Samuel Kaski

Professor, Academy Professor

Research outputs

  1. 2020
  2. Accepted/In press

    Human Strategic Steering Improves Performance of Interactive Optimization

    Colella, F., Daee, P., Jokinen, J., Oulasvirta, A. & Kaski, S., 13 May 2020, (Accepted/In press) Proceedings of the 28th ACM Conference on User Modeling, Adaptation and Personalization: UMAP 2020. 5 p.

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

  3. Accepted/In press

    Learning spectrograms with convolutional spectral kernels

    Shen, Z., Heinonen, M. & Kaski, S., 2020, (Accepted/In press) The 23rd International Conference on Artificial Intelligence and Statistic. (Proceedings of Machine Learning Research).

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

  4. Published

    Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium

    Arredondo-Alonso, S., Top, J., McNally, A., Puranen, S., Pesonen, M., Pensar, J., Marttinen, P., Braat, J., Rogers, M., van Schaik, W., Kaski, S., Willems, R. J. L., Corander, J. & Schürch, A., 2020, In : MBIO. 11, 1, e03284-19.

    Research output: Contribution to journalArticleScientificpeer-review

  5. 2019
  6. Published

    Machine Teaching of Active Sequential Learners

    Peltola, T., Çelikok, M. M., Daee, P. & Kaski, S., 28 Nov 2019, 33rd Conference on Neural Information Processing Systems: NeurIPS 2019 . Neural Information Processing Systems Foundation, p. 11202-11213 12 p. (Advances in Neural Information Processing Systems).

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

  7. Accepted/In press

    Scalable Probabilistic Matrix Factorization with Graph-­Based Priors

    Strahl, J., Peltonen, J., Mamitsuka, H. & Kaski, S., 22 Nov 2019, (Accepted/In press) Proceedings of AAAI-20, AAAI Conference on Artificial Intelligence. AAAI, 9 p.

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

  8. Published

    Modelling G×E with historical weather information improves genomic prediction in new environments

    Gillberg, J., Marttinen, P., Mamitsuka, H. & Kaski, S., 15 Oct 2019, In : Bioinformatics (Oxford, England). 35, 20, p. 4045-4052 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Published

    Local dimension reduction of summary statistics for likelihood-free inference

    Siren, J. & Kaski, S., 4 Oct 2019, In : STATISTICS AND COMPUTING. 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published
  11. Published

    Bayesian metabolic flux analysis reveals intracellular flux couplings

    Heinonen, M., Osmala, M., Mannerström, H., Wallenius, J., Kaski, S., Rousu, J. & Lähdesmäki, H., 15 Jul 2019, In : Bioinformatics. 35, 14, p. i548-i557 btz315.

    Research output: Contribution to journalArticleScientificpeer-review

  12. Published

    Block HSIC Lasso: Model-free biomarker detection for ultra-high dimensional data

    Climente-González, H., Azencott, C. A., Kaski, S. & Yamada, M., 15 Jul 2019, In : Bioinformatics. 35, 14, p. i427-i435 btz333.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Published

    Representation transfer for differentially private drug sensitivity prediction

    Niinimäki, T., Heikkilä, M. A., Honkela, A. & Kaski, S., 15 Jul 2019, In : Bioinformatics. 35, 14, p. i218-i224 btz373.

    Research output: Contribution to journalArticleScientificpeer-review

  14. Published

    Learning Image Relations with Contrast Association Networks

    Lu, Y., Yang, Z., Kannala, J. & Kaski, S., 1 Jul 2019, 2019 International Joint Conference on Neural Networks, IJCNN 2019. IEEE, 7 p. 8852344. (Proceedings of the International Joint Conference on Neural Networks; vol. 2019-July).

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

  15. Published

    Human-in-the-loop Active Covariance Learning for Improving Prediction in Small Data Sets

    Afrabandpey, H., Peltola, T. & Kaski, S., Jul 2019, Proceedings of the 28th International Joint Conference on Artificial Intelligence, IJCAI 2019. p. 1959-1966 8 p. (IJCAI International Joint Conference on Artificial Intelligence).

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

  16. Published

    Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

    AstraZeneca-Sanger Drug Combination DREAM Consortium, Kaski, S. & Marttinen, P., 17 Jun 2019, In : Nature Communications. 10, 1, p. 1-17 17 p., 2674.

    Research output: Contribution to journalArticleScientificpeer-review

  17. Published

    Parameter Inference for Computational Cognitive Models with Approximate Bayesian Computation

    Kangasrääsiö, A., Jokinen, J. P. P., Oulasvirta, A., Howes, A. & Kaski, S., 1 Jun 2019, In : COGNITIVE SCIENCE. 43, 6, 40 p., 12738.

    Research output: Contribution to journalArticleScientificpeer-review

  18. Published

    Harmonizable mixture kernels with variational Fourier features

    Shen, Z., Heinonen, M. & Kaski, S., May 2019, The 22nd International Conference on Artificial Intelligence and Statistic. p. 1812-1821 (Proceedings of Machine Learning Research; vol. 89).

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

  19. Published

    Discovering heritable modes of MEG spectral power

    Leppäaho, E., Renvall, H., Salmela, E., Kere, J., Salmelin, R. & Kaski, S., 1 Apr 2019, In : Human Brain Mapping . 40, 5, p. 1391-1402 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  20. Published

    Deep learning with differential Gaussian process flows

    Hegde, P., Heinonen, M., Lähdesmäki, H. & Kaski, S., Apr 2019, The 22nd International Conference on Artificial Intelligence and Statistic. Vol. 89. p. 1-15 16 p. (Proceedings of Machine Learning Research; vol. 89).

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

  21. Published

    Integrating neurophysiologic relevance feedback in intent modeling for information retrieval

    Jacucci, G., Barral, O., Daee, P., Wenzel, M., Serim, B., Ruotsalo, T., Pluchino, P., Freeman, J., Gamberini, L., Kaski, S. & Blankertz, B., 12 Mar 2019, In : JOURNAL OF THE ASSOCIATION FOR INFORMATION SCIENCE AND TECHNOLOGY. 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    Distributed Bayesian matrix factorization with limited communication

    Qin, X., Blomstedt, P., Leppäaho, E., Parviainen, P. & Kaski, S., 1 Jan 2019, In : Machine Learning. p. 1-26

    Research output: Contribution to journalArticleScientificpeer-review

  23. Published

    Scalable Bayesian non-linear matrix completion

    Qin, X., Blomstedt, P. & Kaski, S., 1 Jan 2019, Proceedings of the 28th International Joint Conference on Artificial Intelligence, IJCAI 2019. Kraus, S. (ed.). p. 3275-3281 7 p. (IJCAI International Joint Conference on Artificial Intelligence; vol. 2019-August).

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

  24. Published

    Aaltovaikutus = The Aalto Effect

    Hölttä, M. (ed.), Flowers, A. (ed.), Hopiavaara, R. (ed.), Särkisilta-Lundberg, R. (ed.), Tolonen, A. (ed.), Seppälä, H. (ed.), Norjamäki, N. (ed.), Rosin, S. (ed.), Ollikainen, T. (ed.), Kinnunen, K. (ed.), Aulanko-Jokirinne, T. (ed.), Syri, S., Lundström, M., Malmi, T., Saarimaa, T., Helke, S., Kaski, S., Mäkelä, M., Mladenovic, M. & Remes, H., 2019, Aalto University. 198 p. (Aalto-yliopiston julkaisusarja CROSSOVER; vol. 2019, no. 4)

    Research output: Book/ReportAnthologyProfessional

  25. Published

    Active Learning for Decision-Making from Imbalanced Observational Data

    Sundin, I., Schulam, P., Siivola, E., Vehtari, A., Saria, S. & Kaski, S., 2019, 36th International Conference on Machine Learning, ICML 2019. p. 10578-10587 10 p. (Proceedings of Machine Learning Research; vol. 97).

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

  26. Accepted/In press

    Deep convolutional Gaussian process

    Blomqvist, K., Kaski, S. & Heinonen, M., 2019, (Accepted/In press) Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases.

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

  27. Published

    Embarrassingly parallel MCMC using deep invertible transformations

    Mesquita, D., Blomstedt, P. & Kaski, S., 2019, 35th Conference on Uncertainty in Artificial Intelligence (UAI 2019) . AUAI Press

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

  28. Published
  29. Published

    Interactive AI with a Theory of Mind

    Peltola, T., Çelikok, M. M., Daee, P. & Kaski, S., 2019. 6 p.

    Research output: Contribution to conferencePaperScientificpeer-review

  30. Published
  31. 2018
  32. Published

    Depression, depressive symptoms and treatments in women who have recently given birth: UK cohort study

    Petersen, I., Peltola, T., Kaski, S., Walters, K. R. & Hardoon, S., 24 Oct 2018, In : BMJ Open. 8, 10, p. 1-8 8 p., e02215.

    Research output: Contribution to journalArticleScientificpeer-review

  33. Published

    Inverse reinforcement learning from summary data

    Kangasrääsiö, A. & Kaski, S., Sep 2018, In : Machine Learning. 107, 8-10, p. 1517–1535

    Research output: Contribution to journalArticleScientificpeer-review

  34. Published

    ELFI: Engine for likelihood-free inference

    Lintusaari, J., Vuollekoski, H., Kangasrääsiö, A., Skytén, K., Järvenpää, M., Marttinen, P., Gutmann, M. U., Vehtari, A., Corander, J. & Kaski, S., 1 Aug 2018, In : Journal of Machine Learning Research. 19, p. 1-7 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  35. Published

    Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge

    Sundin, I., Peltola, T., Micallef, L., Afrabandpey, H., Soare, M., Majumder, M. M., Daee, P., He, C., Serim, B., Havulinna, A., Heckman, C., Jacucci, G., Marttinen, P. & Kaski, S., 27 Jun 2018, In : Bioinformatics. 34, 13, p. i395-i403

    Research output: Contribution to journalArticleScientificpeer-review

  36. Published

    User Modelling for Avoiding Overfitting in Interactive Knowledge Elicitation for Prediction

    Daee, P., Peltola, T., Vehtari, A. & Kaski, S., 8 Mar 2018, IUI 2018 - Proceedings of the 23rd International Conference on Intelligent User Interfaces. ACM, p. 305-310 6 p.

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

  37. Published

    Phenotype-driven identification of epithelial signalling clusters

    Marques, E., Peltola, T., Kaski, S. & Klefström, J., 5 Mar 2018, In : Scientific Reports. 8, 1, p. 1-13 4034.

    Research output: Contribution to journalArticleScientificpeer-review

  38. Published

    Efficient differentially private learning improves drug sensitivity prediction

    Honkela, A., Das, M., Nieminen, A., Dikmen, O. & Kaski, S., 6 Feb 2018, In : BIOLOGY DIRECT. 13, 1, p. 1-12

    Research output: Contribution to journalArticleScientificpeer-review

  39. Published

    AI is far from ready

    Kaski, S., 2018, 1 p. AALTO-YLIOPISTO.

    Research output: Other contributionProfessional

  40. Published

    Deep Transfer Learning of Representations for Differentially Private Learning

    Niinimäki, T., Heikkilä, M., Kaski, S. & Honkela, A., 2018.

    Research output: Contribution to conferencePaperScientificpeer-review

  41. Published

    Interactive Intent Modeling for Exploratory Search

    Ruotsalo, T., Peltonen, J., Eugster, M. JA., Glowacka, D., Floréen, P., Myllymäki, P., Jacucci, G. & Kaski, S., 2018, In : ACM TRANSACTIONS ON INFORMATION SYSTEMS. 36, 4, p. 1-46 44.

    Research output: Contribution to journalArticleScientificpeer-review

  42. Published

    Likelihood-free inference via classification

    Gutmann, M. U., Dutta, R., Kaski, S. & Corander, J., 2018, In : STATISTICS AND COMPUTING. 28, 2, p. 411–425 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  43. Published

    Probabilistic Formulation of the Take The Best Heuristic

    Peltola, T., Jokinen, J. & Kaski, S., 2018, CogSci 2018 Proceedings . COGNITIVE SCIENCE SOCIETY, p. 2214-2219

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

  44. Published

    Using counterfactual queries to improve models for decision-support

    Sundin, I., Schulam, P., Siivola, E., Vehtari, A., Saria, S. & Kaski, S., 2018.

    Research output: Contribution to conferenceAbstractScientificpeer-review

  45. Published

    Variational zero-inflated Gaussian processes with sparse kernels

    Hegde, P., Heinonen, M. & Kaski, S., 2018, 34th Conference on Uncertainty in Artificial Intelligence 2018, UAI 2018. AUAI Press, Vol. 1. p. 361-371 148

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

  46. 2017
  47. Published

    Inference of Strategic Behavior based on Incomplete Observation Data

    Kangasrääsiö, A. & Kaski, S., 8 Dec 2017, NIPS17 Workshop: Learning in the Presence of Strategic Behavior. Carnegie Mellon University, 4 p.

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

  48. Published

    A Mutually-Dependent Hadamard Kernel for Modelling Latent Variable Couplings

    Remes, S., Heinonen, M. & Kaski, S., Nov 2017, Proceedings of the 9th Asian Conference on Machine Learning. Zhang, M-L. & Noh, Y-K. (eds.). p. 455-470 16 p. (Proceedings of Machine Learning Research; vol. 77).

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

  49. Published

    The inconvenience of data of convenience: Computational research beyond post-mortem analyses

    Azencott, C. A., Aittokallio, T., Roy, S., Norman, T., Friend, S., Stolovitzky, G., Goldenberg, A., Agrawal, A., Barillot, E., Bessonov, N., Chasman, D., Czerwinska, U., Siahpirani, A. F., Greenberg, J., Huber, M., Kaski, S., Kurz, C., Mailick, M., Merzenich, M., Morozova, N. & 16 others, Movaghar, A., Nahum, M., Nordling, T. E. M., Penner, R., Saha, K., Salim, A., Sorooshyari, S., Soumelis, V., Stark-Inbar, A., Sterling, A., Shiju, S. S., Tang, J., Tosenberger, A., Van Vieet, T., Wennerberg, K. & Zinovyev, A., 1 Oct 2017, In : Nature Methods. 14, 10, p. 937-938 2 p.

    Research output: Contribution to journalLetterScientific

  50. Published

    MediSyn: Uncertainty-aware Visualization of Multiple Biomedical Datasets to Support Drug Treatment Selection

    He, C., Micallef, L., Tanoli, Z-U-R., Kaski, S., Aittokallio, T. & Jacucci, G., 13 Sep 2017, In : BMC Bioinformatics. 18, p. 1-12 393.

    Research output: Contribution to journalArticleScientificpeer-review

  51. Published

    Convex factorization machine for toxicogenomics prediction

    Yamada, M., Lian, W., Goyal, A., Chen, J., Wimalawarne, K., Khan, S. A., Kaski, S., Mamitsuka, H. & Chang, Y., 13 Aug 2017, KDD 2017 - Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. ACM, p. 1215-1224 10 p.

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

  52. Published

    Localized Lasso for High-Dimensional Regression

    Yamada, M., Koh, T., Iwata, T., Shawe-Taylor, J. & Kaski, S., 1 Aug 2017, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. Singh, A. & Zhu, J. (eds.). Fort Lauderdale, FL, USA, p. 325-333 9 p. (Proceedings of Machine Learning Research; vol. 54).

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

  53. Published

    Knowledge elicitation via sequential probabilistic inference for high-dimensional prediction

    Daee, P., Peltola, T., Soare, M. & Kaski, S., 12 Jul 2017, In : Machine Learning. 106, 9, p. 1599-1620 22 p.

    Research output: Contribution to journalArticleScientificpeer-review

  54. Published

    Interactive Prior Elicitation of Feature Similarities for Small Sample Size Prediction

    Afrabandpey, H., Peltola, T. & Kaski, S., 10 Jul 2017, Proceedings of the 25th Conference on User Modeling, Adaptation and Personalization . Bratislava, Slovakia: ACM, p. 265-269 4 p.

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

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