Statistical Machine Learning and Bioinformatics research group / Samuel Kaski

  • PL 68 (Gustaf Hällströmin katu 2b), A343

    HELSINGIN YLIOPISTO

    Finland

Publications 2001 2015

2015

Advances in Independent Component Analysis and Learning Machines

Bingham, E. E. (ed.), Kaski, S. J. I. (ed.), Laaksonen, J. (ed.) & Lampinen, J. (ed.), 2015, Amsterdam: Elsevier Scientific Publ. Co. 296 p.

Research output: Book/ReportAnthology or special issueScientificpeer-review

Developing a Symbiotic System for Scientific Information Seeking: The MindSee Project

Gamberini, L., Spagnolli, A., Blankertz, B., Kaski, S., Freeman, J., Acqualagna, L., Barral, O., Bellio, M., Chech, L., Eugster, M., Ferrari, E., Negri, P., Orso, V., Pluchino, P., Minelle, F., Serim, B., Wenzel, M. & Jacucci, G., 2015, Symbiotic Interaction : 4th International Workshop, Symbiotic 2015 Berlin, Germany, October 7–8, 2015 Proceedings. Blankertz, B., Jacucci, G., Gamberini, L., Spagnolli, A. & Freeman, J. (eds.). Cham: Springer International Publishing AG, p. 68-80 13 p. (Lecture Notes in Computer Science; vol. 9359).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Exploring Peripheral Physiology As a Predictor of Perceived Relevance in Information Retrieval

Barral, O., Eugster, M. J. A., Ruotsalo, T., Spapé, M. M., Kosunen, I., Ravaja, N., Kaski, S. & Jacucci, G., 2015, Proceedings of the 20th International Conference on Intelligent User Interfaces. Atlanta, Georgia, USA: ACM, p. 389-399 11 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Improving controllability and predictability of interactive recommendation interfaces for exploratory search

Kangasrääsiö, A., Głowacka, D. & Kaski, S., 2015, IUI '15 Proceedings of the 20th International Conference on Intelligent User Interfaces . New York, NY: ACM , p. 247-251 5 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Interactive intent modeling: Information discovery beyond search

Ruotsalo, T., Jacucci, G., Myllymäki, P. & Kaski, S., Jan 2015, In : Communications of the ACM. 58, 1, p. 86-92 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Majorization-Minimization for Manifold Embedding

Yang, Z., Peltonen, J. T. & Kaski, S. J. I., 10 May 2015, Proceedings of the Eighteenth International Conference on Artificial Intelligence and Statistics. Lebanon, G. & Vishwanathan, S. V. N. (eds.). Cambridge, MA: Journal of Machine Learning Research, p. 1088-1097 10 p. (JMLR: Workshop and Conference Proceedings series; vol. 38).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Towards brain-activity-controlled information retrieval: Decoding image relevance from MEG signals

Kauppi, J-P., Kandemir, M., Saarinen, V-M., Hirvenkari, L., Parkkonen, L., Klami, A., Hari, R. & Kaski, S., 15 May 2015, In : NeuroImage. 112, p. 288-298 11 p.

Research output: Contribution to journalArticleScientificpeer-review

2014

Bayesian multi-view tensor factorization

Khan, S. A. & Kaski, S., 2014, Machine Learning and Knowledge Discovery in Databases: European Conference, ECML PKDD 2014, Nancy, France, September 15-19, 2014. Proceedings. Calders, T., Esposito, F., Hüllermeier, E. & Meo, R. (eds.). Heidelberg: Springer-Verlag, Vol. 1. p. 656-671 16 p. (Lecture Notes in Computer Science; vol. 8724).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Computational statistics approaches to study metabolic syndrome

Huopaniemi, I. & Kaski, S., 2014, A systems biology approach to study metabolic syndrome. Orešic, M. & Vidal-Puig, A. (eds.). Dordrecht: Springer, p. 319-339 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Cross-organism toxicogenomics with group factor analysis

Suvitaival, T., Parkkinen, J., Virtanen, S. & Kaski, S., 2014, In : Systems Biomedicine. 2, 4, p. 71-80 10 p., e29291.

Research output: Contribution to journalArticleScientificpeer-review

Intentradar: search user interface that anticipates user's search intents

Ruotsalo, T., Peltonen, J., Eugster, M., Glowacka, D., Reijonen, A., Jacucci, G., Myllymäki, P. & Kaski, S., 2014, CHI EA '14 CHI '14 Extended Abstracts on Human Factors in Computing Systems . New York: ACM, p. 455-458 4 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Multi-task and multi-view learning of user state

Kandemir, M., Vetek, A., Gönen, M., Klami, A. & Kaski, S., 2 Sep 2014, In : Neurocomputing. 139, p. 97-106

Research output: Contribution to journalArticleScientificpeer-review

Optimal Neighborhood Preserving Visualization by Maximum Satisfiability

Bunte, K., Järvisalo, M., Berg, O., Myllymäki, P., Peltonen, J. & Kaski, S., 2014, Proceedings of the 28th AAAI Conference on Artificial Intelligence (AAAI 2014). Brodley, C. E. & Stone, P. (eds.). AAAI Press, p. 1694-1700 7 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Optimization Equivalence of Divergences Improves Neighbor Embedding

Yang, Z., Peltonen, J. & Kaski, S., 2014, Proceedings of ICML 2014, the 31st International Conference on Machine Learning. Xing, E. P. & Jebara, T. (eds.). Journal of Machine Learning Research, p. 460-468 9 p. (JMLR Workshop and Conference Proceedings; vol. 32).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Predicting term-relevance from brain signals

Eugster, M., Ruotsalo, T., Spape, M., Kosunen, I., Barral Mery de Bellegarde, O., Ravaja, N., Jacucci, G. & Kaski, S., 2014, SIGIR '14 Proceedings of the 37th international ACM SIGIR conference on Research & development in information retrieval. New York, NY, USA: ACM, p. 425-434

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Probabilistic drug connectivity mapping

Parkkinen, J. A. & Kaski, S., 17 Apr 2014, In : BMC Bioinformatics. 15, 10 p., 113.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics: AISTATS 2014

Kaski, S. (ed.) & Corander, J. (ed.), 2014, Journal of Machine Learning Research. (JMLR W&CP; vol. 33)

Research output: Book/ReportAnthology or special issueScientificpeer-review

Retrieval of experiments by efficient comparison of marginal likelihoods

Seth, S., Shawe-Taylor, J. & Kaski, S., 2014, Neural Information Processing: 21st International Conference, ICONIP 2014, Kuching, Malaysia, November 3-6, 2014 : Proceedings. Loo, C. K., Yap, K. S., Wong, K. W., Teon, A. & Huang, K. (eds.). Cham: Springer, Vol. II. p. 135-142 8 p. (Lecture Notes in Computer Science; vol. 8835).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations

Suvitaival, T., Rogers, S. & Kaski, S., 1 Sep 2014, In : Bioinformatics. 30, 17, p. I461-I467 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Stronger findings from mass spectral data through multi-peak modeling

Suvitaival, T., Rogers, S. & Kaski, S., 19 Jun 2014, In : BMC Bioinformatics. 15, 11 p., 208.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Toward computational cumulative biology by combining models of biological datasets

Faisal, A., Peltonen, J., Georgii, E., Rung, J. & Kaski, S., 2014, In : PLoS One. 9, 11, e113053.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2013

Bayesian Information Sharing Between Noise And Regression Models Improves Prediction of Weak Effects

Gillberg, J., Marttinen, P., Pirinen, M., Kangas, A. J., Soininen, P., Järvelin, M-R., Ala-Korpela, M. & Kaski, S., 16 Oct 2013, In : arXiv.org . 1310.4362v1 , 9 p.

Research output: Contribution to journalArticleScientific

Directing Exploratory Search with Interactive Intent Modeling

Ruotsalo, T., Jaakko, P., Eugster, M. J. A., Glowacka, D., Konyushkova, K., Athukorala, K., Kosunen, I., Reijonen, A., Myllymäki, P., Jacucci, G. & Kaski, S., 2013, ACM International Conference on Information and Knowledge Management (CIKM 2013). New York: ACM, p. 1759-1764 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Identifying fragments of natural speech from the listener's MEG signals

Koskinen, M., Viinikanoja, J., Kurimo, M., Klami, A., Kaski, S. & Hari, R., Jun 2013, In : Human Brain Mapping. 34, 6, p. 1477-1489 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Information Retrieval Perspective to Interactive Data Visualization

Peltonen, J., Sandholm, M. & Kaski, S., 2013, Proceedings of the Eurographics Conference on Visualization (Eurovis 2013). Hlawitschka, M. & Weinkauf, T. (eds.). The Eurographics Association, p. 49-53 5 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

SciNet: A System for Browsing Scientific Literature through Keyword Manipulation

Glowacka, D., Ruotsalo, T., Konyushkova, K., Athukorala, K., Kaski, S. & Jacucci, G., 2013, Proceedings of the International Conference on Intelligent User Interfaces (IUI'13 Companion). ACM, p. 61-62 2 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2012

Bayesian Group Factor Analysis

Virtanen, S., Klami, A., Khan, S. A. & Kaski, S., 2012, In : JMRL : Workshop and Conference Proceedings. 22, p. 1269-1277 9 p.

Research output: Contribution to journalConference articleScientificpeer-review

Focused multi-task learning in a Gaussian process framework

Leen, G., Peltonen, J. & Kaski, S., 1 Oct 2012, In : Machine Learning. 89, 1-2, SI, p. 157-182 26 p.

Research output: Contribution to journalArticleScientificpeer-review

2011

An Augmented Reality Interface to Contextual Information

Ajanki, A., Billinghurst, M., Gamper, H., Järvenpää, T., Kandemir, M., Kaski, S., Koskela, M., Kurimo, M., Laaksonen, J., Puolamäki, K., Ruokolainen, T. & Tossavainen, T., 2011, In : Virtual Reality. 15, 2-3, p. 161-173

Research output: Contribution to journalArticleScientificpeer-review

Artificial Neural Networks and Machine Learning - Proceedings of ICANN 2011 - 21st International Conference on Artificial Neural Networks, Part I

Honkela, T. (ed.), Duch, W. (ed.), Girolami, M. A. (ed.) & Kaski, S. (ed.), 2011, Springer.

Research output: Book/ReportAnthology or special issueScientificpeer-review

Artificial Neural Networks and Machine Learning - Proceedings of ICANN 2011 - 21st International Conference on Artificial Neural Networks, Part II

Honkela, T. (ed.), Duch, W. (ed.), Girolami, M. A. (ed.) & Kaski, S. (ed.), 2011, Springer.

Research output: Book/ReportAnthology or special issueScientificpeer-review

Artificial Neural Networks and Machine Learning Research - ICANN 2011: 21st International Conference on Artificial Neural Networks, Espoo, Finland, June 14-17, 2011, Proceedings

Honkela, T. (ed.), Duch, W. (ed.), Girolami, M. (ed.) & Kaski, S. (ed.), 2011, Springer-Verlag. (Lecture Notes in Computer Science; vol. 6971)

Research output: Book/ReportAnthology or special issueScientificpeer-review

Artificial Neural Networks and Machine Learning Research - ICANN 2011: 21st International Conference on Artificial Neural Networks, Espoo, Finland, June 14-17, 2011, Proceedings

Honkela, T., Duch, W., Girolami, M. & Kaski, S., 2011, Springer-Verlag. (Lecture Notes in Computer Science; vol. 6792)

Research output: Book/ReportAnthology or special issueScientificpeer-review

Bayesian CCA via Group Sparsity

Virtanen, S., Klami, A. & Kaski, S., 2011, In : Journal of Machine Learning Research. p. 457-464 8 p.

Research output: Contribution to journalConference articleScientificpeer-review

Biomarker discovery via dependency analysis of multi-view functional genomics data

Faisal, A., Louhimo, R., Lahti, L. M., Kaski, S. & Hautaniemi, S., Dec 2011, Personalized medicine workshop, NIPS 2011. 7 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionProfessional

Cross-Species Translation of Multi-way Biomarkers

Suvitaival, T., Huopaniemi, I., Oresic, M. & Kaski, S., 2011, Artificial neural networks and machine learning - ICANN 2011: 21st International Conference on Artificial Neural Networks, Espoo, Finland, June 14-17, 2011, Proceedings. Springer-Verlag, Vol. 1. p. 209-216 8 p. (Lecture Notes in Computer Science; vol. 6791).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Focused Multi-task Learning Using Gaussian Processes

Leen, G., Peltonen, J. & Kaski, S., 2011, Machine Learning and Knowledge Discovery in Databases: European Conference, ECML PKDD 2011 Athens, Greece, September 5-9, 2011 Proceedings. Gunopulos, D., Hofmann, T., Malerba, D. & Vazirgiannis, M. (eds.). Vol. 2. p. 310-325 16 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Generative Modeling for Maximizing Precision and Recall in Information Visualization

Peltonen, J. & Kaski, S., 2011, In : Journal of Machine Learning Research. 15, p. 597-587 9 p.

Research output: Contribution to journalConference articleScientificpeer-review

High Density Lipoprotein Structural Changes and Drug Response in Lipidomic Profiles following the Long-Term Fenofibrate Therapy in the FIELD Substudy

Yetukuri, L., Huopaniemi, I., Koivuniemi, A., Maranghi, M., Hiukka, A., Nygren, H., Kaski, S., Taskinen, M-R., Vattulainen, I., Jauhiainen, M. & Oresic, M., 2011, In : PLoS One. 6, p. e23589 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Introduction to the special issue on mining and learning with graphs

Vishwanathan, S. V. N., Kaski, S., Neville, J. & Wrobel, S., 2011, In : Machine Learning. 82, 2, p. 91-93 3 p.

Research output: Contribution to journalArticleScientific

Machine learning: Special issue on mining and learning with graphs

Vishwanathan, S. V. N., Kaski, S., Neville, J. & Wrobel, S., 2011, Springer-Verlag. (Machine learning; vol. 82, no. 2)

Research output: Book/ReportAnthology or special issueScientificpeer-review

Multitask Learning Using Regularized Multiple Kernel Learning

Gönen, M., Kandemir, M. & Kaski, S., 2011, Neural Information Processing: 18th International Conference, ICONIP 2011 Shanghai, China, November 13-17, 2011 Proceedings. Lu, B-L., Zhang, L. & Kwok, J. (eds.). Vol. 2. p. 500-509 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Probabilistic proactive timeline browser

Ajanki, A. & Kaski, S., 2011, Artificial neural networks and machine learning - ICANN 2011: 21st International Conference on Artificial Neural Networks, Espoo, Finland, June 14-17, 2011, Proceedings. Honkela, T., Duch, W., Girolami, M. & Kaski, S. (eds.). Springer-Verlag, Vol. 2. p. 357-364 8 p. (Lecture Notes in Computer Science; vol. 6792).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2010

Graph Visualization With Latent Variable Models

Parkkinen, J., Nybo, K., Peltonen, J. & Kaski, S., 2010, Proceedings of the Eighth Workshop on Mining and Learning with Graphs: MLG-2010. ACM, p. 94-101

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Hierarchical generative biclustering for microRNA expression analysis

Caldas, J. & Kaski, S., 2010, Research in Computational Molecular Biology: Proceedings of 14th Annual International Conference RECOMB 2010, Lisbon, Portugal, April 25-28. Berger, B. (ed.). Springer, p. 65-79 (Lecture Notes in Computer Science; vol. 6044).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2002

Exploratory Clustering Of Gene Expression Profiles Of Mutated Yeast Strains

Oja, M., Nikkilä, J., Törönen, P., Wong, G. & Kaski, S., 2002

Research output: Book/ReportAnthology or special issueScientificpeer-review

2001

Analysis and Visualization of Gene Expression Data Using Self-Organizing Maps

Kaski, S., Nikkilä, J., Törönen, P., Castrén, E. & Wong, G., 2001

Research output: Book/ReportAnthology or special issueScientificpeer-review