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2020

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

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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)

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.

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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

2019

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.

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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.

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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.

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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

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.

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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.

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1 Citation (Scopus)
76 Downloads (Pure)

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.

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24 Citations (Scopus)
88 Downloads (Pure)

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.

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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

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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

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5 Citations (Scopus)
103 Downloads (Pure)

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

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5 Citations (Scopus)
113 Downloads (Pure)

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

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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

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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)

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

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3 Citations (Scopus)
156 Downloads (Pure)
Open Access

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

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Maternal pre- and postnatal anxiety symptoms and infant attention disengagement from emotional faces

Kataja, E. L., Karlsson, L., Parsons, C. E., Pelto, J., Pesonen, H., Häikiö, T., Hyönä, J., Nolvi, S., Korja, R. & Karlsson, H., 15 Jan 2019, In : Journal of Affective Disorders. 243, p. 280-289 10 p.

Research output: Contribution to journalArticleScientificpeer-review

5 Citations (Scopus)

Meta-analysis of Bayesian analyses

Blomstedt, P., Parente Paiva Mesquita, D., Lintusaari, J., Sivula, T., Corander, J. & Kaski, S., 2019, (Submitted) In : Submitted.

Research output: Contribution to journalArticleScientificpeer-review

Mobile Brainwaves: On the Interchangeability of Simple authentication Tasks with Low-Cost, Single-Electrode EEG Devices

Haukipuro, E-S., Kolehmainen, V., Myllärinen, J., Remander, S., Salo, J., Takko, T., Nguyen, L., Sigg, S. & Findling, R., 1 Apr 2019, In : IEICE Transactions on Communications. E102-B, 4, p. 760-767 8 p.

Research output: Contribution to journalArticleScientificpeer-review

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

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1 Citation (Scopus)
38 Downloads (Pure)

NetGO: improving large-scale protein function prediction with massive network information

You, R., Yao, S., Xiong, Y., Huang, X., Sun, F., Mamitsuka, H. & Zhu, S., 2 Jul 2019, In : Nucleic Acids Research. 47, W1, p. W379-W387

Research output: Contribution to journalArticleScientificpeer-review

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6 Citations (Scopus)
58 Downloads (Pure)

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

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5 Citations (Scopus)
115 Downloads (Pure)

Privacy-preserving data sharing via probabilistic modelling

Jälkö, J., Lagespetz, E., Haukka, J., Tarkoma, S., Kaski, S. & Honkela, A., 2019, (Submitted) In : Submitted.

Research output: Contribution to journalArticleScientificpeer-review

Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches

Nguyen, D. H., Nguyen, C. H. & Mamitsuka, H., 27 Nov 2019, In : BRIEFINGS IN BIOINFORMATICS. 20, 6, p. 2028-2043 16 p.

Research output: Contribution to journalArticleScientificpeer-review

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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

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Scaling up the effects of inbreeding depression from individuals to metapopulations

Nonaka, E., Sirén, J., Somervuo, P., Ruokolainen, L., Ovaskainen, O. & Hanski, I., Aug 2019, In : Journal of Animal Ecology. 88, 8, p. 1202-1214

Research output: Contribution to journalArticleScientificpeer-review

1 Citation (Scopus)

Single-subject analysis of N400 event-related potential component with five different methods

Kallionpää, R. E., Pesonen, H., Scheinin, A., Sandman, N., Laitio, R., Scheinin, H., Revonsuo, A. & Valli, K., 1 Oct 2019, In : International Journal of Psychophysiology. 144, p. 14-24 11 p.

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Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation: Spatially variable opportunities for outcrossing in an obligate pathogen

Laine, A. L., Barrès, B., Numminen, E. & Sirén, J. P., 1 Jun 2019, In : ELIFE. 8

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Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation

Laine, A-L., Barres, B., Numminen, E. & Siren, J. P., 18 Jun 2019, In : ELIFE. 8, p. 1-17 17 p., 47091.

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2018

A Combined PLS and Negative Binomial Regression Model for Inferring Association Networks from Next-generation Sequencing Count Data

Pesonen, M., Nevalainen, J., Potter, S., Datta, S. & Datta, S., 1 May 2018, In : IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 15, 3, p. 760-773 14 p.

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2 Citations (Scopus)
159 Downloads (Pure)

Approximate message passing for nonconvex sparse regularization with stability and asymptotic analysis

Sakata, A. & Xu, Y., 13 Mar 2018, In : Journal of Statistical Mechanics: Theory and Experiment. 2018, 3, p. 1-35 033404.

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2 Citations (Scopus)
118 Downloads (Pure)

Bacmeta: Simulator for genomic evolution in bacterial metapopulations

Sipola, A., Marttinen, P. & Corander, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. 2308-2310 3 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
2 Citations (Scopus)

Binary patterns encoded convolutional neural networks for texture recognition and remote sensing scene classification

Anwer, R. M., Khan, F. S., van de Weijer, J., Molinier, M. & Laaksonen, J., 1 Apr 2018, In : ISPRS Journal of Photogrammetry and Remote Sensing. 138, p. 74-85 12 p.

Research output: Contribution to journalArticleScientificpeer-review

50 Citations (Scopus)

Biosignals reflect pair-dynamics in collaborative work: EDA and ECG study of pair-programming in a classroom environment

Ahonen, L., Cowley, B. U., Hellas, A. & Puolamäki, K., 1 Dec 2018, In : Scientific Reports. 8, 1, p. 1-16 3138.

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14 Citations (Scopus)
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Characteristic functions of quantum heat with baths at different temperatures

Aurell, E., 7 Jun 2018, In : Physical Review E. 97, 6, p. 1-9 062117.

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5 Citations (Scopus)
125 Downloads (Pure)

Correlation-compressed direct-coupling analysis

Gao, C. Y., Zhou, H. J. & Aurell, E., 11 Sep 2018, In : Physical Review E. 98, 3, p. 1-15 032407.

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3 Citations (Scopus)
165 Downloads (Pure)