Pekka Marttinen

University of Helsinki, Helsinki

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Papers48 papers

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Learning Global Pairwise Interactions with Bayesian Neural Networks

Tianyu Cui,Pekka Marttinen,Samuel Kaski

ECAI, pp.1087-1094, (2020)

EIBibtex

Population analysis of Legionella pneumophila reveals the basis of resistance to complement-mediated killing

Bryan A. Wee, Joana Alves,Diane S. J. Lindsay, Ross L. Cameron, Amy Pickering, Jamie Gorzynski,Jukka Corander,Pekka Marttinen,Andrew J. Smith,J. Ross Fitzgerald

Bibtex

Parallel Gaussian Process Surrogate Bayesian Inference with Noisy Likelihood Evaluations

Marko Järvenpää,Michael U. Gutmann,Aki Vehtari,Pekka Marttinen

Bayesian Analysis, (2020)

Cited by5Bibtex

Informative Gaussian Scale Mixture Priors for Bayesian Neural Networks

Cui Tianyu, Havulinna Aki,Marttinen Pekka,Kaski Samuel

Bibtex

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

Järvenpää Marko,Vehtari Aki,Marttinen Pekka

UAI, pp.779-788, (2019)

EIBibtex

Parallel Gaussian process surrogate method to accelerate likelihood-free inference

Marko Järvenpää,Michael Gutmann,Aki Vehtari,Pekka Marttinen

arXiv: Machine Learning, (2019)

Cited by1EIBibtex

Modelling G×E with historical weather information improves genomic prediction in new environments

Jussi Gillberg,Pekka Marttinen,Hiroshi Mamitsuka,Samuel Kaski

BIOINFORMATICS, no. 20 (2019): 4045-4052

Cited by3WOSEIBibtex

Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome

Sergio Arredondo-Alonso,Janetta Top,Anita C Schürch,Alan McNally,Santeri Puranen, Maiju Pesonen,Johan Pensar,Pekka Marttinen,Johanna C Braat,Malbert Rc Rogers,Willem van Schaik,Samuel Kaski

bioRxiv, pp.530725-44, (2019)

Bibtex

Recovering Pairwise Interactions Using Neural Networks

Tianyu Cui,Pekka Marttinen,Samuel Kaski

arXiv: Learning, (2019)

EIBibtex

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact

Rebecca A Gladstone,Stephanie W Lo, John A Lees,Nicholas J Croucher,Andries J van Tonder,Jukka Corander, Andrew J Page,Pekka Marttinen, Leon J Bentley,Theresa J Ochoa,Pak Leung Ho,Mignon du Plessis

EBioMedicine, (2019): 338-346

WOSBibtex

A Bayesian model of acquisition and clearance of bacterial colonization

Marko Järvenpää, Mohamad R. Abdul Sater, Georgia K. Lagoudas,Paul C. Blainey,Loren G. Miller,James A. McKinnell,Susan S. Huang,Yonatan H. Grad,Pekka Marttinen

arXiv: Populations and Evolution, (2018)

EIBibtex

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

Marko Järvenpää,Mohamad Sater, Georgia Lagoudas,Paul C. Blainey,Loren G. Miller,James A. McKinnell,Susan S. Huang,Yonatan H. Grad,Pekka Marttinen

PLoS Computational Biology, no. 4 (2018): 429464-24

WOSEIBibtex

Gaussian process modelling in approximate Bayesian computation to estimate horizontal gene transfer in bacteria

Marko Järvenpää,Michael U. Gutmann, A. K.I. Vehtari,Pekka Marttinen

ANNALS OF APPLIED STATISTICS, no. 4 (2018): 2228-2251

Bibtex

Efficient acquisition rules for model-based approximate Bayesian computation

Marko Järvenpää,Michael U. Gutmann, Arijus Pleska,Aki Vehtari,Pekka Marttinen

Bayesian Analysis, no. 2 (2018): 595-622

Cited by30Bibtex

ELFI: Engine for Likelihood-Free Inference

Jarno Lintusaari, Henri Vuollekoski,Antti Kangasrääsiö, Kusti Skytén, Marko Järvenpää,Pekka Marttinen,Michael U. Gutmann,Aki Vehtari,Jukka Corander,Samuel Kaski

Journal of Machine Learning Research, (2018)

Cited by23EIBibtex

Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge

Iiris Sundin,Tomi Peltola,Luana Micallef,Homayun Afrabandpey, Marta Soare,Muntasir Mamun Majumder,Pedram Daee,Chen He, Baris Serim,Aki S. Havulinna,Caroline Heckman,Giulio Jacucci

BIOINFORMATICS, no. 13 (2018): 395-403

Cited by4EIWOSBibtex

Bacmeta: simulator for genomic evolution in bacterial metapopulations

Aleksi Sipola,Pekka Marttinen,Jukka Corander

BIOINFORMATICS, no. 13 (2018): 2308-2310

Cited by3EIWOSBibtex

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

Rafal Mostowy,Nicholas J Croucher,Cheryl P Andam,Jukka Corander,William P Hanage,Pekka Marttinen

MOLECULAR BIOLOGY AND EVOLUTION, no. 5 (2017): 1167-1182

Cited by16WOSBibtex

Gaussian process modeling in approximate Bayesian computation to estimate horizontal gene transfer in bacteria

Marko Järvenpää,Michael U. Gutmann,Aki Vehtari,Pekka Marttinen

The Annals of Applied Statistics, (2017)

Cited by20Bibtex

biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements

Matti Pirinen,Christian Benner,Pekka Marttinen,Marjo-Riitta Järvelin,Manuel A. Rivas,Samuli Ripatti

BIOINFORMATICS, no. 15 (2017): 2405-2407

Cited by5EIWOSBibtex

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Pekka MarttinenBinding

Papers48 papers

Pekka Marttinen