Statistical Machine Learning and Exploratory Data Analysis research group (SMiLE)

The SMiLE research group researches advanced statistical (probabilistic) machine learning methods for data analysis, especially methods for learning from multiple sources of data and methods for interactive analysis including nonlinear dimensionality reduction and visualization of high-dimensional data. Application areas include bioinformatics, telecommunications, intelligent information access, and information retrieval.

Group Members

Jaakko Peltonen
associate professor, group leader1
Md. Hijbul Alam
postdoctoral researcher
Trung Hieu Nguyen
postdoctoral researcher
Ziyuan Lin
doctoral student1
Chien Lu
postgraduate student
Jonathan Strahl
doctoral student1

Co-affiliates through joint projects:
Joonas Kauppinen
doctoral student (joint supervision)
Olli Kuparinen
doctoral student2 (joint supervision)
Essi Syrjälä
doctoral student3 (joint supervision)
Elizaveta Zimina
doctoral student4 (joint supervision)
1also affiliated with Probabilistic Machine Learning group at Aalto University, Department of Computer Science
2affiliated with University of Tampere, Faculty of Communication Sciences
3affiliated with University of Tampere, Faculty of Social Sciences
4affiliated with University of Tampere, Research Center for Information and Systems

Recent Publications

  1. Dominik Sacha, Leishi Shang, Michael Sedlmair, John A. Lee, Jaakko Peltonen, Daniel Weiskopf, Stephen North, and Daniel A. Keim. Visual interaction with dimensionality reduction: a structured literature analysis. IEEE Transactions on Visualization and Computer Graphics, to appear.

  2. Jaakko Peltonen and Ziyuan Lin. Peacock Bundles: Bundle Coloring for Graphs with Globality-Locality Trade-off. In Proceedings of GD 2016, The 24th International Symposium on Graph Drawing & Network Visualization, accepted for publication.

  3. Ziyuan Lin* and Jaakko Peltonen*. An Information Retrieval Approach to Finding Dependent Subspaces of Multiple Views. ArXiv preprint, arXiv:1511.06423 [stat], 2015. (* equal contributions)

  4. Antti Honkela, Jaakko Peltonen, Hande Topa, Iryna Charapitsa, Filomena Matarese, Korbinian Grote, Hendrik G. Stunnenberg, George Reid, Neil D. Lawrence, and Magnus Rattray. Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays. In proceedings of the NIPS 2015 workshop on Machine Learning for Computational Biology, 2015.

  5. Antti Honkela*, Jaakko Peltonen*, Hande Topa, Iryna Charapitsa, Filomena Matarese, Korbinian Grote, Hendrik G. Stunnenberg, George Reid, Neil D. Lawrence, and Magnus Rattray. Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays. Proceedings of the National Academy of Sciences of the United States of America, 112(42):13115-13120, 2015. (* A.H. and J.P. contributed equally to this work.) (final article on publisher webpages)

  6. Tuukka Ruotsalo, Jaakko Peltonen, Manuel J. A. Eugster, Dorota Glowacka, Aki Reijonen, Giulio Jacucci, Petri Myllymäki, and Samuel Kaski. SciNet: Interactive intent modeling for information discovery. In Proceedings of SIGIR'15, the 38th International ACM SIGIR Conference on Research and Development in Information Retrieval, pages 1043-1044. ACM, New York, NY, 2015. Refereed abstract (2 pages). (PDF)

  7. Antti Honkela, Jaakko Peltonen, Hande Topa, Iryna Charapitsa, Filomena Matarese, Korbinian Grote, Hendrik G. Stunnenberg, George Reid, Neil D. Lawrenc$ Genome-wide modelling of transcription kinetics reveals patterns of RNA processing delays. ArXiv preprint, arXiv:1503.01081 [q-bio.GN], 2015.

  8. Jaakko Peltonen and Ziyuan Lin. Information Retrieval Approach to Meta-visualization. Machine Learning, 99(2):189-229, 2015. (final article on publisher webpages)

  9. Chirayu Wongchockprasitti, Jaakko Peltonen, Tuukka Ruotsalo, Payel Bandyopadhyay, Giulio Jacucci and Peter Brusilovsky. User Model In a Box: Cross-System User Model Transfer for Resolving Cold Start Problems. In Proceedings of UMAP'15, The 23rd Conference on User Modelling, Adaptation and Personalization, pages 289-301, Springer, 2015. (final paper on publisher pages, slides, presentation in UMAP conference navigator)

  10. Zhirong Yang, Jaakko Peltonen, and Samuel Kaski. Majorization-Minimization for Manifold Embedding. In Proceedings of AISTATS'15, The 18th International Conference on Artificial Intellgence and Statistics, JMLR W&CP, pp. 1088-1097, 2015. (abstract on publisher webpages, paper on publisher webpages, supplementary information on publisher webpages)

  11. Salvatore Andolina, Khalil Klouche, Jaakko Peltonen, Mohammad Hoque, Tuukka Ruotsalo, Diogo Cabral, Arto Klami, Dorota Glowacka, Patrik Floreen, and Giulio Jacucci. IntentStreams: Smart Parallel Search Streams for Branching Exploratory Search. In Proceedings of ACM IUI 2015, The 20th ACM Conference on Intelligent User Interfaces, pp. 300-305, 2015. (final paper on publisher pages, YouTube video of the system)

  12. Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, and Samuel Kaski. Toward computational cumulative biology by combining models of biological datasets. PLOS ONE, 9(11), 2014. (preprint pdf, final article on publisher webpages)

  13. Joni Pajarinen, Ari Hottinen, and Jaakko Peltonen. Optimizing spatial and temporal reuse in wireless networks by decentralized partially observable Markov decision processes. IEEE Transactions on Mobile Computing, 13(4):866-879, 2014. (preprint pdf, final pdf on publisher pages)

  14. Zhirong Yang, Jaakko Peltonen, and Samuel Kaski. Optimization Equivalence of Divergences Improves Neighbor Embedding. In Proceedings of ICML 2014, The 31st International Conference on Machine Learning, 2014. (final pdf on publisher pages, supplemental document, code)

  15. Kerstin Bunte, Matti Järvisalo, Jeremias Berg, Petri Myllymäki, Jaakko Peltonen and Samuel Kaski. Optimal Neighborhood Preserving Visualization by Maximum Satisfiability. In Proceedings of AAAI-14, The Twenty-Eighth AAAI Conference on Artificial Intelligence, 2014. (preprint pdf, final pdf on publisher pages)

  16. Jaakko Peltonen, Ali Faisal, Elisabeth Georgii, Johan Rung and Samuel Kaski. Toward computational cumulative biology by combining models of biological datasets. In NIPS 2014 Workshop on Machine Learning in Computational Biology, 2014.

  17. Tuukka Ruotsalo, Jaakko Peltonen, Manuel J. A. Eugster, Dorota Glowacka, Ksenia Konyushkova, Kumaripaba Athukorala, Ilkka Kosunen, Aki Reijonen, Petri Myllymaki, Giulio Jacucci, Samuel Kaski. Bayesian Optimization in Interactive Scientific Search. In NIPS 2014 Workshop on Bayesian Optimization in Academia and Industry, 2014.

  18. Kerstin Bunte, Matti Järvisalo, Jeremias Berg, Petri Myllymäki, Jaakko Peltonen and Samuel Kaski. Optimal Neighborhood Preserving Visualization by Maximum Satisfiability. In Proceedings of RCRA 2014, 21st RCRA International Workshop on Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion, 2014.

  19. Antti Kangasrääsiö, Dorota Glowacka, Tuukka Ruotsalo, Jaakko Peltonen, Manuel J. A. Eugster, Ksenia Konyushkova, Kumaripaba Athukorala, Ilkka Kosunen, Aki Reijonen, Petri Myllymäki, Giulio Jacucci, and Samuel Kaski. Interactive Visualization of Search Intent for Exploratory Information Retrieval. In ICML 2014 Workshop on Crowdsourcing and Human Computing, 2014.

  20. Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, and Samuel Kaski. Toward computational cumulative biology by combining models of biological datasets. ArXiv preprint, arXiv:1404.0329v1 [q-bio.QM], 2014.

  21. Tuukka Ruotsalo, Jaakko Peltonen, Aki Reijonen, Giulio Jacucci, Manuel J.A. Euster, and Samuel Kaski. IntentRadar: Interactive Search User Interface that Anticipates User's Search Intents. Refereed extended abstract (4 pages) in CHI Interactivity 2014, 2014.

Recent Research Talks

This is a partial list of recent research talks given by the group.
  • Jaakko Peltonen, University of Pittsburgh, September 2, 2015: An information retrieval approach to visualization of high-dimensional data. An overview of selected visualization works. (pdf slides, announcement of the talk in the CoMeT system)
  • Jaakko Peltonen, University of Pittsburgh, September 1, 2015: Lost in Publications? How to Find Your Way in 50 Million Scientific Documents. Describes the work on information seeking and cross-system transfer of open user models contained in the CIKM 2013 and UMAP 2015 publications. (pdf slides, announcement of the talk in the CoMeT system)