Research Output

2020

A high-performance implementation of bayesian matrix factorization with limited communication

Vander Aa, T., Qin, X., Blomstedt, P., Wuyts, R., Verachtert, W. & Kaski, S., 1 Jan 2020, Computational Science – ICCS 2020 - 20th International Conference, Proceedings. Krzhizhanovskaya, V. V., Závodszky, G., Lees, M. H., Sloot, P. M. A., Sloot, P. M. A., Sloot, P. M. A., Dongarra, J. J., Brissos, S. & Teixeira, J. (eds.). SPRINGER , p. 3-16 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12142 LNCS).

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

Open Access

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

Computing Tight Differential Privacy Guarantees Using FFT

Koskela, A., Jälkö, J. & Honkela, A., 2020, (Accepted/In press) AISTATS.

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

Deep Contextual Attention for Human-Object Interaction Detection

Wang, T., Anwer, R. M., Khan, M. H., Khan, F. S., Pang, Y., Shao, L. & Laaksonen, J., Feb 2020, Proceedings of the International Conference on Computer Vision (ICCV2019). IEEE, p. 5694-5702 (Proceedings of the IEEE International Conference on Computer Vision; vol. 2019-October).

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

Open Access
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1 Citation (Scopus)
27 Downloads (Pure)

Deep Convolutional Gaussian Processes

Blomqvist, K., Kaski, S. & Heinonen, M., 1 Jan 2020, Machine Learning and Knowledge Discovery in Databases - European Conference, ECML PKDD 2019, Proceedings. Brefeld, U., Fromont, E., Hotho, A., Knobbe, A., Maathuis, M. & Robardet, C. (eds.). SPRINGER , p. 582-597 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11907 LNAI).

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

Differentially private cross-silo federated learning

Heikkilä, M., Koskela, A., Shimizu, K., Kaski, S. & Honkela, A., 2020, (Submitted) In : Submitted.

Research output: Contribution to journalArticleScientificpeer-review

Expectation propagation as a way of life: A framework for Bayesian inference on partitioned data

Vehtari, A., Gelman, A., Sivula, T., Jylänki, 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

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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FullMeSH: Improving large-scale MeSH indexing with full text

Dai, S., You, R., Lu, Z., Huang, X., Mamitsuka, H. & Zhu, S., 1 Mar 2020, In : Bioinformatics. 36, 5, p. 1533-1541 9 p.

Research output: Contribution to journalArticleScientificpeer-review

High-dimensional structure learning of binary pairwise Markov networks: A comparative numerical study

Pensar, J., Xu, Y., Puranen, S., Pesonen, M., Kabashima, Y. & Corander, J., 1 Jan 2020, In : Computational Statistics and Data Analysis. 141, p. 62-76 15 p.

Research output: Contribution to journalArticleScientificpeer-review

1 Citation (Scopus)

Human Strategic Steering Improves Performance of Interactive Optimization

Colella, F., Daee, P., Jokinen, J., Oulasvirta, A. & Kaski, S., 13 May 2020, Proceedings of the 28th ACM Conference on User Modeling, Adaptation and Personalization: UMAP 2020. New York, NY, United States: ACM, p. 293-297 5 p.

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

Open Access

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

Likelihood-Free Inference with Deep Gaussian Processes

Aushev, A., Pesonen, H., Heinonen, M., Corander, J. & Kaski, S., 18 Jun 2020, (Submitted).

Research output: Contribution to conferencePaperScientific

Linking serial homicide – towards an ecologically valid application

Pakkanen, T., Sirén, J., Zappalà, A., Jern, P., Bosco, D., Berti, A. & Santtila, P., 2020, In : Journal of Criminological Research, Policy and Practice.

Research output: Contribution to journalArticleScientificpeer-review

Multiplicative chaos and the characteristic polynomial of the CUE: The L1-Phase

Nikula, M., Saksman, E. & Webb, C., Jun 2020, In : Transactions of the American Mathematical Society. 373, 6, p. 3905-3965 61 p.

Research output: Contribution to journalArticleScientificpeer-review

1 Citation (Scopus)

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

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

Open Access
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34 Downloads (Pure)

Projective Preferential Bayesian Optimization

Mikkola, P., Todorovic, M., Järvi, J., Rinke, P. & Kaski, S., 1 Jun 2020, (Accepted/In press). 9 p.

Research output: Contribution to conferencePaperScientificpeer-review

Robust parallel hybrid artificial bee colony algorithms for the multi-dimensional numerical optimization

Dokeroglu, T., Pehlivan, S. & Avenoglu, B., 9 Jan 2020, In : JOURNAL OF SUPERCOMPUTING.

Research output: Contribution to journalArticleScientificpeer-review

Scaled coupled norms and coupled higher-order tensor completion

Wimalawarne, K., Yamada, M. & Mamitsuka, H., 1 Feb 2020, In : Neural Computation. 32, 2, p. 447-484 38 p.

Research output: Contribution to journalLetterScientificpeer-review

Open Access
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9 Downloads (Pure)

Solving Analogies on Words based on Minimal Complexity Transformation

Murena, P-A., Al-Ghossein, M., Dessalles, J-L. & Cornuéjols, A., Jul 2020, Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, IJCAI. p. 1848-1854

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

2019

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

Open Access

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation

Järvenpää, M., Sater, M. R. A., Lagoudas, G. K., Blainey, P. C., Miller, L. G., McKinnell, J. A., Huang, S. S., Grad, Y. H. & Marttinen, P., 1 Apr 2019, In : PLoS computational biology. 15, 4, p. 1-25 e1006534.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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103 Downloads (Pure)

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

Open Access
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14 Downloads (Pure)

ADAPTIVE: LeArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra

Nguyen, D. H., Nguyen, C. H. & Mamitsuka, H., 15 Jul 2019, In : Bioinformatics. 35, 14, p. i164-i172 btz319.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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5 Citations (Scopus)
64 Downloads (Pure)

A Faster Tree-Decomposition Based Algorithm for Counting Linear Extensions

Kangas, K., Koivisto, M. & Salonen, S., 1 Jan 2019, In : Algorithmica.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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32 Downloads (Pure)

AI4TV 2019: 1st international workshop on AI for smart TV content production, access and delivery

Troncy, R., Laaksonen, J., Tavakoli, H. R., Nixon, L. & Mezaris, V., 15 Oct 2019, MM 2019 - Proceedings of the 27th ACM International Conference on Multimedia. ACM, p. 2716-2717 2 p. (MM 2019 - Proceedings of the 27th ACM International Conference on Multimedia).

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

A Multi-Task Bayesian Deep Neural Net for Detecting Life-Threatening Infant Incidents From Head Images

Wang, T-J. J., Laaksonen, J., Liao, Y-P., Wu, B-Z. & Shen, S-Y., 2019, 2019 IEEE International Conference on Image Processing, ICIP 2019 - Proceedings. IEEE, p. 3006-3010 5 p. 8803332

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

Open Access
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37 Downloads (Pure)

Artificial Neural Networks with Random Weights for Incomplete Datasets

Mesquita, D. P. P., Gomes, J. P. P. & Rodrigues, L. R., 1 Jan 2019, In : Neural Processing Letters. 28 p.

Research output: Contribution to journalArticleScientificpeer-review

2 Citations (Scopus)

A sparse linear regression model for incomplete datasets

Veras, M. B. A., Mesquita, D. P. P., Mattos, C. L. C. & Gomes, J. P. P., 4 Dec 2019, In : Pattern Analysis and Applications.

Research output: Contribution to journalArticleScientificpeer-review

AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification

You, R., Zhang, Z., Wang, Z., Dai, S., Mamitsuka, H. & Zhu, S., Dec 2019, ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 32 (NIPS 2019). Wallach, H., Larochelle, H., Beygelzimer, A., d'Alche-Buc, F., Fox, E. & Garnett, R. (eds.). 11 p. (Advances in Neural Information Processing Systems; vol. 32).

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

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

Open Access
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86 Downloads (Pure)

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

Open Access
File
1 Citation (Scopus)
76 Downloads (Pure)

Bottom-Up Attention, Models of

Borji, A., Rezazadegan Tavakoli, H. & Bylinskii, Z., 2019, Encyclopedia of Computational Neuroscience .

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

Open Access

CalCleaveMKL: a Tool for Calpain Cleavage Prediction

duVerle, D. A. & Mamitsuka, H., 1 Jan 2019, Calpain. p. 121-147 27 p. (Methods in molecular biology; vol. 1915).

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

1 Citation (Scopus)

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

Kaski, S. & Marttinen, P., 17 Jun 2019, In : Nature Communications. 10, 1, p. 1-17 17 p., 2674.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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24 Citations (Scopus)
88 Downloads (Pure)

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

Open Access

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

Open Access
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27 Downloads (Pure)

Differentially Private Markov Chain Monte Carlo

Heikkilä, M., Jälkö, J., Dikmen, O. & Honkela, A., 2019, 33rd Conference on Neural Information Processing Systems: NeurIPS 2019 . Neural Information Processing Systems Foundation, 11 p. (Advances in Neural Information Processing Systems).

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

Open Access

Digging deeper into egocentric gaze prediction

Tavakoli, H. R., Rahtu, E., Kannala, J. & Borji, A., 4 Mar 2019, Proceedings - 2019 IEEE Winter Conference on Applications of Computer Vision, WACV 2019. IEEE, p. 273-282 10 p. 8658619

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

Open Access
3 Citations (Scopus)

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

Open Access
File
2 Citations (Scopus)
105 Downloads (Pure)

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

Open Access
File
2 Citations (Scopus)
105 Downloads (Pure)

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

Open Access
File
5 Citations (Scopus)
103 Downloads (Pure)

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

Open Access

Emergence of ceftazidime-avibactam-resistant Klebsiella pneumoniae during treatment, Finland, December 2018

Räisänen, K., Koivula, I., Ilmavirta, H., Puranen, S., Kallonen, T., Lyytikäinen, O. & Jalava, J., 1 May 2019, In : EUROSURVEILLANCE. 24, 19, p. 1-3

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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4 Citations (Scopus)
113 Downloads (Pure)

Fast and Robust Multi-View Multi-Task Learning via Group Sparsity

Sun, L., Nguyen, C. H. & Mamitsuka, H., 2019, Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence, IJCAI 2019, Macao, China, August 10-16, 2019. p. 3499-3505 7 p.

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

Fuzzy least squares twin support vector machines

Sartakhti, J. S., Afrabandpey, H. & Ghadiri, N., 1 Oct 2019, In : ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE. 85, p. 402-409 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
4 Citations (Scopus)

Gaussian kernels for incomplete data

Mesquita, D. P. P., Gomes, J. P. P., Corona, F., Souza, A. H. & Nobre, J. S., 1 Apr 2019, In : Applied Soft Computing Journal. 77, p. 356-365 10 p.

Research output: Contribution to journalArticleScientificpeer-review

2 Citations (Scopus)

Genome-wide epistasis and co-selection study using mutual information

Pensar, J., Puranen, S., Arnold, B., MacAlasdair, N., Kuronen, J., Tonkin-Hill, G., Pesonen, M., Xu, Y., Sipola, A., Sánchez-Busó, L., Lees, J. A., Chewapreecha, C., Bentley, S. D., Harris, S. R., Parkhill, J., Croucher, N. J. & Corander, J., 10 Oct 2019, In : Nucleic Acids Research. 47, 18, p. 1-14 e112.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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44 Downloads (Pure)

Geometry-aware relational exemplar attention for dense captioning

Wang, T. J. J., Tavakoli, H. R., Sjöberg, M. & Laaksonen, J., 15 Oct 2019, MULEA 2019 - 1st International Workshop on Multimodal Understanding and Learning for Embodied Applications, co-located with MM 2019. ACM, p. 3-11 9 p.

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

Open Access
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39 Downloads (Pure)

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

Open Access
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23 Downloads (Pure)