PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

EPrints submitted by Juho Rousu

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Number of EPrints submitted by this user: 20

Efficient Computation of Gapped Substring Kernels on Large Alphabets
Juho Rousu and John Shawe-Taylor
Journal of Machine Learning Research 2004.

On Maximum Margin Hierarchical Multilabel Classification
Juho Rousu, Craig Saunders, Sandor Szedmak and John Shawe-Taylor
In: NIPS'2004 Workshop on Learning with Structured Outputs, 18 Dec 2004, Whistler, Canada.

Kernel-based Learning of Hierarchical Multilabel Classification Models
Juho Rousu, Craig Saunders, Sandor Szedmak and John Shawe-Taylor
Journal of Machine Learning Research 2005.

Efficient algorithms for max-margin structured classification
Craig Saunders, Sandor Szedmak, John Shawe-Taylor and Juho Rousu
In: Predicting Structured Data Neural Information Processing . (2007) MIT Press , Cambridge, Usa , pp. 105-128. ISBN 0262026178

Probabilistic Modeling and Machine Learning in Structural and Systems Biology
Juho Rousu, Samuel Kaski and Esko Ukkonen, ed. (2006) Series of Publications B, University of Helsinki, Department of Computer Science , Volume B-2006-4 . Helsinki University Press , Helsinki, Finland . ISBN 952-10-3277-4

Towards Structured Output Prediction of Enzyme Function
Katja Astikainen, Liisa Holm, Esa Pitkänen, Sandor Szedmak and Juho Rousu
In: Machine Learning in Systems Biology, 24-25 Sep 2007, Evry, France.

Towards structured output prediction of enzyme function
Katja Astikainen, Liisa Holm, Esa Pitkänen, Sandor Szedmak and Juho Rousu
BMC Proceedings Volume 2, Number Suppl 4, 2008. ISSN 1753-6561

Reaction kernels: structured output prediction approaches for novel enzyme function
Katja Astikainen, Esa Pitkänen, Juho Rousu, Liisa Holm and Sandor Szedmak
In: Bioinformatics 2010, 19-23 Jan 2010, Valencia, Spain.

Inferring branching pathways in genome-scale metabolic networks
Esa Pitkänen, Paula Jouhten and Juho Rousu
BMC Systems Biology Volume 3, Number 103, 2009. ISSN 1752-0509

Machine Learning in Systems Biology. Proc. 3rd International Workshop
Saso Dzeroski, Pierre Geurts and Juho Rousu
(2009) Technical Report. Helsinki University Printing House, Helsinki, Finland.

Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism
Heinonen Markus, Lappalainen Sampsa, Taneli Mielikäinen and Juho Rousu
Journal of Computational Biology 2009.

Minimum mutation algorithm for gapless metabolic network evolution
Esa Pitkänen, Juho Rousu and Mikko Arvas
In: International Conference on Bioinformatics Models, Methods and Algorithms, 26 Jan - 29 Jan 2011, Rome, Italy.

Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism
Markus Heinonen, Sampsa Lappalainen, Taneli Mielikäinen and Juho Rousu
Journal of Computational Biology Volume 18, Number 1, pp. 43-58, 2011.

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels
Katja Astikainen, Liisa Holm, Esa Pitkänen, Sandor Szedmak and Juho Rousu
In: BIOMEDICAL ENGINEERING SYSTEMS AND TECHNOLOGIES COMMUNICATIONS IN COMPUTER AND INFORMATION SCIENCE , 127 . (2011) Springer , pp. 367-379.

Computational methods for metabolic reconstruction
Esa Pitkänen, Juho Rousu and Esko Ukkonen
Current Opinion in Biotechnology Volume 21, Number 1, pp. 70-77, 2010.

Multilabel Classification of Drug-like Molecules via Max-Margin Conditional Random Fields
Hongyu Su, Markus Heinonen and Juho Rousu
In: Fifth European Workshop on Probabilistic Graphical Models (PGM-2010), 13-15 Sep 2010, Helsinki.

Structured Output Prediction of Anti-cancer Drug Activity
Hongyu Su, Markus Heinonen and Juho Rousu
In: 5th International Conference on Pattern Recognition in Bioinformatics, 22-24 Sep 2010, Nijmegen, The Netherlands.

Multi-Task Drug Bioactivity Classification with Graph Labeling Ensembles
Hongyu Su and Juho Rousu
In: 6th International Conference on Pattern Recognition in Bioinformatics, 2-4 Nov 2011, Delft, The Netherlands.

Sparse Canonical Correlation Analysis for Biomarker Discovery : A Case Study in Tuberculosis
Juho Rousu, Daniel D. Agranoff, John Shawe-Taylor and Delmiro Fernandez-Reyes
In: Machine Learning in Systems Biology : Proceedings of the Fifth International Workshop, 20-21 Jul 2011, Vienna, Austria.

Efficient Path Kernels for Reaction Function Prediction
Markus Heinonen, Niko Välimäki, Veli Mäkinen and Juho Rousu
In: 3rd International Conference on Bioinformatics Models, Methods and Algorithms, 1-4 Feb 2012, Algarve, Portugal.