Antti Honkela
Cited by
Cited by
A community effort to assess and improve drug sensitivity prediction algorithms
JC Costello, LM Heiser, E Georgii, M Gönen, MP Menden, NJ Wang, ...
Nature biotechnology 32 (12), 1202-1212, 2014
Identifying differentially expressed transcripts from RNA-seq data with biological variation
P Glaus, A Honkela, M Rattray
Bioinformatics 28 (13), 1721-1728, 2012
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
JA Lees, M Vehkala, N Välimäki, SR Harris, C Chewapreecha, ...
Nature communications 7 (1), 12797, 2016
Bayesian non-linear independent component analysis by multi-layer perceptrons
H Lappalainen, A Honkela
Advances in independent component analysis, 93-121, 2000
Approximate Riemannian conjugate gradient learning for fixed-form variational Bayes
A Honkela, T Raiko, M Kuusela, M Tornio, J Karhunen
The Journal of Machine Learning Research 11, 3235-3268, 2010
Model-based method for transcription factor target identification with limited data
A Honkela, C Girardot, EH Gustafson, YH Liu, EEM Furlong, ...
Proceedings of the National Academy of Sciences 107 (17), 7793-7798, 2010
Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities
P Gao, A Honkela, M Rattray, ND Lawrence
Bioinformatics 24 (16), i70-i75, 2008
Computing tight differential privacy guarantees using FFT
A Koskela, J Jälkö, A Honkela
International Conference on Artificial Intelligence and Statistics, 2560-2569, 2020
Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays
A Honkela, J Peltonen, H Topa, I Charapitsa, F Matarese, K Grote, ...
Proceedings of the National Academy of Sciences 112 (42), 13115-13120, 2015
Variational learning and bits-back coding: an information-theoretic view to Bayesian learning
A Honkela, H Valpola
IEEE transactions on Neural Networks 15 (4), 800-810, 2004
A generative approach for image-based modeling of tumor growth
BH Menze, K Van Leemput, A Honkela, E Konukoglu, MA Weber, ...
Information Processing in Medical Imaging: 22nd International Conference …, 2011
Unsupervised variational Bayesian learning of nonlinear models
A Honkela, H Valpola
Advances in neural information processing systems 17, 2004
Differentially private Bayesian learning on distributed data
M Heikkilä, E Lagerspetz, S Kaski, K Shimizu, S Tarkoma, A Honkela
Advances in neural information processing systems, 3226-3235, 2017
Seasonal variation in genome-wide DNA methylation patterns and the onset of seasonal timing of reproduction in great tits
HM Viitaniemi, I Verhagen, ME Visser, A Honkela, K Van Oers, A Husby
Genome Biology and Evolution 11 (3), 970-983, 2019
Nonlinear independent component analysis using ensemble learning: Experiments and discussion
H Valpola, X Giannakopoulos, A Honkela, J Karhunen
Proc. Second International Workshop on Independent Component Analysis and …, 2000
On-line variational Bayesian learning
A Honkela, H Valpola
4th International Symposium on Independent Component Analysis and Blind …, 2003
Differentially private variational inference for non-conjugate models
J Jälkö, O Dikmen, A Honkela
arXiv preprint arXiv:1610.08749, 2016
Tight differential privacy for discrete-valued mechanisms and for the subsampled Gaussian mechanism using FFT
A Koskela, J Jälkö, L Prediger, A Honkela
International Conference on Artificial Intelligence and Statistics, 3358-3366, 2021
Natural conjugate gradient in variational inference
A Honkela, M Tornio, T Raiko, J Karhunen
Neural Information Processing: 14th International Conference, ICONIP 2007 …, 2008
Gaussian process test for high-throughput sequencing time series: application to experimental evolution
H Topa, Á Jónás, R Kofler, C Kosiol, A Honkela
Bioinformatics 31 (11), 1762-1770, 2015
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