Antti Honkela
Antti Honkela
Associate Professor, University of Helsinki
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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, 2014
Bayesian non-linear independent component analysis by multi-layer perceptrons
H Lappalainen, A Honkela
Advances in independent component analysis, 93-121, 2000
Identifying differentially expressed transcripts from RNA-seq data with biological variation
P Glaus, A Honkela, M Rattray
Bioinformatics 28 (13), 1721-1728, 2012
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
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
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), 1-8, 2016
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
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
Unsupervised variational Bayesian learning of nonlinear models
A Honkela, H Valpola
Advances in neural information processing systems, 593-600, 2005
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
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
A generative approach for image-based modeling of tumor growth
BH Menze, K Van Leemput, A Honkela, E Konukoglu, MA Weber, ...
Biennial International Conference on Information Processing in Medical …, 2011
On-line variational Bayesian learning
A Honkela, H Valpola
4th International Symposium on Independent Component Analysis and Blind …, 2003
Nonlinear blind source separation by variational Bayesian learning
H Valpola, E Oja, A Ilin, A Honkela, J Karhunen
IEICE Transactions on Fundamentals of Electronics, Communications and …, 2003
Natural conjugate gradient in variational inference
A Honkela, M Tornio, T Raiko, J Karhunen
International Conference on Neural Information Processing, 305-314, 2007
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
Blind separation of nonlinear mixtures by variational Bayesian learning
A Honkela, H Valpola, A Ilin, J Karhunen
Digital Signal Processing 17 (5), 914-934, 2007
Fast and accurate approximate inference of transcript expression from RNA-seq data
J Hensman, P Papastamoulis, P Glaus, A Honkela, M Rattray
Bioinformatics 31 (24), 3881-3889, 2015
Accelerating cyclic update algorithms for parameter estimation by pattern searches
A Honkela, H Valpola, J Karhunen
Neural Processing Letters 17 (2), 191-203, 2003
Nonlinear switching state-space models
A Honkela
Master's thesis, Helsinki University of Technology, Espoo, Finland, 2001
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