukuri, Ilkka Huopaniemi, Artturi Koivuniemi, Marianna Maranghi, Anne Hiukka, Heli Nygren, Samuel Kaski, Marja-Riitta Taskinen, Ilpo Vattulainen, Matti Jauhiainen, and Matej Orešic. 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, 2011.
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2010

219Antti Ajanki, Mark Billinghurst, Toni Järvenpää, Melih Kandemir, Samuel Kaski, Markus Koskela, Mikko Kurimo, Jorma Laaksonen, Kai Puolamäki, Teemu Ruokolainen, and Timo Tossavainen. Contextual information access with augmented reality. In Proceedings of MLSP 2010, IEEE International Workshop on Machine Learning for Signal Processing, pages 95–100. IEEE, August 2010.
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218Antti Ajanki, Mark Billinghurst, Melih Kandemir, Samuel Kaski, Markus Koskela, Mikko Kurimo, Jorma Laaksonen, Kai Puolamäki, and Timo Tossavainen. Ubiquitous contextual information access with proactive retrieval and augmentation. In The Fourth International Workshop on Ubiquitous Virtual Reality (IWUVR2010), 2010.
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217Peter Auer, Zakria Hussain, Samuel Kaski, Arto Klami, Jussi Kujala, Jorma Laaksonen, Alex P. Leung, Kitsuchart Pasupa, and John Shawe-Taylor. Pinview: Implicit feedback in content-based image retrieval. In Tom Diethe, Nello Cristianini, and John Shawe-Taylor, editors, Proceedings of Workshop on Applications of Pattern Analysis, volume 11 of JMLR Workshop and Conference Proceedings, pages 51–57, 2010.
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216José Caldas and Samuel Kaski. Hierarchical generative biclustering for microRNA expression analysis. In Bonnie Berger, editor, Research in Computational Molecular Biology, Proceedings of 14th Annual International Conference RECOMB 2010, Lisbon, Portugal, April 25-28, pages 65–79, Berlin, 2010. Springer.
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215Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Orešic, and Samuel Kaski. Multivariate multi-way analysis of multi-source data. Bioinformatics, 26:i391–i398, 2010. (ISMB 2010).
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214Ilkka Huopaniemi, Tommi Suvitaival, Matej Orešic, and Samuel Kaski. Graphical multi-way models. In José Balcázar, Francesco Bonchi, Aristides Gionis, and Michèle Sebag, editors, Machine Learning and Knowledge Discovery in Databases. Proceedings of European Conference, ECML PKDD 2010, Barcelona, Spain, September 20-24, 2010, volume I, pages 538–553, Berlin, 2010. Springer.
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213Melih Kandemir, Veli-Matti Saarinen, and Samuel Kaski. Inferring object relevance from gaze in dynamic scenes. In Proceedings of ETRA 2010, ACM Symposium on Eye Tracking Research & Applications, Austin, TX, USA, March 22-24, pages 105–108, New York, NY, 2010. ACM.
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212Samuel Kaski. Self-organizing maps. In Claude Sammut and Geoffrey I. Webb, editors, Encyclopedia of Machine Learning, pages 886–888. Springer, Berlin, 2010.
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211Samuel Kaski. Three paths to relevance. In Akitoshi Hanazawa, Tsutom Miki, and Keiichi Horio, editors, Brain-Inspired Information Technology, pages 11–13. Springer, Berlin Heidelberg, 2010.
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210Samuel Kaski, David J. Miller, Erkki Oja, and Antti Honkela, editors. Proceedings of the 2010 IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010). IEEE, Piscataway, NJ, 2010.
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209Arto Klami, Seppo Virtanen, and Samuel Kaski. Bayesian exponential family projections for coupled data sources. In Peter Grunwald and Peter Spirtes, editors, Proceedings of the Twenty-Sixth Conference on Uncertainty in Artificial Intelligence (2010), pages 286–293, Corvallis, Oregon, 2010. AUAI Press.
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208Leo Lahti, Juha E. A. Knuuttila, and Samuel Kaski. Global modeling of transcriptional responses in interaction networks. Bioinformatics, 26:2713–2720, 2010. Implementations in R and Matlab available at http://netpro.r-forge.r-project.org/.
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207Juuso Parkkinen and Samuel Kaski. Searching for functional gene modules with interaction component models. BMC Systems Biology, 4:4, 2010.
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206Juuso Parkkinen, Kristian Nybo, Jaakko Peltonen, and Samuel Kaski. Graph visualization with latent variable models. In Proceedings of MLG-2010, the Eighth Workshop on Mining and Learning with Graphs, pages 94–101, New York, NY, USA, 2010. ACM. DOI: http://doi.acm.org/10.1145/1830252.1830265.
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205Jaakko Peltonen, Yusuf Yaslan, and Samuel Kaski. Relevant subtask learning by constrained mixture models. Intelligent Data Analysis, 14:641–662, 2010.
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204Jaakko Peltonen, Helena Aidos, Nils Gehlenborg, Alvis Brazma, and Samuel Kaski. An information retrieval perspective on visualization of gene expression data with ontological annotation. In Proceedings of ICASSP 2010, IEEE International Conference on Acoustics, Speech and Signal Processing, pages 2178–2181, Piscataway, NJ, 2010. IEEE.
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203Jaakko Peltonen and Samuel Kaski. Generative modeling for maximizing precision and recall in information visualization. Technical Report TKK-ICS-R38, Aalto University, Department of Information and Computer Science, Espoo, Finland, 2010.
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202Simon Rogers, Arto Klami, Janne Sinkkonen, Mark Girolami, and Samuel Kaski. Infinite factorization of multiple non-parametric views. Machine Learning, 79(1-2):201–226, 2010.
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201Jarkko 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.
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200Jaakko Viinikanoja, Arto Klami, and Samuel Kaski. Variational Bayesian mixture of robust CCA models. In Aristides Gionis José Luis Balcázar, Francesco Bonchi and Michèle Sebag, editors, Machine Learning and Knowledge Discovery in Databases. Proceedings of European Conference, ECML PKDD 2010, Barcelona, Spain, September 20-24, 2010, volume III, pages 370–385, Berlin, 2010. Springer. Implementation in Matlab available at http://research.ics.tkk.fi/mi/software/vbcca/.
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2009

199Antti Ajanki, Mark Billinghurst, Melih Kandemir, Samuel Kaski, Markus Koskela, Mikko Kurimo, Jorma Laaksonen, Kai Puolamäki, and Timo Tossavainen. Ubiquitous contextual information access with proactive retrieval and augmentation. Technical Report TKK-ICS-R27, Helsinki University of Technology, Department of Information and Computer Science, Espoo, Finland, December 2009.
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198Kristian Nybo, Juuso Parkkinen, and Samuel Kaski. Graph visualization with latent variable models. Technical Report TKK-ICS-R20, Helsinki University of Technology, Department of Information and Computer Science, Espoo, September 2009.
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197Juuso Parkkinen, Janne Sinkkonen, Adam Gyenge, and Samuel Kaski. A block model suitable for sparse graphs. In Proceedings of the 7th International Workshop on Mining and Learning with Graphs (MLG 2009), Leuven, Belgium, July 2-4 2009. Extended Abstract.
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196Eerika Savia, Kai Puolamäki, and Samuel Kaski. On two-way grouping by one-way topic models. Technical Report TKK-ICS-R15, Helsinki University of Technology, Department of Information and Computer Science, Espoo, May 2009.
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195Antti Ajanki, David R. Hardoon, Samuel Kaski, Kai Puolamäki, and John Shawe-Taylor. Can eyes reveal interest?—Implicit queries from gaze patterns. User Modeling and User-Adapted Interaction: The Journal of Personalization Research, 19:307–339, 2009.
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194Farid Benachenhou, Patric Jern, Merja Oja, Göran Sperber, Vidar Blikstad, Panu Somervuo, Samuel Kaski, and Jonas Blomberg. Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data. PLoS ONE, 4(4):e5179, 2009.
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193José 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).
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192José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, and Samuel Kaski. Probabilistic retrieval and visualization of biologically relevant microarray experiments. BMC Bioinformatics, 10:P1, 2009. Poster abstract for the 5th ISCB Student Council. Best poster award.
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191Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Orešic, and Samuel Kaski. Two-way analysis of high-dimensional collinear data. Data Mining and Knowledge Discovery, 19:261–276, 2009.
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190Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Orešic, and Samuel Kaski. Multi-way, multi-view learning. In NIPS 2009 workshop on Learning from Multiple Sources with Applications to Robotics, 2009. Extended Abstract.
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189László Kozma, Arto Klami, and Samuel Kaski. GaZIR: Gaze-based zooming interface for image retrieval. In Proceedings of ICMI-MLMI 2009, The Eleventh International Conference on Multimodal Interfaces and The Sixth Workshop on Machine Learning for Multimodal Interaction, pages 305–312, New York, NY, USA, 2009. ACM.
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188Leo Lahti, Samuel Myllykangas, Sakari Knuutila, and Samuel Kaski. Dependency detection with similarity constraints. In Proceedings of MLSP 2009, IEEE International Workshop on Machine Learning for Signal Processing, pages 89–94. IEEE, 2009.
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187Gayle Leen, David R. Hardoon, and Samuel Kaski. Automatic choice of control measurements. In Z.-H. Zhou and T. Washio, editors, Advances in Machine Learning (Proc. ACML'09, The 1st Asian Conference on Machine Learning), volume 5828 of Lecture Notes in Computer Science, pages 206–219. Springer, 2009.
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186Jaakko Peltonen, Jarkko Venna, and Samuel Kaski. Visualizations for assessing convergence and mixing of Markov chain Monte Carlo simulations. Computational Statistics and Data Analysis, 53:4453–4470, 2009.
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185Kitsuchart Pasupa, Craig Saunders, Sandor Szedmak, Arto Klami, Samuel Kaski, and Steve Gunn. Learning to rank images from eye movements. In IEEE International Workshop on Human-Computer Interaction (HCI2009), October 4, 2009, Kyoto, Japan, pages 2009–2016, 2009.
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184Jaakko Peltonen, Helena Aidos, and Samuel Kaski. Supervised nonlinear dimensionality reduction by neighbor retrieval. In Proceedings of ICASSP 2009, the IEEE International Conference on Acoustics, Speech, and Signal Processing, pages 1809–1812. IEEE, 2009.
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183Kai Puolamäki and Samuel Kaski. Bayesian solutions to the label switching problem. In N. Adams, C. Robardet, A. Siebes, and J.-F. Boulicaut, editors, Advances in Intelligent Data Analysis VIII, Proceedings of the 8th International Symposium on Intelligent Data Analysis, IDA 2009, pages 381–392, Berlin, 2009. Springer.
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182Eerika Savia, Arto Klami, and Samuel Kaski. Fast dependent components for fMRI analysis. In Proceedings of ICASSP 09, the International Conference on Acoustics, Speech, and Signal Processing, pages 1737–1740. IEEE, 2009.
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181Eerika Savia, Kai Puolamäki, and Samuel Kaski. Two-way grouping by one-way topic models. In N. Adams, C. Robardet, A. Siebes, and J.-F. Boulicaut, editors, Advances in Intelligent Data Analysis VIII, Proceedings of the 8th International Symposium on Intelligent Data Analysis, IDA 2009, Lecture Notes in Computer Science, pages 178–189, Berlin, 2009. Springer.
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180Eerika Savia, Kai Puolamäki, and Samuel Kaski. Latent grouping models for user preference prediction. Machine Learning, 74:75–109, 2009. Published online: 3 September 2008.
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179Suvi Savola, Arto Klami, Abhishek Tripathi, Tarja Niini, Massimo Serra, Piero Picci, Samuel Kaski, Diana Zambelli, Katia Scotlandi, and Sakari Knuutila. Combined use of expression and CGH arrays pinpoints novel candidate genes in ewing sarcoma family of tumors. BMC Cancer, 9:17, 2009.
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178Abhishek Tripathi, Arto Klami, and Samuel Kaski. Using dependencies to pair samples for multi-view learning. In Proceedings of ICASSP 09, the International Conference on Acoustics, Speech, and Signal Processing, pages 1561–1564. IEEE, 2009.
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177Keisuke Yamazaki and Samuel Kaski. An analysis of generalization error in relevant subtask learning. In Mario K?pen, Nikola Kasabov, and George Coghill, editors, Advances in Neuro-Information Processing, 15th International Conference, ICONIP 2008, pages 629–637, Berlin Heidelberg, 2009. Springer-Verlag.
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176Jarkko Ylipaavalniemi, Eerika Savia, Sanna Malinen, Riitta Hari, Ricardo Vigário, and Samuel Kaski. Dependencies between stimuli and spatially independent fMRI sources: Towards brain correlates of natural stimuli. NeuroImage, 48:176–185, 2009.
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2008

175Janne Sinkkonen, Juuso Parkkinen, Janne Aukia, and Samuel Kaski. A simple infinite topic mixture for rich graphs and relational data. In Proceedings of the NIPS 2008 Workshop on Analyzing Graphs: Theory and Applications, December 12 2008. Extended Abstract.
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174José Caldas and Samuel Kaski. Bayesian biclustering with the plaid model. In José Príncipe, Deniz Erdogmus, and Tulay Adali, editors, Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing XVIII, pages 291–296. IEEE, 2008.
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173Arto Klami and Samuel Kaski. Probabilistic approach to detecting dependencies between data sets. Neurocomputing, 72:39–46, 2008.
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172Arto Klami, Craig Saunders, Teófilo de Campos, and Samuel Kaski. Can relevance of images be inferred from eye movements?. In MIR '08: Proceeding of the 1st ACM International Conference on Multimedia Information Retrieval, pages 134–140. ACM, New York, NY, 2008.
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171Janne Nikkilä, Marko Sysi-Aho, Andrey Ermolov, Tuulikki Seppänen-Laakso, Olli Simell, Samuel Kaski, and Matej Orešic. Gender dependent progression of systemic metabolic states in early childhood. Molecular Systems Biology, 4:197, 2008.
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170Jaakko Peltonen, Yusuf Yaslan, and Samuel Kaski. Variational Bayes learning from relevant tasks only. In Learning from Multiple Sources Workshop, 13 December 2008, Whistler Canada, 2008. Proceedings at http://web.mac.com/davidrh/LMSworkshop08/Schedule.html.
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169Kai Puolamäki, Antti Ajanki, and Samuel Kaski. Learning to learn implicit queries from gaze patterns. In Andrew McCallum and Sam Roweis, editors, Proceedings of ICML 2008, Twenty-Fifth International Conference on Machine Learning, pages 760–767, Madison, WI, 2008.
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168Kai Puolamäki and Samuel Kaski. Bayesian solutions to the label switching problem. TKK Reports in Information and Computer Science TKK-ICS-R7, Helsinki University of Technology, Espoo, Finland, 2008.
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167Tapani Raiko, Kai Puolamäki, Juha Karhunen, Jaakko Hollmén, Antti Honkela, Samuel Kaski, Heikki Mannila, Erkki Oja, and Olli Simula. Macadamia: Master's programme in machine learning and data mining. In Teaching Machine Learning Workshop 2008, May 6-7, Sait-Étienne, France, 2008. Papers at http://labh-curien.univ-st-etienne.fr/informatique/tml08/programme.php.
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166Simon Rogers, Janne Sinkkonen, Arto Klami, Mark Girolami, and Samuel Kaski. Two-level infinite mixture for multi-domain data. In Learning from Multiple Sources Workshop, 13 December 2008, Whistler Canada, 2008. Proceedings at http://web.mac.com/davidrh/LMSworkshop08/Schedule.html.
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165Janne Sinkkonen, Janne Aukia, and Samuel Kaski. Infinite mixtures for multi-relational categorical data. In Samuel Kaski, S. V. N. Vishwanathan, and Stefan Wrobel, editors, 6th International Workshop on Mining and Learning with Graphs (MLG 2008), 2008. Proceedings at http://www.cis.hut.fi/MLG08.
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164Abhishek Tripathi, Arto Klami, and Samuel Kaski. Simple integrative preprocessing preserves what is shared in data sources. BMC Bioinformatics, 9:111, 2008.
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163Abhishek Tripathi, Arto Klami, and Samuel Kaski. Using dependencies to pair samples for multi-view learning. TKK Reports in Information and Computer Science TKK-ICS-R8, Helsinki University of Technology, Espoo, Finland, 2008.
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162Keisuke Yamazaki and Samuel Kaski. On asymmetric generalization error of asymmetric multitask learning. In Learning from Multiple Sources Workshop, 13 December 2008, Whistler Canada, 2008. Proceedings at http://web.mac.com/davidrh/LMSworkshop08/Schedule.html.
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2007

161Juuso Parkkinen and Samuel Kaski. Searching for functional gene modules with interaction component models. In Proceedings of the NIPS 2007 workshop on Machine Learning in Computational Biology, Whistler, BC, Canada, December 7 2007. Extended Abstract.
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160Merja Oja, Jaakko Peltonen, Jonas Blomberg, and Samuel Kaski. Estimating human endogeneous retrovirus activities in various tissues with a hidden Markov mixture model. In Intelligent Systems for Molecular Biology & European Conference on Computational Biology 2007 (ISMB/ECCB 2007), Vienna, Austria, July 21-25 2007. Poster.
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159Antti Ajanki, Janne Nikkilä, and Samuel Kaski. Discovering condition-dependent Bayesian networks for gene regulation. In Proceedings of GENSIPS 2007, The Fifth IEEE International Workshop on Genomic Signal Processing and Statistics, Tuusula, Finland, 10-12 June, 2007.
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158Janne Aukia, Samuel Kaski, and Janne Sinkkonen. Inferring vertex properties from topology in large networks. In NIPS'07 Workshop on Statistical Models of Networks, 2007.
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157David R. Hardoon, John Shawe-Taylor, Antti Ajanki, Kai Puolamäki, and Samuel Kaski. Information retrieval by inferring implicit queries from eye movements. In Marina Meila and Xiaotong Shen, editors, Proceedings of AISTATS 2007, the 11th International Conference on International Conference on Artificial Intelligence and Statistics. Omnipress, 2007. JMLR Workshop and Conference Proceedings, Volume 2: AISTATS 2007.
Info
See jmlr.csail.mit.edu ...
156Samuel Kaski and Jaakko Peltonen. Learning from relevant tasks only. In Joost N. Kok, Jacek Koronacki, Ramon Lopez de Mantaras, Stan Matwin, Dunja Mladenic, and Andrzej Skowron, editors, Machine Learning: ECML 2007 (Proceedings of the 18th European Conference on Machine Learning), pages 608–615, Berlin, 2007. Springer-Verlag.
Info
See dx.doi.org ...
155Samuel Kaski, Juho Rousu, and Esko Ukkonen, editors. BMC Bioinformatics, Special Issue on Probabilistic Modeling and Machine Learning in Structural and Systems Biology, 8(Suppl 2), 2007.
Info
See www.biomedcentral.com ...
154Samuel Kaski, Juho Rousu, and Esko Ukkonen. Probabilistic modeling and machine learning in structural and systems biology. BMC Bioinformatics, 8(Suppl 2):S1, 2007.
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153Arto Klami and Samuel Kaski. Local dependent components. In Zoubin Ghahramani, editor, Proceedings of ICML 2007, the 24th International Conference on Machine Learning, pages 425–432. Omnipress, 2007.
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152Kristian Nybo, Jarkko Venna, and Samuel Kaski. The self-organizing map as a visual information retrieval method. In Proceedings of WSOM'07, 6th International Workshop on Self-Organizing Maps, Bielefeld, Germany, 2007. Bielefeld University.
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151Penny Nymark, Pamela M Lindholm, Mikko V Korpela, Leo Lahti, Salla Ruosaari, Samuel Kaski, Jaakko Hollmen, Sisko Anttila, Vuokko L Kinnula, and Sakari Knuutila. Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines. BMC Genomics, 8:62, 2007.
Info
See www.biomedcentral.com ...
150Merja Oja, Jaakko Peltonen, Jonas Blomberg, and Samuel Kaski. Methods for estimating human endogenous retrovirus activities from EST databases. BMC Bioinformatics, 8(Suppl 2):S11, 2007.
Info
See www.biomedcentral.com ...
149Merja Oja, Jaakko Peltonen, and Samuel Kaski. A hidden Markov model for estimating retrovirus activities from expressed sequence databases. In European Conference on Computational Biology (ECCB 2006), Eilat, Israel, January 21-24 2007. Poster.
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148Jaakko Peltonen, Jacob Goldberger, and Samuel Kaski. Fast semi-supervised discriminative component analysis. In Konstantinos Diamantaras, Tülay Adali, Ioannis Pitas, Jan Larsen, Theophilos Papadimitriou, and Scott Douglas, editors, Machine Learning for Signal Processing XVII, pages 312–317. IEEE, 2007. Preprint pdf at http://www.cis.hut.fi/projects/mi/papers/mlsp07.pdf.
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147Janne Sinkkonen, Janne Aukia, and Samuel Kaski. Inferring vertex properties from topology in large networks. In MLG'07, the 5th International Workshop on Mining and Learning with Graphs, Firenze, Aug 1-3, 2007, 2007.
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146Jarkko Venna and Samuel Kaski. Nonlinear dimensionality reduction as information retrieval. In Marina Meila and Xiaotong Shen, editors, Proceedings of AISTATS 2007, the 11th International Conference on International Conference on Artificial Intelligence and Statistics. Omnipress, 2007. JMLR Workshop and Conference Proceedings, Volume 2: AISTATS 2007.
Info
See jmlr.csail.mit.edu ...
145Jarkko Venna and Samuel Kaski. Comparison of visualization methods for an atlas of gene expression data sets. Information Visualization, 6:139–154, 2007.
Info
144Jarkko Ylipaavalniemi, Eerika Savia, Ricardo Vigário, and Samuel Kaski. Functional elements and networks in fMRI. In Proceedings of ESANN 2007, the 15th European Symposium on Artificial Neural Networks, pages 561–566, Bruges, Belgium, 2007. d-side.
Info
See www.dice.ucl.ac.be ...

2006

143Samuel Kaski. Ydintehtävät kunniaan. Polysteekki, N/A(3):19, 2006. (Commentary on the role of TKK in research in TKK's magazine.).
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142Arto Klami and Samuel Kaski. Generative models that discover dependencies between data sets. In Proceedings of MLSP'06, IEEE International Workshop on Machine Learning for Signal Processing, pages 123–128. IEEE, 2006.
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141Janne Nikkilä, Antti Honkela, and Samuel Kaski. Exploring the independence of gene regulatory modules. In Juho Rousu, Samuel Kaski, and Esko Ukkonen, editors, Proceedings of Probabilistic Modeling and Machine Learning in Structural and Systems Biology (PMSB 2006), pages 131–136, Helsinki, Finland, 2006. Poster.
Info
140Merja Oja, Jaakko Peltonen, and Samuel Kaski. Estimation of human endogeneous retrovirus activities from expressed sequence databases. In Juho Rousu, Samuel Kaski, and Esko Ukkonen, editors, Probabilistic Modeling and Machine Learning in Structural and Systems Biology. Workshop Proceedings; Tuusula, Finland, June 17-18, pages 50–54, Helsinki, Finland, 2006. University of Helsinki.
Info
See www.cis.hut.fi ...
139Jaakko Peltonen, Jacob Goldberger, and Samuel Kaski. Fast discriminative component analysis for comparing examples. In NIPS'06 Workshop on Learning to Compare Examples, December 8, 2006, Whistler, BC, Canada, 2006. http://www.idiap.ch/lce/.
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138Jaakko Peltonen and Samuel Kaski. Learning when only some of the training data are from the same distribution as test data. In NIPS 2006 Workshop on Learning when Test and Training Inputs Have Different Distributions, 2006. Extended abstract at http://www.cis.hut.fi/projects/mi/papers/nips06_did_abstract.pdf, poster at http://www.cis.hut.fi/projects/mi/papers/nips06_did_poster.pdf.
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137Kai Puolamäki and Samuel Kaski, editors. Proceedings of the NIPS 2005 Workshop on Machine Learning for Implicit Feedback and User Modeling. Helsinki University of Technology, Espoo, Finland, 2006.
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136Kai Puolam?i, Jarkko Salojarvi, Eerika Savia, and Samuel Kaski. Discriminative MCMC. Publications in Computer and Information Science E1, Helsinki University of Technology, Espoo, Finland, 2006.
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135Juho Rousu, Samuel Kaski, and Esko Ukkonen, editors. Probabilistic Modeling and Machine Learning in Structural and Systems Biology. Workshop Proceedings; Tuusula, Finland, June 17-18. University of Helsinki, Helsinki, Finland, 2006.
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134Jarkko Salojärvi, Kai Puolamäki, Jaana Simola, Lauri Kovanen, Ilpo Kojo, and Samuel Kaski. Inferring relevance from eye movements: Feature extraction. In Kai Puolamäki and Samuel Kaski, editors, Proceedings of the NIPS 2005 Workshop on Machine Learning for Implicit Feedback and User Modeling, pages 45–67. Helsinki University of Technology, Espoo, Finland, 2006.
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133Udo Seiffert, Barbara Hammer, Samuel Kaski, and Thomas Villmann. Neural networks and machine learning in bioinformatics—theory and applications. In Proceedings of ESANN'06, 14th European Symposium on Artificial Neural Networks, pages 521–532, Evere, Belgium, 2006. d-side.
Info
132Jarkko Venna and Samuel Kaski. Local multidimensional scaling. Neural Networks, 19:889–899, 2006.
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131Jarkko Venna and Samuel Kaski. Visualizing gene interaction graphs with local multidimensional scaling. In Proceedings of ESANN'06, 14th European Symposium on Artificial Neural Networks, pages 557–562, Evere, Belgium, 2006. d-side. Poster.
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130Jarkko Venna and Samuel Kaski. Nonlinear dimensionality reduction viewed as information retrieval. In NIPS 2006 Workshop on Novel Applications of Dimensionality Reduction, 2006. Extended abstract at http://www.cis.hut.fi/projects/mi/papers/nips06_nldrws.pdf.
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129Jarkko Venna and Samuel Kaski. Nonlinear dimensionality reduction as information retrieval. Publications in Computer and Information Science E5, Helsinki University of Technology, 2006.
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128Jarkko Ylipaavalniemi, Eerika Savia, Ricardo Vig?io, and Samuel Kaski. Functional elements and networks in fmri. Publications in Computer and Information Science E7, Helsinki University of Technology, 2006.
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2005

127Janne Sinkkonen, Samuel Kaski, Janne Nikkilä, and Leo Lahti. Associative clustering (AC): Technical details. Publications in Computer and Information Science A84, Helsinki University of Technology, Espoo, Finland, April 2005.
Info
126Catherine Bounsaythip, Jaakko Hollmén, Samuel Kaski, and Matej Orešic, editors. Proceedings of KRBIO05, Symposium on Knowledge Representation in Bioinformatics. Helsinki University of Technology, Espoo, Finland, 2005.
Info
125Samuel Kaski. From learning metrics towards dependency exploration. In Proceedings of WSOM'05, 5th Workshop On Self-Organizing Maps, pages 307–314, Paris, 2005.
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124Samuel Kaski. Proactive information retrieval by monitoring eye movements. In Abstracts of BrainIT, The Second International Conference on Brain-Inspired Information Technology, page 28, Kitakuyshu, Japan, 2005. Kyushu Institute of Technology. Abstract of an invited talk.
Info
123Samuel Kaski, Petri Myllymäki, and Ilpo Kojo. User models from implicit feedback for proactive information retrieval. In Colin de la Higuera and Thierry Artières, editors, Proceedings of Workshop 4 of the 10th International Conference on User Modeling; Machine Learning for User Modeling: Challenges, pages 25–26, 2005.
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122Samuel Kaski and Janne Nikkilä. Dependency exploration in computational systems biology. In Tiina Manninen, Marja-Leena Linne, and Olli Yli-Harja, editors, Proceedings of The 3rd TICSP Workshop on Computational Systems Biology, TICSP Series #29, pages 49–50, Tampere, Finland, 2005. Tampere University of Technology.
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121Samuel Kaski and Janne Nikkilä. Of mice and men and yeast, and dependency exploration. CSCnews, Information Technology for Science in Finland, N/A(4):24–26, 2005.
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120Samuel Kaski, Janne Nikkil?and Eerika Savia, and Christophe Roos. Discriminative clustering of yeast stress response. In Udo Seiffert, Lakhmi Jain, and Patric Schweizer, editors, Bioinformatics using Computational Intelligence Paradigms, pages 75–92, Berlin, 2005. Springer.
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119Samuel Kaski, Janne Nikkilä, Janne Sinkkonen, Leo Lahti, Juha Knuuttila, and Christophe Roos. Associative clustering for exploring dependencies between functional genomics data sets. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2(3):203–216, 2005.
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118Samuel Kaski, Eerika Savia, and Kai Puolamäki. Predicting binding of transcriptional regulators with a two-way latent grouping model. Poster in ISMB 2005, the 13th Annual International Conference on Intelligent Systems for Molecular Biology, Detroit, Michigan, June 25-29, 2005.
Info
See www.iscb.org ...
117Samuel Kaski, Janne Sinkkonen, and Arto Klami. Discriminative clustering. Neurocomputing, 69:18–41, 2005.
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116Arto Klami and Samuel Kaski. Non-parametric dependent components. In Proceedings of ICASSP 2005, IEEE International Conference on Acoustics, Speech, and Signal Processing, pages V–209–V–212. IEEE, 2005.
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115Arto Klami, Janne Nikkilä, Christophe Roos, and Samuel Kaski. Extracting yeast stress genes by dependencies between stress treatments, 2005. Abstract in web, http://tinyurl.com/98kcx.
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114Janne Nikkilä, Tapio Rinnet, Antti Ajanki, and Samuel Kaski. Stress in yeast knockout experiments. In ICSB 2005, 6th International Conference on Systems Biology, abstract proceedings, page 249, 2005. Poster abstract.
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113Janne Nikkilä, Christophe Roos, and Samuel Kaski. Integration of transcription factor binding and gene expression by associative clustering. In Catherine Bounsaythip, Jaakko Hollmén, Samuel Kaski, and Matej Orešic, editors, Proceedings of KRBIO05, Symposium on Knowledge Representation in Bioinformatics, pages 22–29, Espoo, Finland, 2005. Helsinki University of Technology.
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112Janne Nikkilä, Christophe Roos, Eerika Savia, and Samuel Kaski. Explorative modeling of yeast stress response and its regulation with gCCA and associative clustering. International Journal of Neural Systems, 15(4):237–246, 2005.
Info
See dx.doi.org ...
111Merja Oja, Göran O. Sperber, Jonas Blomberg, and Samuel Kaski. Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups. International Journal of Neural Systems, 15:163–180, 2005.
Info
110Jaakko Peltonen and Samuel Kaski. Discriminative components of data. IEEE Transactions on Neural Networks, 16:68–83, 2005. Preprint pdf at http://www.cis.hut.fi/projects/mi/papers/tnn04_preprint.pdf.
Info
See dx.doi.org ...
109Kai Puolamäki, Jarkko Salojärvi, Eerika Savia, Jaana Simola, and Samuel Kaski. Combining eye movements and collaborative filtering for proactive information retrieval. In Gary Marchionini, Alistair Moffat, John Tait, Ricardo Baeza-Yates, and Novio Ziviani, editors, Proceedings of SIGIR 2005, Twenty-Eighth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, pages 146–153, New York, NY, 2005. ACM.
Info
See www.cis.hut.fi ...
108Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski. On discriminative joint density modeling. In Jo? Gama, Rui Camacho, Pavel Brazdil, Al?io Jorge, and Lu? Torgo, editors, Proceedings of ECML 2005, 16th European Conference on Machine Learning, pages 341–352, Berlin, 2005. Springer.
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107Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski. Expectation maximization algorithms for conditional likelihoods. In Luc De Raedt and Stefan Wrobel, editors, Proceedings of ICML 2005, the 22nd International Conference on Machine Learning, pages 753–760, New York, NY, 2005. ACM Press.
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106Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski. Implicit relevance feedback from eye movements. In Włodzisław Duch, Janusz Kacprzyk, Erkki Oja, and Sławomir Zadrozny, editors, Artificial Neural Networks: Biological Inspirations — ICANN 2005, volume I, pages 513–518, Berlin, 2005. Springer.
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105Jarkko Salojärvi, Kai Puolamäki, Jaana Simola, Lauri Kovanen, Ilpo Kojo, and Samuel Kaski. Inferring relevance from eye movements: Feature extraction. Publications in Computer and Information Science A82, Helsinki University of Technology, Espoo, Finland, 2005.
Info
104Eerika Savia, Kai Puolamäki, Janne Sinkkonen, and Samuel Kaski. Two-way latent grouping model for user preference prediction. In Fahiem Bachus and Tommi Jaakkola, editors, Proceedings of UAI 2005, Uncertainty in Artificial Intelligence, pages 518–525, Corvallis, OH, 2005. AUAI Press.
Info
See www.cis.hut.fi ...
103Jarkko Venna and Samuel Kaski. Visualized atlas of a gene expression databank. In Catherine Bounsaythip, Jaakko Hollmén, Samuel Kaski, and Matej Orešic, editors, Proceedings of KRBIO05, Symposium on Knowledge Representation in Bioinformatics, pages 30–36, Espoo, Finland, 2005. Helsinki University of Technology.
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102Jarkko Venna and Samuel Kaski. Local multidimensional scaling with controlled tradeoff between trustworthiness and continuity. In Proceedings of WSOM'05, 5th Workshop On Self-Organizing Maps, pages 695–702, Paris, 2005.
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2004

101Samuel Kaski. Bubbly bioinformatics. In From Genes to Ethics. Research for a New Millennium. Final Report of the Life 2000 Research Programme, Publications of the Academy of Finland 5/04, pages 48–51, Helsinki, Finland, 2004. Academy of Finland.
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100Samuel Kaski and Janne Sinkkonen. Principle of learning metrics for exploratory data analysis. Journal of VLSI Signal Processing, special issue on Machine Learning for Signal Processing, 37:177–188, 2004.
Info
99Krista Lagus, Samuel Kaski, and Teuvo Kohonen. Mining massive document collections by the WEBSOM method. Information Sciences, 163:135–156, 2004.
Info
98Janne Nikkilä, Christophe Roos, and Samuel Kaski. Exploring dependencies between yeast stress genes and their regulators. In Zheng Rong Yang, Richard Everson, and Hujun Yin, editors, Proceedings of IDEAL04, Intelligent Data Engineering and Automated Learning, pages 92–98, Berlin, 2004. Springer-Verlag.
Info
97Merja Oja, Göran Sperber, Jonas Blomberg, and Samuel Kaski. Grouping and visualizing human endogenous retroviruses by bootstrapping median self-organizing maps. In Proceedings of CIBCB'04, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pages 95–101, Piscataway, NJ, 2004. IEEE.
Info
96Jaakko Peltonen, Arto Klami, and Samuel Kaski. Improved learning of Riemannian metrics for exploratory analysis. Neural Networks, 17:1087–1100, 2004. Invited paper. Preprint postscript file at http://www.cis.hut.fi/projects/mi/papers/nn04_preprint.ps.gz.
Errata 
Info
See dx.doi.org ...
95Jaakko Peltonen, Janne Sinkkonen, and Samuel Kaski. Sequential information bottleneck for finite data. In Russ Greiner and Dale Schuurmans, editors, Proceedings of ICML 2004, the Twenty-First International Conference on Machine Learning, pages 647–654, Madison, WI, 2004. Omnipress.
Info
See www.cis.hut.fi ...
94Kai Puolamäki, Eerika Savia, Janne Sinkkonen, and Samuel Kaski. Two-way latent grouping model for user preference prediction. Publications in Computer and Information Science A80, Helsinki University of Technology, Espoo, Finland, 2004.
Info
93Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski. Relevance feedback from eye movements for proactive information retrieval. In Janne Heikkilä, Matti Pietikäinen, and Olli Silvén, editors, Proceedings of PSIPS 2004, Workshop on Processing Sensory Information for Proactive Systems, pages 37–42. Infotech Oulu, Oulu, Finland, 2004.
Info
92Eerika Savia, Samuel Kaski, Ville Tuulos, and Petri Myllymäki. On text-based estimation of document relevance. In Proceedings of IJCNN'04, International Joint Conference on Neural Networks, pages 3275–3280. IEEE, Piscataway, NJ, 2004.
Info
See www.cis.hut.fi ...
91Janne Sinkkonen, Janne Nikkilä, Leo Lahti, and Samuel Kaski. Associative clustering. In Jean-Francois Boulicaut, Floriana Esposito, Fosca Giannotti, and Dino Pedreschi, editors, Machine Learning: ECML'04. Proceedings of the 15th European Conference on Machine Learning, pages 396–405, Berlin, 2004. Springer.
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2003

90Janne Sinkkonen, Janne Nikkilä, Leo Lahti, and Samuel Kaski. Associative clustering by maximizing a Bayes factor. Publications in Computer and Information Science A68, Helsinki University of Technology, Espoo, Finland, June 2003.
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89Samuel Kaski. Discriminative clustering. In Bulletin of the International Statistical Institute. Invited Paper Proceedings of the 54th Session, volume 2, pages 270–273. International Statistical Institute, 2003.
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88Samuel Kaski and Janne Nikkil?and Teuvo Kohonen. Methods for exploratory cluster analysis. In P. S. Szczepaniak, J. Segovia, J. Kacprzyk, and L. A. Zadeh, editors, Intelligent Exploration of the Web, pages 136–151, Heidelberg, 2003. Physica-Verlag.
Info
87Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna, Petri Törönen, and Eero Castrén. Trustworthiness and metrics in visualizing similarity of gene expression. BMC Bioinformatics, 4(48), 2003.
Info
86Samuel Kaski and Jaakko Peltonen. Informative discriminant analysis. In Tom Fawcett and Nina Mishra, editors, Proceedings of ICML-2003, the Twentieth International Conference on Machine Learning, pages 329–336, Menlo Park, CA, 2003. AAAI Press.
Info
See www.cis.hut.fi ...
85Samuel Kaski and Janne Sinkkonen. Discriminative clustering: Vector quantization in learning metrics. In M. Schader, W. Gaul, and M. Vichi, editors, Between Data Science and Applied Data Analysis, pages 456–463, Berlin, 2003. Springer.
Info
84Samuel Kaski, Janne Sinkkonen, and Arto Klami. Regularized discriminative clustering. In Christophe Molina, Tülay Adali, Jan Larsen, Marc Van Hulle, Scott Douglas, and Jean Rouat, editors, Neural Networks for Signal Processing XIII, pages 289–298, New York, NY, 2003. IEEE. Poster.
Info
83Janne Nikkilä, Christophe Roos, Janne Sinkkonen, and Samuel Kaski. Associative clustering to find dependencies between expression profiles and transcription factor binding. In Catherine Christophe, Hans-Peter Lenhof, and Marie-France Sagot, editors, Proceedings of ECCB'2003, European Conference on Computational Biology, pages 433–434, 2003.
Info
82Merja Oja, Samuel Kaski, and Teuvo Kohonen. Bibliography of self-organizing map (SOM) papers: 1998–2001 addendum. Neural Computing Surveys, 3:1–156, 2003. Available in electronic form at http://www.soe.ucsc.edu/NCS/.
Info
81Merja Oja, Panu Somervuo, Samuel Kaski, and Teuvo Kohonen. Clustering of human endogenous retrovirus sequences with median self-organizing map. In Proceedings of WSOM'03, Workshop on Self-Organizing Maps, pages 134–139, Kitakyushu, Japan, 2003. Kyushu Institute of Technology. (Proceedings on CD-ROM).
Info
80Jaakko Peltonen, Arto Klami, and Samuel Kaski. Learning metrics for information visualization. In Proceedings of WSOM'03, Workshop on Self-Organizing Maps, pages 213–218, Kitakyushu, Japan, 2003. Kyushu Institute of Technology. (Proceedings on CD-ROM).
Info
See www.cis.hut.fi ...
79Jarkko Salojärvi, Samuel Kaski, and Janne Sinkkonen. Discriminative clustering in Fisher metrics. In O. Kaynak, E. Alpaydin, E. Oja, and L. Xu, editors, Artificial Neural Networks and Neural Information Processing—Supplementary proceedings ICANN/ICONIP, pages 161–164, 2003.
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78Jarkko Salojärvi, Ilpo Kojo, Jaana Simola, and Samuel Kaski. Can relevance be inferred from eye movements in information retrieval?. In Proceedings of WSOM'03, Workshop on Self-Organizing Maps, pages 261–266, Kitakyushu, Japan, 2003. Kyushu Institute of Technology. (Proceedings on CD-ROM).
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77Jarkko Saloj?vi, Kai Puolamäki, and Samuel Kaski. Relevance feedback from eye movements for proactive information retrieval. In Machine Learning Meets the User Interface, A workshop at NIPS 2003, 2003. (2-page abstract).
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76Jarkko Salojärvi, Kai Puolamäki, and Samuel Kaski. Relevance feedback from eye movements for proactive information retrieval. Publications in Computer and Information Science A73, Helsinki University of Technology, Espoo, Finland, 2003.
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75Jarkko Venna and Samuel Kaski. Visualizing high-dimensional posterior distributions in Bayesian modeling. In Artificial Neural Networks and Neural Information Processing—Supplementary proceedings ICANN/ICONIP, pages 165–168, 2003.
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74Jarkko Venna, Samuel Kaski, and Jaakko Peltonen. Visualizations for assessing convergence and mixing of MCMC. In N. Lavrac, D. Gamberger, H. Blockeel, and L. Todorovski, editors, Proceedings of ECML-2003, 14th European Conference on Machine Learning, pages 432–443, Berlin, 2003. Springer. Preprint postscript at http://www.cis.hut.fi/projects/mi/papers/ecml03.ps.gz.
Info
See dx.doi.org ...

2002

73Pekka Ala-Siuru and Samuel Kaski, editors. STeP 2002—Intelligence, the Art of Natural and Artificial. Proceedings of the 10th Finnish Artificial Intelligence Conference. Finnish Artificial Intelligence Society, Oulu, Finland, 2002.
Info
72Jukka Iivarinen, Samuel Kaski, and Erkki Oja, editors. Neljännesvuosisata Hatutusta: Hahmontunnistustutkimus Suomessa 1977–2002. Suomen hahmontunnistustutkimuksen seura ry, Otaniemi, 2002.
Info
71Samuel Kaski. Learning metrics. In 3rd Conference of the International Society for Ecological Informatics, Grottaferrata, Italy, page 42, 2002. (Abstract of a plenary talk).
Info
70Arto Klami, Jaakko Peltonen, and Samuel Kaski. Accurate self-organizing maps in learning metrics. In Pekka Ala-Siuru and Samuel Kaski, editors, STeP 2002—Intelligence, the Art of Natural and Artificial. Proceedings of the 10th Finnish Artificial Intelligence Conference, pages 41–49, Oulu, Finland, 2002. Finnish Artificial Intelligence Society.
Info
69Janne Nikkilä, Petri Törönen, Samuel Kaski, Jarkko Venna, Eero Castrén, and Garry Wong. Analysis and visualization of gene expression data using self-organizing maps. Neural Networks, 15:953–966, 2002.
Info
68Merja Oja, Janne Nikkilä, Petri Törönen, Eero Castrén, and Samuel Kaski. Learning metrics for visualizing gene functional similarities. In Pekka Ala-Siuru and Samuel Kaski, editors, STeP 2002—Intelligence, the Art of Natural and Artificial. Proceedings of the 10th Finnish Artificial Intelligence Conference, pages 31–40, Oulu, Finland, 2002. Finnish Artificial Intelligence Society.
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67Merja Oja, Janne Nikkilä, Petri Törönen, Garry Wong, Eero Castrén, and Samuel Kaski. Exploratory clustering of gene expression profiles of mutated yeast strains. In Wei Zhang and Ilya Shmulevich, editors, Computational and Statistical Approaches to Genomics, pages 65–78, Boston, MA, 2002. Kluwer.
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66Ville Ollikainen, Christer Bäckström, and Samuel Kaski. Electronic editor: Automatic content-based sequential compilation of newspaper articles. Neurocomputing, 43:91–106, 2002.
Info
65Jaakko Peltonen, Arto Klami, and Samuel Kaski. Learning more accurate metrics for self-organizing maps. In J. R. Dorronsoro, editor, Artificial Neural Networks—ICANN 2002, pages 999–1004, Berlin, 2002. Springer. Preprint postscript at http://www.cis.hut.fi/projects/mi/papers/icann02.ps.gz.
Info
See dx.doi.org ...
64Jaakko Peltonen, Janne Sinkkonen, and Samuel Kaski. Discriminative clustering of text documents. In Lipo Wang, Jagath C. Rajapakse, Kunihiko Fukushima, Soo-Young Lee, and Xin Yao, editors, Proceedings of ICONIP'02, 9th International Conference on Neural Information Processing, pages 1956–1960, Piscataway, NJ, 2002. IEEE. Preprint postscript at http://www.cis.hut.fi/projects/mi/papers/iconip02.ps.gz.
Info
See ieeexplore.ieee.org ...
63Jarkko Salojärvi and Samuel Kaski. Mixture density from autonomous experts. International Journal of Knowledge Based Intelligent Engineering Systems, 6:48–55, 2002.
Info
62Janne Sinkkonen and Samuel Kaski. Clustering based on conditional distributions in an auxiliary space. Neural Computation, 14:217–239, 2002.
Info
61Janne Sinkkonen, Samuel Kaski, and Janne Nikkilä. Discriminative clustering: optimal contingency tables by learning metrics. In Tapio Elomaa, Heikki Mannila, and Hannu Toivonen, editors, Machine Learning: ECML 2002, pages 418–430, Berlin, 2002. Springer.
Info

2001

60Samuel Kaski and Jarkko Salojärvi. Generative mixture modeling by autonomous estimators. In N. Baba, L. C. Jain, and R. J. Howlett, editors, Knowledge-Based Intelligent Information Engineering Systems & Allied Technologies, Proceedings of KES'2001, volume 1, pages 250–254, Amsterdam, 2001. IOS Press.
Info
59Janne Nikkilä, Petri Törönen, Janne Sinkkonen, and Samuel Kaski. Analysis of gene expression data using semi-supervised clustering. In Proceedings of Bioinformatics 2001, Skövde, Sweden, March 29-April 1, pages 2–3, 2001. (Abstract).
Info
58Samuel Kaski, Janne Sinkkonen, and Janne Nikkilä. Clustering gene expression data by mutual information with gene function. In Georg Dorffner, Horst Bischof, and Kurt Hornik, editors, Artificial Neural Networks—ICANN 2001, pages 81–86, Berlin, 2001. Springer.
Info
57Jarkko Venna and Samuel Kaski. Neighborhood preservation in nonlinear projection methods: An experimental study. In Georg Dorffner, Horst Bischof, and Kurt Hornik, editors, Artificial Neural Networks—ICANN 2001, pages 485–491, Berlin, 2001. Springer.
Info
56Samuel Kaski. Learning metrics for exploratory data analysis. In David Miller, Tülay Adali, Jan Larsen, Marc Van Hulle, and Scott Douglas, editors, Neural Networks for Signal Processing XI, Proceedings of the 2001 IEEE Signal Processing Society Workshop, pages 53–62, New York, NY, 2001. IEEE.
Info
55Samuel Kaski, Janne Sinkkonen, and Jaakko Peltonen. Data visualization and analysis with self-organizing maps in learning metrics. In Yahiko Kambayashi, Werner Winiwarter, and Masatoshi Arikawa, editors, Proceedings of DaWaK'01, Third International Conference on Data Warehousing and Knowledge Discovery, pages 162–173, Berlin, 2001. Springer. (LNCS 2114).
Info
See link.springer.de ...
54Samuel Kaski, Janne Sinkkonen, and Jaakko Peltonen. Learning metrics for self-organizing maps. In Proceedings of IJCNN'01, International Joint Conference on Neural Networks, pages 914–919, Piscataway, NJ, 2001. IEEE. Preprint postscript at http://www.cis.hut.fi/projects/mi/papers/ijcnn01.ps.gz.
Info
See dx.doi.org ...
53Samuel Kaski. SOM-based exploratory analysis of gene expression data. In Nigel Allinson, Hujun Yin, Lesley Allinson, and Jon Slack, editors, Advances in Self-Organizing Maps, pages 124–131, London, 2001. Springer.
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52Samuel Kaski and Janne Sinkkonen. A topography-preserving latent variable model with learning metrics. In Nigel Allinson, Hujun Yin, Lesley Allinson, and Jon Slack, editors, Advances in Self-Organizing Maps, pages 224–229, London, 2001. Springer.
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51Samuel Kaski, Janne Sinkkonen, and Jaakko Peltonen. Bankruptcy analysis with self-organizing maps in learning metrics. IEEE Transactions on Neural Networks, 12:936–947, 2001. Preprint postscript at http://www.cis.hut.fi/projects/mi/papers/trnn00_preprint.ps.gz.
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50Samuel Kaski, Janne Nikkilä, Petri Törönen, Eero Castren, and Garry Wong. Analysis and visualization of gene expression data using self-organizing maps. In Proceedings of NSIP-01, IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing, 03.06.2001 - 06.06.2001, Baltimore, Maryland USA, 2001. Proceedings on CD-ROM.
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2000

49Samuel Kaski. Convergence of a stochastic semisupervised clustering algorithm. Technical Report A62, Helsinki University of Technology, Publications in Computer and Information Science, Espoo, Finland, November 2000.
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48Samuel Kaski, Jarkko Venna, and Teuvo Kohonen. Coloring that reveals cluster structures in multivariate data. Australian Journal of Intelligent Information Processing Systems, 6:82–88, 2000.
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47Samuel Kaski. Kohti uutta luovan ajattelun opettamista. In Irene Hein and Riikka Lauhia, editors, protect, Dokumentoitua opetuksen kehitt?ist? Teknillisess?korkeakoulussa 1999-2000, pages 9–14. Teknillinen korkeakoulu, Opetuksen ja opiskelun tuen julkaisuja 3/2000, Helsinki, Finland, 2000.
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46Samuel Kaski, Janne Nikkilä, and Teuvo Kohonen. Methods for exploratory cluster analysis. In Proceedings of SSGRR 2000, International Conference on Advances in Infrastructure for Electronic Business, Science, and Education on the Internet, L'Aquila, July 31–August 6. Scuola Superiore G. Reiss Romoli, 2000. (Proceedings on CD-ROM, ISBN 88-85280-52-8).
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45Samuel Kaski and Janne Sinkkonen. Metrics that learn relevance. In Proceedings of IJCNN-2000, International Joint Conference on Neural Networks, volume V, pages 547–552, Piscataway, NJ, 2000. IEEE Service Center.
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44Teuvo 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.
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43Ville Ollikainen, Christer Bäckström, and Samuel Kaski. Automatic content-based sequential ordering of newspaper articles for electronic books. In Dimitris Tsaptsinos, editor, Engineering Problems, Neural Network Solutions; Proceedings of EANN-2000, International Conference on Engineering Applications of Neural Networks, pages 183–190, Kingston Upon Thames, England, 2000. Neural Network Centre, Kingston University.
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42Janne Sinkkonen and Samuel Kaski. Clustering by similarity in an auxiliary space. In Kwong Sak Leung, Lai-Wan Chan, and Helen Meng, editors, Proceedings of IDEAL 2000, Second International Conference on Intelligent Data Engineering and Automated Learning, pages 3–8, Berlin, 2000. Springer.
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1999

41Krista Lagus, Timo Honkela, Samuel Kaski, and Teuvo Kohonen. WEBSOM for textual data mining. Artificial Intelligence Review, 13:345–364, 1999.
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40Samuel Kaski, Jarkko Venna, and Teuvo Kohonen. Coloring that reveals high-dimensional structures in data. In T. Gedeon, P. Wong, S. Halgamuge, N. Kasabov, D. Nauck, and K. Fukushima, editors, Proceedings of ICONIP'99, 6th International Conference on Neural Information Processing, volume II, pages 729–734, Piscataway, NJ, 1999. IEEE Service Center.
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39Samuel Kaski. Fast winner search for SOM-based monitoring and retrieval of high-dimensional data. In Proceedings of ICANN99, Ninth International Conference on Artificial Neural Networks, volume 2, pages 940–945, London, 1999. IEE.
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38Krista Lagus and Samuel Kaski. Keyword selection method for characterizing text document maps. In Proceedings of ICANN99, Ninth International Conference on Artificial Neural Networks, volume 1, pages 371–376, London, 1999. IEE.
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37Erkki Oja and Samuel Kaski, editors. Kohonen Maps. Elsevier, Amsterdam, 1999.
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36Teuvo 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.
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1998

35Jari Kangas and Samuel Kaski. 3043 works that have been based on the self-organizing map (SOM) method developed by Kohonen. Technical Report A49, Helsinki University of Technology, Laboratory of Computer and Information Science, Espoo, Finland, February 1998.
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34Samuel Kaski, Jari Kangas, and Teuvo Kohonen. Bibliography of self-organizing map (SOM) papers: 1981–1997. Neural Computing Surveys, 1(3&4):1–176, 1998. Available in electronic form at http://www.icsi.berkeley.edu/protectjagota/NCS/: Vol 1, pp. 102–350.
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33Samuel Kaski, Timo Honkela, Krista Lagus, and Teuvo Kohonen. WEBSOM—self-organizing maps of document collections. Neurocomputing, 21:101–117, 1998.
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32Timo Honkela, Krista Lagus, and Samuel Kaski. Self-organizing maps of large document collections. In Guido Deboeck and Teuvo Kohonen, editors, Visual Explorations in Finance with Self-Organizing Maps, pages 168–178. Springer, London, 1998.
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31Samuel Kaski, Janne Nikkilä, and Teuvo Kohonen. Methods for interpreting a self-organized map in data analysis. In Michel Verleysen, editor, Proceedings of ESANN'98, 6th European Symposium on Artificial Neural Networks, Bruges, April 22-24, pages 185–190. D-Facto, Brussels, Belgium, 1998.
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30Samuel Kaski. Dimensionality reduction by random mapping: Fast similarity computation for clustering. In Proceedings of IJCNN'98, International Joint Conference on Neural Networks, volume 1, pages 413–418. IEEE Service Center, Piscataway, NJ, 1998.
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1997

29Samuel Kaski. Data exploration using self-organizing maps. Acta Polytechnica Scandinavica, Mathematics, Computing and Management in Engineering Series No. 82, March 1997. Dr.Tech. Thesis, Helsinki University of Technology, Finland.
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28Timo Honkela, Samuel Kaski, Krista Lagus, and Teuvo Kohonen. WEBSOM—self-organizing maps of document collections. In Proceedings of WSOM'97, Workshop on Self-Organizing Maps, Espoo, Finland, June 4-6, pages 310–315. Helsinki University of Technology, Neural Networks Research Centre, Espoo, Finland, 1997.
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27Teuvo Kohonen, Samuel Kaski, Harri Lappalainen, and Jarkko Saloj?vi. 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.
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26Teuvo Kohonen, Samuel Kaski, and Harri Lappalainen. Self-organized formation of various invariant-feature filters in the adaptive-subspace SOM. Neural Computation, 9:1321–1344, 1997.
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25Samuel Kaski. Computationally efficient approximation of a probabilistic model for document representation in the WEBSOM full-text analysis method. Neural Processing Letters, 5:139–151, 1997.
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1996

24Janne Sinkkonen, Samuel Kaski, Minna Huotilainen, Risto J. Ilmoniemi, Risto Näätänen, and Kai Kaila. Optimal resource allocation for novelty detection in a human auditory memory. Neuroreport, 7:2479–2482, 1996.
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23Samuel Kaski, Timo Honkela, Krista Lagus, and Teuvo Kohonen. Creating an order in digital libraries with self-organizing maps. In Proceedings of WCNN'96, World Congress on Neural Networks, September 15-18, San Diego, California, pages 814–817. Lawrence Erlbaum and INNS Press, Mahwah, NJ, 1996.
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22Krista Lagus, Timo Honkela, Samuel Kaski, and Teuvo Kohonen. Self-organizing maps of document collections: A new approach to interactive exploration. In Evangelios Simoudis, Jiawei Han, and Usama Fayyad, editors, Proceedings of the Second International Conference on Knowledge Discovery and Data Mining, pages 238–243. AAAI Press, Menlo Park, California, 1996.
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21Jari Kangas and Samuel Kaski. Compression of vector quantization code sequences based on code frequencies and spatial redundancies. In Proceedings of ICIP'96, IEEE International Conference on Image Processing, Lausanne, Switzerland, September 16-19, volume III, pages 463–466. IEEE Service Center, Piscataway, NJ, 1996.
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20Krista Lagus, Timo Honkela, Samuel Kaski, and Teuvo Kohonen. WEBSOM – a status report. In Jarmo Alander, Timo Honkela, and Matti Jakobsson, editors, Proceedings of STeP'96, Finnish Artificial Intelligence Conference, pages 73–78. Finnish Artificial Intelligence Society, Vaasa, Finland, 1996.
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19Teuvo Kohonen, Samuel Kaski, Krista Lagus, and Timo Honkela. Very large two-level SOM for the browsing of newsgroups. In C. von der Malsburg, W. von Seelen, J. C. Vorbrüggen, and B. Sendhoff, editors, Proceedings of ICANN96, International Conference on Artificial Neural Networks, Bochum, Germany, July 16-19, 1996, Lecture Notes in Computer Science, vol. 1112, pages 269–274. Springer, Berlin, 1996.
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18Samuel Kaski and Krista Lagus. Comparing self-organizing maps. In C. von der Malsburg, W. von Seelen, J. C. Vorbrüggen, and B. Sendhoff, editors, Proceedings of ICANN96, International Conference on Artificial Neural Networks, Bochum, Germany, July 16-19, Lecture Notes in Computer Science, vol. 1112, pages 809–814. Springer, Berlin, 1996.
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17Timo Honkela, Samuel Kaski, Krista Lagus, and Teuvo Kohonen. Exploration of full-text databases with self-organizing maps. In Proceedings of the ICNN96, International Conference on Neural Networks, volume I, pages 56–61. IEEE Service Center, Piscataway, NJ, 1996.
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16Krista Lagus, Samuel Kaski, Timo Honkela, and Teuvo Kohonen. Browsing digital libraries with the aid of self-organizing maps. In Proceedings of the Fifth International World Wide Web Conference WWW5, May 6-10, Paris, France, volume Poster Proceedings, pages 71–79. EPGL, 1996.
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15Timo Honkela, Samuel Kaski, Krista Lagus, and Teuvo Kohonen. Self-organizing maps of document collections. ALMA, 1(2), 1996. Electronic Journal, address http://www.diemme.it/ luigi/alma.html.
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14Timo Honkela, Samuel Kaski, Krista Lagus, and Teuvo Kohonen. Newsgroup exploration with WEBSOM method and browsing interface. Technical Report A32, Helsinki University of Technology, Laboratory of Computer and Information Science, Espoo, Finland, 1996.
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13Samuel Kaski and Teuvo Kohonen. Exploratory data analysis by the self-organizing map: Structures of welfare and poverty in the world. In Apostolos-Paul N. Refenes, Yaser Abu-Mostafa, John Moody, and Andreas Weigend, editors, Neural Networks in Financial Engineering. Proceedings of the Third International Conference on Neural Networks in the Capital Markets, London, England, 11-13 October, 1995, pages 498–507. World Scientific, Singapore, 1996.
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1995

12Sirkka-Liisa Joutsiniemi, Samuel Kaski, and Andreo Larsen. Self-organizing map in recognition of topographic patterns of EEG spectra. IEEE Transactions on Biomedical Engineering, 42:1062–1068, 1995.
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11Samuel Kaski and Teuvo Kohonen. Structures of welfare and poverty in the world discovered by the self-organizing map. Technical Report A24, Helsinki University of Technology, Laboratory of Computer and Information Science, Espoo, Finland, 1995.
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1994

10Jukka Iivarinen, Teuvo Kohonen, Jari Kangas, and Samuel Kaski. Visualizing the clusters on the self-organizing map. In Christer Carlsson, Timo Järvi, and Tapio Reponen, editors, Proceedings of the Conference on Artificial Intelligence Research in Finland, number 12 in Publications of the Finnish Artificial Intelligence Society, pages 122–126. Finnish Artificial Intelligence Society, Helsinki, Finland, 1994.
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9Samuel Kaski and Teuvo Kohonen. Winner-take-all networks for physiological models of competitive learning. Neural Networks, 7:973–984, 1994.
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1993

8Samuel Kaski. Hermoverkkomalleissa tapahtuvaan kilpailuoppimiseen liittyvät mekanismit (Mechanisms connected with competitive learning in neural network models). Master's thesis, Helsinki University of Technology, 1993. (In Finnish).
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7Karin Portin, Riitta Salmelin, and Samuel Kaski. Analysis of magnetoencephalographic data with self-organizing maps. In T. Kuusela, editor, Proceedings of the XXVII Annual Conference of the Finnish Physical Society, page 15.2, Turku, 1993. Finnish Physical Society. Report TURKU-SFL-R5, Department of Applied Physics, University of Turku.
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6Samuel Kaski and Sirkka-Liisa Joutsiniemi. Monitoring EEG signal with the self-organizing map. In Stan Gielen and Bert Kappen, editors, Proceedings of the International Conference on Artificial Neural Networks (ICANN93), Amsterdam, September 13-16, pages 974–977, London, 1993. Springer-Verlag.
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1992

5Samuel Kaski. Viivemukautuvat topografiset komponentit: Tuntoärsykkeisiin liittyvät aivojen jännitevasteet uudella menetelmällä analysoituina (Latency-adjusting topographic components model: An analysis of somatosensory evoked potentials with a novel method). Master's thesis, University of Helsinki, 1992. (In Finnish).
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4Pekka Utela, Kari Torkkola, Lea Leinonen, Jari Kangas, Samuel Kaski, and Teuvo Kohonen. Speech recognition and analysis. In Proceedings of the Fifth Finnish Artificial Intelligence Conference (SteP-92): New Directions in Artificial Intelligence, Espoo, Finland, June 9-11, volume 2, pages 178–182. Finnish Artificial Intelligence Society (FAIS), 1992.
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3Pekka Utela, Samuel Kaski, and Kari Torkkola. Using phoneme group specific LVQ-codebooks with HMMs. In Proceedings of the 1992 International Conference on spoken language processing (ICSLP 92). Banff, Alberta, Canada, October 12-16, pages 551–554, Edmonton, Canada, 1992. Personal Publishing Ltd.
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2Teuvo Kohonen and Samuel Kaski. The self-organizing map as a model for the formation of memory representations. In Abstracts of the 15th Annual Meeting of the European Neuroscience Association. Munich, September 13-17, page 280. Oxford University Press, 1992. Supplement No. 5 to the European Journal of Neuroscience.
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1991

1Kari Torkkola, Jari Kangas, Pekka Utela, Samuel Kaski, Mikko Kokkonen, Mikko Kurimo, and Teuvo Kohonen. Status report of the Finnish phonetic typewriter project. In T. Kohonen, K. Mäkisara, O. Simula, and J. Kangas, editors, Artificial Neural Networks, pages 771–776, Amsterdam, 1991. North-Holland.
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