Aki Vehtari

Professor (Associate Professor)

Research outputs

  1. 2020
  2. Accepted/In press

    Parallel Gaussian process surrogate Bayesian inference with noisy likelihood evaluations

    Järvenpää, M., Gutmann, M., Vehtari, A. & Marttinen, P., Feb 2020, (Accepted/In press) In : Bayesian Analysis.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Published

    Minimum mode saddle point searches using Gaussian process regression with inverse-distance covariance function

    Koistinen, O-P., Ásgeirsson, V., Vehtari, A. & Jonsson, H., 14 Jan 2020, In : Journal of Chemical Theory and Computation. 16, 1, p. 499-509

    Research output: Contribution to journalArticleScientificpeer-review

  4. Accepted/In press

    Batch simulations and uncertainty quantification in Gaussian process surrogate approximate Bayesian computation

    Järvenpää, M., Vehtari, A. & Marttinen, P., 2020, (Accepted/In press) Conference on Uncertainty in Artificial Intelligence (UAI 2020).

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

  5. Published

    Expectation Propagation as a Way of Life: A Framework for Bayesian Inference on Partitioned Data

    Vehtari, A., Gelman, A., Sivula, T., Jylanki, P., Tran, D., Sahai, S., Blomstedt, P., Cunningham, J. P., Schiminovich, D. & Robert, C. P., 2020, In : Journal of Machine Learning Research. 21, p. 1-53 53 p.

    Research output: Contribution to journalArticleScientificpeer-review

  6. 2019
  7. Published

    Nudged elastic band calculations accelerated with Gaussian process regression based on inverse interatomic distances

    Koistinen, O-P., Ásgeirsson, V., Vehtari, A. & Jonsson, H., 10 Dec 2019, In : Journal of Chemical Theory and Computation. 15, 12, p. 6738-6751

    Research output: Contribution to journalArticleScientificpeer-review

  8. Published

    Efficient acquisition rules for model-based approximate Bayesian computation

    Järvenpää, M., Gutmann, M. U., Pleska, A., Vehtari, A. & Marttinen, P., Jun 2019, In : Bayesian Analysis. 14, 2, p. 595-622 28 p.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Published

    Deep Learning Spectroscopy: Neural Networks for Molecular Excitation Spectra

    Ghosh, K., Stuke, A., Todorović, M., Jørgensen, P. B., Schmidt, M. N., Vehtari, A. & Rinke, P., 3 May 2019, In : Advanced Science. 6, 9, p. 1-7 7 p., 1801367.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published

    An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data

    Cheng, L., Ramchandran, S., Vatanen, T., Lietzén, N., Lahesmaa, R., Vehtari, A. & Lähdesmäki, H., 17 Apr 2019, In : Nature Communications. 10, 1, p. 1-11 11 p., 1798.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Published

    Variable selection for Gaussian processes via sensitivity analysis of the posterior predictive distribution

    Paananen, T., Piironen, J., Andersen, M. & Vehtari, A., 16 Apr 2019, Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics. 10 p. (Proceedings of Machine Learning Research; vol. 89).

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

  12. Published

    Visualization in Bayesian workflow

    Gabry, J., Simpson, D., Vehtari, A., Betancourt, M. & Gelman, A., 1 Feb 2019, In : Journal of the Royal Statistical Society. Series A: Statistics in Society. 182, 2, p. 389-402 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Published

    R-squared for Bayesian regression models

    Gelman, A., Goodrich, B., Gabry, J. & Vehtari, A., 1 Jan 2019, In : AMERICAN STATISTICIAN. p. 1-6 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  14. 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

  15. Published

    Bayesian leave-one-out cross-validation for large data

    Magnusson, M., Andersen, M., Jonasson, J. & Vehtari, A., 2019, 36th International Conference on Machine Learning, ICML 2019. 10 p. (Proceedings of Machine Learning Research; vol. 97).

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

  16. 2018
  17. Published

    Characterization and non-parametric modeling of the developing serum proteome during infancy and early childhood

    Lietzén, N., Cheng, L., Moulder, R., Siljander, H., Laajala, E., Härkönen, T., Peet, A., Vehtari, A., Tillmann, V., Knip, M., Lähdesmäki, H. & Lahesmaa, R., 1 Dec 2018, In : Scientific Reports. 8, 1, p. 1-13 5883.

    Research output: Contribution to journalArticleScientificpeer-review

  18. Published

    Gaussian process modelling in approximate bayesian computation to estimate horizontal gene transfer in Bacteria

    Järvenpää, M., Gutmann, M. U., Vehtari, A. K. I. & Marttinen, P., 1 Dec 2018, In : Annals of Applied Statistics. 12, 4, p. 2228-2251 24 p.

    Research output: Contribution to journalArticleScientificpeer-review

  19. Accepted/In press

    Bayesian loo for large data

    Magnusson, M., Vehtari, A. & Andersen, M., Dec 2018, (Accepted/In press) Symposium on Advances in Approximate Bayesian Inference. 5 p.

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

  20. Published

    Effectiveness of three interventions for secondary prevention of low back pain in the occupational health setting - A randomised controlled trial with a natural course control

    Rantonen, J., Karppinen, J., Vehtari, A., Luoto, S., Viikari-Juntura, E., Hupli, M., Malmivaara, A. & Taimela, S., Dec 2018, In : BMC Public Health. 18, 1, 598.

    Research output: Contribution to journalArticleScientificpeer-review

  21. Published

    Bayesian aggregation of average data: An application in drug development

    Weber, S., Gelman, A., Lee, D., Betancourt, M., Vehtari, A. & Racine-Poon, A., 1 Sep 2018, In : Annals of Applied Statistics. 12, 3, p. 1583-1604 22 p.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    Using Stacking to Average Bayesian Predictive Distributions (with Discussion)

    Yao, Y., Vehtari, A., Simpson, D. & Gelman, A., Sep 2018, In : Bayesian Analysis. 13, 3, p. 917-1003 87 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. 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

  24. Published

    P95HER2 methionine 611 carboxy-terminal fragment is predictive of trastuzumab adjuvant treatment benefit in the FinHer trial

    Sperinde, J., Huang, W., Vehtari, A., Chenna, A., Kellokumpu-Lehtinen, P. L., Winslow, J., Bono, P., Lie, Y. S., Petropoulos, C. J., Weidler, J. & Joensuu, H., 1 Jul 2018, In : Clinical Cancer Research. 24, 13, p. 3046-3052 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  25. 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

  26. Published

    Yes, but did it work? Evaluating variational inference

    Yao, Y., Vehtari, A., Simpson, D. & Gelman, A., 1 Jan 2018, 35th International Conference on Machine Learning, ICML 2018. Dy, J. & Krause, A. (eds.). Vol. 12. p. 8887-8895 9 p. (Proceedings of Machine Learning Research; no. 80).

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

  27. Published

    Correcting boundary over-exploration deficiencies in Bayesian optimization with virtual derivative sign observations

    Siivola, E., Vehtari, A., Vanhatalo, J., Gonzalez, J. & Andersen, M., 2018, 2018 IEEE 28th International Workshop on Machine Learning for Signal Processing (MLSP) . IEEE, p. 1-6 6 p. 8516936. (Machine learning for signal processing ).

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

  28. Published

    Iterative Supervised Principal Components

    Piironen, J. & Vehtari, A., 2018, International Conference on Artificial Intelligence and Statistics, 9-11 April 2018, Playa Blanca, Lanzarote, Canary Islands. Storkey, A. & Perez-Cruz, F. (eds.). 9 p. (Proceedings of Machine Learning Research; vol. 84).

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

  29. 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

  30. 2017
  31. Published

    Brain-to-brain hyperclassification reveals action-specific motor mapping of observed actions in humans

    Smirnov, D., Lachat, F., Peltola, T., Lahnakoski, J., Koistinen, O-P., Glerean, E., Vehtari, A., Hari, R., Sams, M. & Nummenmaa, L., 11 Dec 2017, In : PloS one. 12, 12, e0189508.

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    Bayesian inference for spatio-temporal spike-and-slab priors

    Andersen, M. R., Vehtari, A., Winther, O. & Kai Hansen, L., 1 Dec 2017, In : Journal of Machine Learning Research. 18, p. 1-58

    Research output: Contribution to journalArticleScientificpeer-review

  33. Published

    Efficient acquisition rules for model-based approximate Bayesian computation

    Järvenpää, M., Gutmann, M., Pleska, A., Vehtari, A. & Marttinen, P., Dec 2017.

    Research output: Contribution to conferencePosterScientificpeer-review

  34. Published
  35. Published

    Uncertainty Quantification for the Horseshoe (with Discussion) comment

    Piironen, J., Betancourt, M., Simpson, D. & Vehtari, A., Dec 2017, In : Bayesian Analysis. 12, 4, p. 1264-1266 3 p.

    Research output: Contribution to journalEditorialScientificpeer-review

  36. Published

    Nudged elastic band calculations accelerated with Gaussian process regression

    Koistinen, O-P., Dagbjartsdóttir, F. B., Ásgeirsson, V., Vehtari, A. & Jonsson, H., 21 Oct 2017, In : Journal of Chemical Physics. 147, 15, p. 1-14 152720.

    Research output: Contribution to journalArticleScientificpeer-review

  37. Published

    Plasma levels of hepatocyte growth factor and placental growth factor predict mortality in a general population: a prospective cohort study

    Santalahti, K., Havulinna, A., Maksimow, M., Zeller, T., Blankenberg, S., Vehtari, A., Joensuu, H., Jalkanen, S., Salomaa, V. & Salmi, M., 1 Oct 2017, In : Journal of Internal Medicine. 282, 4, p. 340-352 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  38. Published

    Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC

    Vehtari, A., Gelman, A. & Gabry, J., Sep 2017, In : STATISTICS AND COMPUTING. 27, 5, p. 1413–1432

    Research output: Contribution to journalArticleScientificpeer-review

  39. Published

    Distributed neural signatures of natural audiovisual speech and music in the human auditory cortex

    Salmi, J., Koistinen, O-P., Glerean, E., Jylänki, P., Vehtari, A., Jääskeläinen, I., Mäkelä, S., Nummenmaa, L., Nummi-Kuisma, K., Nummi, I. & Sams, M., 15 Aug 2017, In : NeuroImage. 157, p. 108-117 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  40. Published

    SLUG transcription factor: A pro-survival and prognostic factor in gastrointestinal stromal tumour

    Pulkka, O. P., Nilsson, B., Sarlomo-Rikala, M., Reichardt, P., Eriksson, M., Hall, K. S., Wardelmann, E., Vehtari, A., Joensuu, H. & Sihto, H., 25 Apr 2017, In : BRITISH JOURNAL OF CANCER. 116, 9, p. 1195-1202 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  41. Published

    Automatic detection of acute kidney injury episodes from primary care data

    Tirunagari, S., Bull, S. C., Vehtari, A., Farmer, C., De Lusignan, S. & Poh, N., 9 Feb 2017, 2016 IEEE Symposium Series on Computational Intelligence, SSCI 2016. IEEE, 6 p. 7849885

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

  42. Published

    Bayesian optimization of unimodal functions

    Andersen, M. R., Siivola, E. & Vehtari, A., 2017, NIPS Workshop on Bayesian Optimization : BayesOpt 2017.

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

  43. Published

    Comment: Consensus Monte Carlo using expectation propagation

    Gelman, A. & Vehtari, A., 2017, In : Brazilian Journal of Probability and Statistics. 31, 4, p. 692-696 5 p.

    Research output: Contribution to journalComment/debateScientificpeer-review

  44. Published

    Comparison of Bayesian predictive methods for model selection

    Piironen, J. & Vehtari, A., 2017, In : STATISTICS AND COMPUTING. 27, 3, p. 711-735 25 p.

    Research output: Contribution to journalArticleScientificpeer-review

  45. Published

    Correcting boundary over-exploration deficiencies in Bayesian optimization with virtual derivative sign observations

    Siivola, E., Vehtari, A., Vanhatalo, J. & González, J., 2017, NIPS Workshop on Bayesian Optimization : BayesOpt 2017.

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

  46. Published

    Effect of KIT and PDGFRA mutations on survival in patients with gastrointestinal stromal tumors treated with adjuvant imatinib: An exploratory analysis of a randomized clinical trial

    Joensuu, H., Wardelmann, E., Sihto, H., Eriksson, M., Sundby Hall, K., Reichardt, A., Hartmann, J. T., Pink, D., Cameron, S., Hohenberger, P., Al-Batran, S-E., Schlemmer, M., Bauer, S., Nilsson, B., Kallio, R., Junnila, J., Vehtari, A. & Reichardt, P., 2017, In : JAMA Oncology. 3, 5, p. 602-609 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    ELFI, a software package for likelihood-free inference

    Lintusaari, J., Vuollekoski, H., Kangasrääsiö, A., Skyten, K., Järvenpää, M., Gutmann, M., Vehtari, A., Corander, J. & Kaski, S., 2017.

    Research output: Contribution to conferencePaperScientific

  48. Published

    Finding minimum energy paths using Gaussian process regression

    Koistinen, O-P., Dagbjartsdóttir, F. B., Ásgeirsson, V., Vehtari, A. & Jónsson, H., 2017, NIPS Workshop on Bayesian Optimization : BayesOpt 2017. Curran Associates, Inc., (Advances in neural information processing systems; vol. 30).

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

  49. Published

    On the hyperprior choice for the global shrinkage parameter in the horseshoe prior

    Piironen, J. & Vehtari, A., 2017, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. 9 p. (Proceedings of Machine Learning Research; vol. 54).

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

  50. Published

    Pareto Smoothed Importance Sampling

    Vehtari, A., Gelman, A. & Gabry, J., 2017.

    Research output: Working paperProfessional

  51. Published

    Sparsity information and regularization in the horseshoe and other shrinkage priors

    Piironen, J. & Vehtari, A., 2017, In : ELECTRONIC JOURNAL OF STATISTICS. 11, 2, p. 5018-5051

    Research output: Contribution to journalArticleScientificpeer-review

  52. 2016
  53. Published

    ELFI: Engine for Likelihood-Free Inference

    Kangasrääsiö, A., Lintusaari, J., Skyten, K., Järvenpää, M., Vuollekoski, H., Gutmann, M., Vehtari, A., Corander, J. & Kaski, S., 9 Dec 2016. 4 p.

    Research output: Contribution to conferencePaperScientific

  54. Published

    SLUG transcription factor promotes cell proliferation and predicts outcome of patients with gastrointestinal stromal tumor

    Sihto, H., Pulkka, O. P., Nilsson, B., Sarlomo-Rikala, M., Reichardt, P., Eriksson, M., Hall, K. S., Wardelmann, E., Vehtari, A. & Joensuu, P. H., Dec 2016, In : EUROPEAN JOURNAL OF CANCER. 69, p. S73 1 p.

    Research output: Contribution to journalMeeting AbstractScientificpeer-review

  55. Published

    Bayesian leave-one-out cross-validation approximations for Gaussian latent variable models

    Vehtari, A., Mononen, T., Tolvanen, V., Sivula, T. & Winther, O., 1 Jun 2016, In : Journal of Machine Learning Research. 17, p. 1-38 38 p.

    Research output: Contribution to journalArticleScientificpeer-review

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