Research Output

2020

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
File
1 Citation (Scopus)
21 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

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
File

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, (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

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

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

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
File
29 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
File
8 Downloads (Pure)
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
File
101 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
File
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
File
4 Citations (Scopus)
63 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
File
25 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
File
35 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

1 Citation (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
File
83 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)
75 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
File
22 Citations (Scopus)
86 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
File
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
2 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)
104 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)
102 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
File
2 Citations (Scopus)
110 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
File
42 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
File
38 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
File
23 Downloads (Pure)

HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks

Gao, J., Liu, L., Yao, S., Huang, X., Mamitsuka, H. & Zhu, S., 23 Dec 2019, In : BMC Medical Genomics . 12, 14 p., 187.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
14 Downloads (Pure)

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

Open Access
Open Access
File
120 Downloads (Pure)

Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis

Kachroo, P., Eraso, J. M., Olsen, R. J., Beres, S. B., Zhu, L., Nasser, W., Bernard, P. E., Cantu, C. C., Saavedra, M. O., Arredondo, M. J., Strope, B., Do, H., Kumaraswami, M., Vuopio, J., Gröndahl-Yli-Hannuksela, K., Kristinsson, K. G., Gottfredsson, M., Pesonen, M., Pensar, J., Davenport, E. R. & 11 others, Clark, A. G., Corander, J., Caugant, D. A., Gaini, S., Magnussen, M. D., Kubiak, S. L., Nguyen, H. A. T., Long, S. W., Porter, A. R., DeLeo, F. R. & Musser, J. M., 1 Mar 2019, In : NATURE GENETICS. 51, 3, p. 548-559 12 p.

Research output: Contribution to journalArticleScientificpeer-review

18 Citations (Scopus)