PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

EPrints submitted by Antti Honkela

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Number of EPrints submitted by this user: 28

Using Kernel PCA for Initialisation of Variational Bayesian Nonlinear Blind Source Separation Method
Antti Honkela, Stefan Harmeling, Leo Lundqvist and Harri Valpola
In: 5th International Conference on Independent Component Analysis and Blind Signal Separation (ICA 2004), 22-24 Sep 2004, Granada, Spain.

Unsupervised variational Bayesian learning of nonlinear models
Antti Honkela and Harri Valpola
In: NIPS 2004, 13-18 Dec 2004, Vancouver, Canada.

Independent variable group analysis in learning compact representations for data
Krista Lagus, Esa Alhoniemi, Jeremias Seppä, Antti Honkela and Paul Wagner
In: AKRR'05, 15-17 Jun 2005, Espoo, Finland.

Advances in Variational Bayesian Nonlinear Blind Source Separation
Antti Honkela
(2005) PhD thesis, Helsinki University of Technology.

Bayes Blocks: An Implementation of the Variational Bayesian Building Blocks Framework
Markus Harva, Tapani Raiko, Antti Honkela, Harri Valpola and Juha Karhunen
In: UAI 2005, 26-29 Jul 2005, Edinburgh, Scotland.

Empirical evidence of the linear nature of magnetoencephalograms
Antti Honkela, Tomas Östman and Ricardo Vigário
In: ESANN 2005, 27-29 Apr 2005, Bruges, Belgium.

State Inference in Variational Bayesian Nonlinear State-Space Models
Tapani Raiko, Matti Tornio, Antti Honkela and Juha Karhunen
In: 6th International Conference on Independent Component Analysis and Blind Signal Separation (ICA 2006), 5-8 Mar 2006, Charleston, South Carolina, USA.

Exploring the independence of gene regulatory modules
Janne Nikkilä, Antti Honkela and Samuel Kaski
In: Probabilistic Modeling and Machine Learning in Structural and Systems Biology (PMSB 2006), 17-18 June 2006, Tuusula, Finland.

Bayes Blocks: A Python Toolbox for Variational Bayesian Learning
Antti Honkela, Markus Harva, Tapani Raiko, Harri Valpola and Juha Karhunen
In: NIPS*2006 Workshop on Machine Learning Open Source Software, 9 Dec 2006, Whistler, B.C., Canada.

Variational Bayes for Continuous-Time Nonlinear State-Space Models
Antti Honkela, Matti Tornio and Tapani Raiko
In: NIPS*2006 Workshop on Dynamical Systems, Stochastic Processes and Bayesian Inference, 9 Dec 2006, Whistler, B.C., Canada.

Time Series Prediction with Variational Bayesian Nonlinear State-Space Models
Matti Tornio, Antti Honkela and Juha Karhunen
In: European Symposium on Time Series Prediction (ESTSP 2007), 7-9 Feb 2007, Espoo, Finland.

Agglomerative Independent Variable Group Analysis
Antti Honkela, Jeremias Seppä and Esa Alhoniemi
In: 15th European Symposium on Artificial Neural Networks (ESANN 2007), 25-27 Apr 2007, Bruges, Belgium.

Compact Modeling of Data Using Independent Variable Group Analysis
Esa Alhoniemi, Antti Honkela, Krista Lagus, Jeremias Seppä, Paul Wagner and Harri Valpola
IEEE Transactions on Neural Networks Volume 18, Number 6, pp. 1762-1776, 2007. ISSN 1045-9227

Blind Separation of Nonlinear Mixtures by Variational Bayesian Learning
Antti Honkela, Harri Valpola, Alexander Ilin and Juha Karhunen
Digital Signal Processing Volume 17, Number 5, pp. 914-934, 2007. ISSN 1051-2004

Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities
Pei Gao, Antti Honkela, Magnus Rattray and Neil Lawrence
Bioinformatics Volume 24, Number 16, i70-i75, 2008. ISSN 1460-2059

Natural Conjugate Gradient in Variational Inference
Antti Honkela, Matti Tornio, Tapani Raiko and Juha Karhunen
In: 14th International Conference on Neural Information Processing (ICONIP 2007), 13-16 Nov 2007, Kitakyushu, Japan.

Agglomerative independent variable group analysis
Antti Honkela, Jeremias Seppä and Esa Alhoniemi
Neurocomputing Volume 71, Number 7-9, pp. 1311-1320, 2008. ISSN 0925-2312

Identifying targets of transcriptionally regulated transcription factors using dynamical models
Antti Honkela, Neil Lawrence and Magnus Rattray
In: Mathematical and Statistical Aspects of Molecular Biology: 19th Annual MASAMB Workshop, 2-3 Apr 2009, London, UK.

Identifying targets of transcriptionally regulated transcription factors using dynamical models
Antti Honkela, Neil Lawrence and Magnus Rattray
In: 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), 27 Jun - 2 Jul 2009, Stockholm, Sweden.

Model-based method for transcription factor target identification with limited data
Antti Honkela, Charles Girardot, E. Hilary Gustafson, Ya-Hsin Liu, Eileen E. M. Furlong, Neil Lawrence and Magnus Rattray
Proceedings of the National Academy of Sciences of the USA Volume 107, Number 17, pp. 7793-7798, 2010. ISSN 0027-8424

Approximate Riemannian conjugate gradient learning for fixed-form variational Bayes
Antti Honkela, Tapani Raiko, Mikael Kuusela, Matti Tornio and Juha Karhunen
Journal of Machine Learning Research Volume 11, Number Nov, pp. 3235-3268, 2010.

tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression for Bioconductor
Antti Honkela, Pei Gao, Jonatan Ropponen, Magnus Rattray and Neil Lawrence
Bioinformatics Volume 27, Number 7, pp. 1026-1027, 2011. ISSN 1367-4803

Variational Inference and Learning for Non-Linear State-Space Models with State-Dependent Observation Noise
Veli Peltola and Antti Honkela
In: 2010 IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010), 29 Aug - 1 Sep 2010, Kittilä, Finland.

Ranking of Gene Regulators through Differential Equations and Gaussian Processes
Antti Honkela, Marta Milo, Matthew Holley, Magnus Rattray and Neil Lawrence
In: 2010 IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010), 29 Aug - 1 Sep 2010, Kittilä, Finland.

Bayesian model of transcript differential expression in RNA-seq data with biological variation
Peter Glaus, Antti Honkela and Magnus Rattray
In: Machine Learning in Computational Biology (MLCB) 2011, 17 Dec 2011, Sierra Nevada, Spain.

Hierarchical Gaussian Process Models of Gene Expression and Transcriptional Regulation
Antti Honkela, James Hensman, Neil Lawrence and Magnus Rattray
In: Mathematical and Statistical Aspects of Molecular Biology: 21st Annual MASAMB Workshop, 11-12 Apr 2011, Vienna, Austria.

Identifying differentially expressed transcripts from RNA-seq data with biological variation
Peter Glaus, Antti Honkela and Magnus Rattray
Bioinformatics Volume 28, Number 13, pp. 1721-1728, 2012. ISSN 1460-2059

Mining Regulatory Network Connections by Ranking Transcription Factor Target Genes Using Time Series Expression Data
Antti Honkela, Magnus Rattray and Neil Lawrence
In: Data Mining for Systems Biology Methods in Molecular Biology , 939 . (2013) Humana Press , pp. 59-67. ISBN 978-1-62703-106-6