Jarno Vanhatalo

Publications of Jarno Vanhatalo

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Full list in pdf format

Preprints:

• Karel Kaurila, Sanna Kuningas, Antti Lappalainen, Jarno Vanhatalo (preprint). Species Distribution Modeling with Expert Elicitation and Bayesian Calibration.
  [link]

Peer-reviewed scientific articles:

1. Ersalman, M., Kunnasranta, M., Ahola, M., Carlsson, A. M., Persson, S., Bäcklin, B.-M., Helle, I., Cervin, L., Vanhatalo J. (in press). Integrated population model reveals human and environment driven changes in Baltic ringed seal (Pusa hispida botnica) demography and behavior. Marine Ecology Progress Series
   [link]
2. Mäkinen, J., Ellis, E., Antão, L. H., Davrinche, A., Laine, A.-L., Saastamoinen, M., Conenna, I., Hällfors, M. H., Santangeli, A., Kaarlejärvi, E., Heliölä, J., Huikkonen, I.-M., Kuussaari, M., Leinonen, R., Lehikoinen, A., Pöyry, J., Suuronen, A., Salemaa, M., Tonteri, T., Vuorio, K. M., Skjelbred, B., Järvinen, M., Drakare, S., Carvalho, L., Welk, E., Seidler, G., Vangansbeke, P., Malis, F., Hédl, R., Auffret, A. G., Plue, J., De Frenne, P., Kalwij, J. M., Vanhatalo, J., and Roslin, T. (2025). Thermal homogenization of boreal communities in response to climate warming.. PNAS, 122(17): e2415260122.
   [link]
3. Goodsell, R., Tack, A., Iwaszkiewicz-Eggebrecht, E., Miraldo, A., van Dijk, L., Ronquist, F., Roslin, T., and Vanhatalo, J. (2025). Moving towards better risk assessment for invertebrate conservation. Ecography, e07819
   [link]
4. Rodrigues, V. A., Rissanen, T., Jones, M., Huikkonen, I.-M.; Huitu, O., Korpimäki, E., Kuussaari, M., Lehikoinen, A., Lindén, A., Pietiäinen, H., Pöyry, J. Sihvonen, P., Suuronen, A., Vuorio, K., Saastamoinen, M., Vanhatalo, J., Laine, A.-L. (in press). Cross-taxa analysis of long-term data reveals a positive biodiversity-stability relationship with taxon-specific mechanistic underpinning. Ecology Letters
   [Link]
5. Schulz, T., Saastamoinen, M., Vanhatalo, J. (2025). Model-based variance partitioning for statistical ecology. Ecological Monographs 95(1): e1646
   [link]
6. Pia, I., Numminen, E., Veneranta, L. and Vanhatalo, J. (2025). Spatially explicit model to disentangle effects of environment on annual fish reproduction. Environmetrics, 36: e2894.
   [link]
7. Lignell, R., Miettunen, E., Kuosa, H., Ropponen, J., Tuomi, L., Puttonen, I., Lukkari, K., Korppoo, M., Huttunen, M., Kaurila, K., Vanhatalo, J., and Thinstad, F. (in press). Modeling how eutrophication in northern Baltic coastal zone is driven by new nutrient inputs, internal loading, and 3D hydrodynamics. Journal of Marine Systems., 249: 104049
   [link]
8. Kaurila, K., Lignell, R., Thingstad, F., Kuosa, H. and Vanhatalo, J. (2025). Bayesian Calibration and Uncertainty Quantification for a Large Nutrient Load Impact Model. Ecological Informatics, 85:102976
   [link]
9. Korrensalo, A., Kettunen, J., Mehtätalo, L., Vanhatalo, J. and Tuittila, E.-S. (2025). Detecting moderate change in species and trait composition and quantifying its uncertainty in a boreal peatland. Journal of Vegetation Science, 36: e70025.
   [link]
10. Kaarlejärvi, E., Itter, M., Tonteri, T., Hamberg, L., Salemaa, M., Merilä, P., Vanhatalo, J., and Laine, A.-L. (2024). Inferring ecological selection from multidimensional community trait distributions along environmental gradients. Ecology, 105(9): e4378.
    [Link]
11. Hamberg, L., Vanhatalo, J., Velmala, S., Taylor, A., MacKay, J., Caron, S., Asiegbu, F., Sievänen, R., Raumonen, P., Hytönen, T., Pennanen, T. (2024). The community of root fungi is associated with the growth rate of Norway spruce (Picea abies). Environmental Microbiology, 26(6), e16662
    [Link]
12. Itter, M., Kaarlejärvi, M., Laine, A.-L., Hamberg, L., Tonteri, T., Vanhatalo, J. (2024). Bayesian joint species distribution model selection for community-level prediction. Global Ecology and Biogeography, 33, e13827.
    [link]
13. Kettunen, J., Mehtätalo, L., Korrensalo, A., Tuittila, E.-S. and Vanhatalo, J. (2024). Joint Species Distribution Modeling of Percentage Cover Data with Exclusive Competition for Space. Environmetrics, 35(2):e2830.
    [link]
14. Santangeli, A., Weigel, B., Antão, L., Kaarlejärvi, E., Hällfors, M., Lehikoinen, A., Lindén, A., Salemaa, M., Tonteri, T., Merilä, P., Vuorio, K., Ovaskainen, O, Vanhatalo, J., Roslin, T., and Saastamoinen,M. (2023). Mixed effects of a national protected area network on terrestrial and freshwater biodiversity. Nature Communications, 14: 5426.
    [link]
15. Thorogood, R., Mustonen, V., Aleixo, A., Aphalo, P. J., Asiegu, F. O., Cabeza, M., Cairns, J., Candolin, Y., Cardoso, P., Eronen, J. T., Hällfors, M., Hovatta, I., Juslen A., Kovalchuk, A., Kulmuni, J., Kuula, L., Mäkipää, R., Ovaskainen, O., Pesonen, A.-K., Primmer, G. R., Saastamoinen, M., Schulman, A. H., Schulman, L., Strona, G., and Vanhatalo, J. (2023). Understanding and applying biological resilience, from genes to ecosystems. npj Biodiversity, 2(16).
    [link]
16. Numminen, E., Jokinen, M., Lindén, A. and Vanhatalo, J. (2023). Species ecology can bias population estimates. Biological Conservation, 283:110-115.
    [link]
17. Mäkinen, J., Numminen, E., Niittynen, P., Luoto, M. and Vanhatalo, J. (2022). Spatial confounding in Bayesian species distribution modeling. Ecography, 2022: e06183.
    [link]
18. Antão, L. H., Weigel, B., Strona, G., Hällfors, M., Kaarlejärvi, E., Dallas, T., OpedalØ. H., Heliölä, J., Henttonen, H., Huitu, O., Korpimäki, E., Kuussaari, M., Lehikoinen, A., Leinonen, R., Lindén, A., Merilä, P., Pietiäinen, H., Pöyry, J., Salemaa, M., Tonteri, T., Vuorio, K., Ovaskainen, O., Saastamoinen, M., Vanhatalo, J., Roslin, T. and Laine, A.-L. (2022). Climate change reshuffles northern species within their niches. Nature Climate Change, 12:587-592.
    [link]
19. Martin Bergström, Thomas Browne, Sören Ehlers, Inari Helle, Hauke Herrnring, Faisal Khan, Jan Kubiczek, Pentti Kujala, Mihkel Kõrgesaar, Bernt Johan Leira, Tuuli Parviainen, Arttu Polojärvi, Mikko Suominen, Rocky Taylor, Jukka Tuhkuri, Jarno Vanhatalo, Brian Veitch (2022). A Comprehensive approach to scenario-based risk management for Arctic Waters. Ship Technology Research - Schiffstechnik
    [Link].
20. Jarno Vanhatalo, Scott D. Foster and Geoffrey R. Hosack (2021). Spatiotemporal Clustering using Gaussian Processes Embedded in a Mixture Model. Environmetrics, 32:e2681
    [Link] [Code].
21. Benjamin Weigel, Jussi Mäkinen, Meri Kallasvuo and Jarno Vanhatalo (2021). Exposing changing phenology of fish larvae by modeling climate effects on temporal early life-stage shifts. Marine Ecology Progress Series, 666:135-148
    [Link].
22. Scott D. Foster , Jarno Vanhatalo, Verena M. Trenkel, Torsti Schulz, Emma Lawrence, Rachel Przeslawski, and Geoffrey R. Hosack (2021). Effects of Ignoring Survey Design Information for Data Reuse. Ecological Applications,31(6):e02360
    [Link].
23. Jarno Vanhatalo, Juri Huuhtanen, Martin Bergström, Inari Helle, Jussi Mäkinen and Pentti Kujala (2021). Probability of a ship becoming beset in ice along the Northern Sea Route - a Bayesian analysis of real-life data. Cold Regions Science and Technology, 184:103238
    [Link].
24. Tommi Perälä, Jarno Vanhatalo and Anna Chrysafi (2020). Calibrating expert assessments using hierarchical Gaussian process models. Bayesian Analysis, 15(4):1251-1280.
    [Link].
25. Jarno Vanhatalo, Marcelo Hartmann and Lari Veneranta (2020). Additive multivariate Gaussian processes for joint species distribution modeling with heterogeneous data. Bayesian Analysis, 15(2):415-447.
    [Link] [data]
26. Inari Helle, Jussi Mäkinen, Maisa Nevalainen, Mawuli Afenyo and Jarno Vanhatalo (2020). Impacts of oil spills on Arctic marine ecosystems: A quantitative and probabilistic risk assessment perspective. Environmental Science & Technology, 54(4):2112-2121.
    [Link]
27. Torsti Schulz, Jarno Vanhatalo and Marjo Saastamoinen (2020). Long-term demographic surveys reveal a consistent relationship between average occupancy and abundance within local populations of a butterfly metapopulation. Ecography, 43: 306-317.
    [Link].
28. Jia Liu and Jarno Vanhatalo (2020). Bayesian model based spatio-temporal sampling designs and partially observed log Gaussian Cox process. Spatial Statistics, 35:100392.
    [Link]
29. Kelsey LaMere, Samu Mäntyniemi, Jarno Vanhatalo and Päivi Haapasaari (2020). Making the Most of Mental Models: Advancing the Methodology for Mental Model Elicitation and Documentation with Expert Stakeholders. Environmental Modelling and Software, 124:104589
    [Link].
30. Skipton Woolley, Scott Foster, Nicolas Bax, Jock Currie, Daniel, Dunn, Cecilie, Hansen, Nicole, Hill, Timothy, O'Hara, Otso Ovaskainen, Roger Sayre, Jarno, Vanhatalo, Piers Dunstan (2020). Bioregions in marine environments: Combining Biological and Environmental Data for Management and Scientific Understanding. BioScience, 70(1):48-59.
    [Link].
31. Malcolm Itter, Jarno Vanhatalo and Andrew Finley (2019). EcoMem: An R package for quantifying ecological memory. Environmental Modelling & Software, 119: 305-308.
    [Link]
32. Maisa Nevalainen, Jarno Vanhatalo and Inari Helle (2019). Index-based approach for estimating vulnerability of Arctic biota to oil spills. Ecosphere, 10(6):e02766.
    [Link]
33. Jarno Vanhatalo, Zitong Li and Mikko Sillanpää (2019). A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotype data. Bioinformatics, 35(19):3684-3692.
    [Link] [Code]
34. Norberg, A., Abrego, N., Blanchet, F. G., Adler, F. R., Anderson, B. J., Anttila, J., Araújo, M. B., Dallas, T., Dunson, D., Elith, J., Foster, S. D., Fox, R., Franklin, J., Godsoe, W., Guisan, A., O'Hara, B., Hill, N. A., Holt, R. D., Hui, F. K. C., Husby, M., Kålås, J. A., Lehikoinen, A., Luoto, M., Mod, H. K., Newell, G., Renner, I., Roslin, T., Soininen, J., Thuiller, W., Vanhatalo, J., Warton, D., White, M., Zimmermann, N. E., Gravel, D., and Ovaskainen, O. (2019). A comprehensive evaluation of predictive performance of 33 species distribution models at species and community levels. Ecological Monographs, 89(3):e01370
    [Link]
35. Haakon Bakka, Jarno Vanhatalo, Janine Illian, Daniel Simpson and Håvard Rue (2019). Non-stationary Gaussian models with physical barriers. Spatial Statistics, 29:268-288
    [Link] [Code]
36. Jonne Kotta, Jarno Vanhatalo, Holger Jänes, Helen Orav-Kotta, Luca Rugiu, Veijo Jormalainen, Ivo Bobsien, Markku Viitasalo, Elina Virtanen, Antonia Nyström Sandman, Martin Isaeus, Sonja Leidenberger, Per Jonsson, and Kerstin Johannesson (2019). Integrating experimental and distribution data to predict future species patterns. Scientific Reports, 9(1): 1821
    [Link]
37. Marcelo Hartmann and Jarno Vanhatalo (2019). Laplace approximation and natural gradient for Gaussian process regression with heteroscedastic Student-t model. Statistics and Computing, 29:753-773.
    [Link] [Code]
38. Jussi Mäkinen and Jarno Vanhatalo (2018). Hierarchical Bayesian model reveals the distributional shifts of Arctic marine mammals. Diversity and Distributions, 24:1381-1394.
    [Link]
39. Maisa Nevalainen, Inari Helle and Jarno Vanhatalo (2018). Estimating the acute impacts of Arctic marine oil spills using expert elicitation. Marine Pollution Bulletin 131,782-792.
    [Link]
40. Eero Siivola, Aki Vehtari, Javier Conzalez, Jarno Vanhatalo, and Michael R. Andersen (2018). Correcting Boundary Over-Exploration Deficiencies In Bayesian Optimization With Virtual Derivative Sign Observations. IEEE 28th International Workshop on Machine Learning for Signal Processing (MLSP)
    [Link]
41. Mikko Kotilainen, Jarno Vanhatalo, Mikko Suominen, and Pentti Kujala (2018). Predicting Local Ice Loads on Ship Bow as a Function of Ice and Operational Conditions in the Southern Sea.. Ship Technology Research - Schiffstechnik 65(2):87-101.
    [Link]
42. Marcelo Hartmann, Geoffrey R. Hosack, Richard M. Hillary and Jarno Vanhatalo (2017). Gaussian processs framework for temporal dependence and discrepancy functions in Ricker-type population growth models. Annals of Applied Statistics, 11(3):1375-1402.
    [Link]
43. Mika Rahikainen, Kirsi-Maaria Hoviniemi, Samu Mäntyniemi, Jarno Vanhatalo, Inari Helle, Maiju Lehtiniemi, Jukka Pönni and Sakari Kuikka (2017). Impacts of eutrophication and oil spills on the Gulf of Finland herring stock. Canadian Journal of Fisheries and Aquatic Sciences, 74(8): 1218-1232.
    [Link]
44. Meri Kallasvuo, Jarno Vanhatalo and Lari Veneranta (2017). Modeling the spatial distribution of larval fish abundance provides essential information for management. Canadian Journal of Fisheries and Aquatic Sciences, 74:636-649
    [Link]
45. Jarno Vanhatalo, Geoffrey R. Hosack and Hugh Sweatman (2017). Spatio-temporal modelling of crown-of-thorns starfish outbreaks on the Great Barrier Reef to inform control strategies. Journal of Applied Ecology, 54:188-197.
    [Link] [code]
46. Maisa Nevalainen, Inari Helle and Jarno Vanhatalo (2017). Preparing for the unprecedented - towards quantitative oil risk assessment in the Arctic marine areas. Marine Pollution Bulletin, 114(1):90-101
    [Link]
47. Mikko Kotilainen, Jarno Vanhatalo, Mikko Suominen, and Pentti Kujala (2017). Predicting ice-induced load amplitudes on ship bow conditional on ice thickness and ship speed in the Baltic Sea.. Cold Regions Science and Technology, 135: 116-126.
    
[Link]
48. Jussi Mäkinen and Jarno Vanhatalo (2016). Hydrographic responses to regional covariates across the Kara Sea. Journal of Geophysical Research - Oceans, 121: 8872-8887.
    [Link]
49. Lari Veneranta, Jarno Vanhatalo and Lauri Urho (2016). Detailed temperature mapping - warming characterizes archipelago zones. Estuarine, Coastal & Shelf science, 182:123-135.
    [Link]
50. Mikko Kotilainen, Jarno Vanhatalo, Mikko Suominen, and Pentti Kujala (2016). Predicting ice loads as a function of ship speed and ice conditions based on ice load measurements taken on S.A. Agulhas II sailing in the Southern Sea. International Conference on Ships and Offshore Structures (ICSOS) 2016, Hamburg, Germany
    
51. Jarno Vanhatalo, Alistair J. Hobday, Richard L. Little. and Claire M. Spillman (2016). Downscaling and extrapolating dynamic seasonal marine forecasts for coastal ocean users. Ocean Modelling, 100:20-30.
    [Link]
52. Bjarke Mølgaard, Jarno Vanhatalo, Pasi Aalto, Nönne L. Prisle and Kaarle Hämeri (2016). Notably improved inversion of Differential Mobility Particle Sizer data obtained under conditions of fluctuating particle number concentrations.. Atmospheric Measurement Techniques, 9:741-751.
    [Link] [code], [code for SMPS inversion]
53. Samu Mäntyniemi, Rebekka Whitlock, Tommi Perälä, Paul Blomstedt, Jarno Vanhatalo, Marcarita M. Rincon, Anna Kuparinen, Henni Pulkkinen, and Sakari Kuikka (2015). General State-space Population Dynamics Model for Bayesian Stock Assessment ICES journal of Marine Sciences 72 (8): 2209-2222.
    [Link]
54. Jarno Vanhatalo, Markus Vetemaa, Annika Herrero, Teija Aho, Raisa Tiilikainen (2014). By-Catch of Grey Seals (Halichoerus grypus) in Baltic Fisheries - A Bayesian Analysis of Interview Survey. PLoS ONE 9(11): e113836.
    [Link] [Press release]
55. Sakari Kuikka, Jarno Vanhatalo, Henni Pulkkinen, Samu Mäntyniemi and Jukka Corander (2014). Experiences in Bayesian Inference in Baltic Salmon management. Statistical Science, 29(1):42-49.
    [Link]
56. Mika Rahikainen, Inari Helle, Päivi Haapasaari, Soile Oinonen, Sakari Kuikka, Jarno Vanhatalo, Samu Mäntyniemi, Kirsi-Maaria Hoviniemi. (2014). Toward Integrative Management Advice of Water Quality, Oil Spills, and Fishery in the Gulf of Finland: A Bayesian Approach. Ambio, 43:115-123.
    [link]
57. Sören Ehlers, Pentti Kujala, Brian Veitch, Faisal Khan, and Jarno Vanhatalo (2014). Scenario based risk management for arctic shipping and operations. ASME 2014 33rd International Conference on Ocean, Offshore and Arctic Engineering : Polar and Arctic Science and Technology. 10(33).
    [Link]
58. Jarno Vanhatalo, Jaakko Riihimäki, Jouni Hartikainen, Pasi Jylänki, Ville Tolvanen, Aki Vehtari (2013). GPstuff: Bayesian Modeling with Gaussian Processes. Journal of Machine Learning Research, 14:1175-1179.
    [link]
59. Lari Veneranta, Richard Hudd and Jarno Vanhatalo (2013). Reproduction areas of sea-spawning Coregonids reflect the environment in shallow coastal waters. Marine Ecology Progress Series, 477:231-250.
    [link] [data]
60. Jarno Vanhatalo, Laura Tuomi, Arto Inkala, Inari Helle, and Heikki Pitkänen (2013). Probabilistic Ecosystem Model for Predicting the Nutrient Concentrations in the Gulf of Finland under Diverse Management Actions. Environmental Science & Technology, 47(1):334-341.
    [link]
61. Heini Ahtiainen and Jarno Vanhatalo (2012). The value of reducing eutrophication in European marine areas - A Bayesian meta-analysis. Ecological Economics, 83:1-10.
    [link]
62. Jarno Vanhatalo, Lari Veneranta and Richard Hudd (2012). Species Distribution Modelling with Gaussian Processes: a Case Study with the Youngest Stages of Sea Spawning Whitefish (Coregonus lavaretus L. s.l.) Larvae. Ecological Modelling, 228:49-58.
    [link] [data]
63. Teppo Juntunen, Jarno Vanhatalo, Heikki Peltonen and Samu Mäntyniemi (2012). Bayesian spatial multispecies modelling to assess pelagic fish stocks from acoustic- and trawl-survey data. ICES Journal of Marine Science, 69: 95-104.
    [link]
64. Pasi Jylänki, Jarno Vanhatalo and Aki Vehtari (2011). Robust Gaussian Process Regression with a Student-t Likelihood. Journal of Machine Learning Research, 12:3227-3257.
    [link]
65. Jarno Vanhatalo, Ville Pietiläinen and Aki Vehtari (2010). Approximate inference for disease mapping with sparse Gaussian processes. Statistics in Medicine , 29(15):1580-1607.
    [link]
66. Jarno Vanhatalo, Pia Mäkelä, ja Aki Vehtari (2010). Alkoholikuolleisuuden alueelliset erot Suomessa 2000-luvun alussa. Yhteiskuntapolitiikka, 75(3):265-273 (in Finnish)
    [link] [Lisï¿œmateriaalia Suomeksi][English translation]
67. Jarno Vanhatalo and Aki Vehtari (2010). Speeding up the binary Gaussian process classification. Proceedings of the 26th Conference on Uncertainty in Artificial Intelligence.
    [link]
68. Jarno Vanhatalo, Pasi Jylänki and Aki Vehtari (2009). Gaussian process regression with Student-t likelihood. Advances in Neural Information Processing Systems 23.
    [link]
69. Jarno Vanhatalo and Aki Vehtari (2008). Modelling local and lobal phenomena with sparse Gaussian processes. Proceedings of the 24th Conference on Uncertainty in Artificial Intelligence.
    [link]
70. Jarno Vanhatalo and Aki Vehtari (2007). Sparse Log Gaussian Processes via MCMC for Spatial Epidemiology. JMLR Workshop and Conference Proceedings, 1:73-89. (Gaussian Processes in Practice)
    [link]

Theses:

• Jarno Vanhatalo (2010). Speeding Up the Inference in Gaussian Process Models. PhD Thesis, Aalto University, School of Science and Technology. (pdf)
• Jarno Vanhatalo (2006). Sparse Log Gaussian Process in Spatial Epidemiology. M.Sc. Thesis, Department of Electrical and Communications Engineering, Helsinki University of Technology. (pdf)

Reports and non-refereed articles

• Kenchington, E., Callery, O., Davidson, F., Grehan, A., Morato, T., Appiott, J., Davis A., Dunstan P., Du Preez, C., Finney, J., González-Irusta, J.M., Howell, K., Knudby, A., Lacharité, M., Lee, J., Murillo, F. J., Beazley, L., Roberts, J.M., Roberts, M., Rooper, C., Rowden, A., Rubidge, E., Stanley, R., Stirling, D., Tanaka, K.R., Vanhatalo, J., Weigel, B., Woolley, S. and Yesson C. (2019). Use of species distribution modeling in the deep sea. Canadian technical report of fisheries and aquatic sciences no. 3296
  [link]
• Lari Veneranta, Richard Hudd and Jarno Vanhatalo (2013). Siiat tarvitsevat puhtaita matalikkoja. Suomen Kalastuslehti 4/2013:8-10.
• Lari Veneranta, Richard Hudd and Jarno Vanhatalo (2013). Merikutuisen siian ja muikun poikastuotantoalueet. RKTL:n tyï¿œraportteja 8/2013, Riista- ja kalatalouden tutkimuslaitos. [link]
• Richard Hudd, Lari Veneranta and Jarno Vanhatalo (2013). Havslekande sikens och siklï¿œjans yngelproduktionsomrï¿œden. Vilt- och fiskeriforskningsinstitutes arbetsrapporter 7/2013, Vilt- och fiskeriforskningsinstitutet. [link]
• Jarno Vanhatalo, Jaakko Riihimï¿œki, Jouni Hartikainen, Pasi Jylï¿œnki, Ville Tolvanen and Aki Vehtari (2012). Bayesian Modeling with Gaussian Processes using the GPstuff Toolbox. arXiv:1206.5754.[link]