PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

EPrints submitted by Samuel Kaski

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Number of EPrints submitted by this user: 61

Visualized atlas of a gene expression databank
Jarkko Venna and Samuel Kaski
In: KRBIO'05, 16 June 2005, Espoo, Finland.

Associative clustering for exploring dependencies between functional genomics data sets
Samuel Kaski, Janne Nikkilä, Janne Sinkkonen, Leo Lahti, Juha Knuutila and Christophe Roos
IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 2, pp. 203-216, 2005.

Proceedings of KRBIO05, Symposium on Knowledge Representation in Bioinformatics
Catherine Bonsaythip, Jaakko Hollmen, Samuel Kaski and Matej Oresic, ed. (2005) Helsinki University of Technology , Espoo, Finland .

From learning metrics towards dependency exploration
Samuel Kaski
In: WSOM'05, 5th Workshop On Self-Organizing Maps, 5-8 Sep 2005, Paris, France.

User models from implicit feedback for proactive information retrieval
Samuel Kaski, Petri Myllymäki and Ilpo Kojo
In: Workshop 4 of the 10th International Conference on User Modeling; Machine Learning for User Modeling: Challenges, Edinburgh, Scotland(2005).

Integration of transcription factor binding and gene expression by associative clustering
Janne Nikkilä, Christophe Roos and Samuel Kaski
In: KRBIO05, Symposium on Knowledge Representation in Bioinformatics, Espoo, Finland(2005).

Proactive information retrieval by monitoring eye movements
Samuel Kaski
In: BrainIT, The Second International Conference on Brain-Inspired Information Technology, 7-9 Oct 2005, Kitakyushu, Japan.

Associative clustering (AC): Technical details
Janne Sinkkonen, Samuel Kaski, Janne Nikkilä and Leo Lahti
(2005) Technical Report. Helsinki University of Technology, Espoo, Finland.

Probabilistic Modeling and Machine Learning in Structural and Systems Biology
Juho Rousu, Samuel Kaski and Esko Ukkonen, ed. (2006) Helsinki University Printing House , Helsinki, Finland . ISBN 952 10 3277 4

Neural networks and machine learning in bioinformatics - theory and applications
Udo Seiffert, Barbara Hammer, Samuel Kaski and Thomas Villmann
In: ESANN 2006, 26-28 April 2006, Brugge, Belgium.

Inferring vertex properties from topology in large networks
Janne Aukia, Samuel Kaski and Janne Sinkkonen
In: NIPS'07 workshop on statistical models of networks, 8 Dec 2007, Whistler, BC.

Learning from relevant tasks only
Samuel Kaski and Jaakko Peltonen
In: Machine Learning: ECML 2007 (Proceedings of the 18th European Conference on Machine Learning) (2007) Springer-Verlag , Berlin , pp. 608-615.

Probabilistic modeling and machine learning in structural and systems biology
Samuel Kaski, Juho Rousu and Esko Ukkonen
(2007) BMC.

The self-organizing map as a visual information retrieval method
Kristian Nybo, Jarkko Venna and Samuel Kaski
In: Proceedings of WSOM'07, 6th International Workshop on Self-Organizing Maps (2007) Bielefeld University , Bielefeld, Germany .

Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines
Penny Nymark, Pamela Lindholm, Mikko Korpela, Leo Lahti, Salla Ruosaari, Samuel Kaski, Jaakko Hollmen, Sisko Anttila, Vuokko Kinnula and Sakari Knuutila
BMC Genomics Volume 8, 62, 2007.

Searching for functional gene modules with interaction component models
Juuso Parkkinen and Samuel Kaski
In: NIPS 2007 workshop on Machine Learning in Computational Biology, 7-8 Dec 2007, Whistler, BC.

Inferring vertex properties from topology in large networks
Janne Sinkkonen, Janne Aukia and Samuel Kaski
In: MLG'07, Mining and Learning with Graphs, 1-3 Aug 2007, Firenze.

Nonlinear dimensionality reduction as information retrieval
Jarkko Venna and Samuel Kaski
In: Proceedings of AISTATS 2007, the 11th International Conference on International Conference on Artificial Intelligence and Statistics (2007) Omnipress .

Comparison of visualization methods for an atlas of gene expression data sets
Jarkko Venna and Samuel Kaski
Information Visualization Volume 6, pp. 139-154, 2007.

Bayesian Biclustering with the Plaid Model
José Caldas and Samuel Kaski
In: Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing XVIII (2008) IEEE , NJ, USA , pp. 291-296.

Gender dependent progression of systemic metabolic states in early childhood
Janne Nikkilä, Marko Sysi-Aho, Andrey Ermolov, Tuulikki Seppänen-Laakso, Olli Simell, Samuel Kaski and Matej Oresic
Molecular Systems Biology Volume 4, Number 197, 2008.

Infinite mixtures for multi-relational categorical data
Janne Sinkkonen, Janne Aukia and Samuel Kaski
In: MLG-2008: 6th International Workshop on Mining and Learning with Graphs, 4-5 July 2008, Helsnki, Finland.

A simple infinite topic mixture for rich graphs and relational data
Janne Sinkkonen, Juuso Parkkinen, Janne Aukia and Samuel Kaski
In: NIPS 2008 Workshop on Analyzing Graphs: Theory and Applications, 12 Dec 2008, Whistler, BC.

On asymmetric generalization error of asymmetric multitask learning
Keisuke Yamazaki and Samuel Kaski
In: NIPS Learning from Multiple Sources Workshop, 13 Dec 2008, Whistler, BC.

Hierarchical generative biclustering for microRNA expression analysis
José Caldas and Samuel Kaski
In: Proceedings of RECOMB (2009) Springer .

Inferring Object Relevance from Gaze in Dynamic Scenes
Melih Kandemir, Veli-Matti Saarinen and Samuel Kaski
In: Proc. ETRA 2010, Eye Tracking Research & Applications (2009) ACM .

Self-Organizing Maps
Samuel Kaski
In: Encyclopedia of Machine Learning (2009) Springer .

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays
Leo Lahti, Laura L. Elo, Tero Aittokallio and Samuel Kaski
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2009. ISSN http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.38

Three Paths to Relevance
Samuel Kaski
In: Brain-Inspired Information Technology (2010) Springer , Berlin , pp. 11-13.

Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data
Farid Benachenhou, Patric Jern, Merja Oja, Göran Sperber, Panu Somervuo, Samuel Kaski and Jonas Blomberg
PLoS ONE Volume 4, Number e5179, 2009.

Probabilistic retrieval and visualization of biologically relevant microarray experiments
José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma and Samuel Kaski
Bioinformatics Volume 25, i145-i153, 2009.

Two-Way Analysis of High-Dimensional Collinear Data
Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Oresic and Samuel Kaski
Data Mining and Knowledge Discovery Volume 19, pp. 261-276, 2009.

Multi-Way, Multi-View Learning
Ilkka Huopaniemi, Tommi Suvitaival, Janne Nikkilä, Matej Oresic and Samuel Kaski
In: NIPS 2009 workshop on Learning from Multiple Sources with Applications to Robotics, Whistler, BC(2009).

Dependency detection with similarity constraints
Leo Lahti, Samuel Myllykangas, Sakari Knuutila and Samuel Kaski
In: Proc. MLSP 2009, IEEE International Workshop on Machine Learning for Signal Processing (2009) IEEE , pp. 89-94.

Graph Visualization with Latent Variable Models
Kristian Nybo, Juuso Parkkinen and Samuel Kaski
(2009) Technical Report. Helsinki University of Technology, Espoo, Finland.

Searching for functional gene modules with interaction component models
Juuso Parkkinen and Samuel Kaski
BMC Systems Biology Volume 4, Number 4, 2010.

A Block Model Suitable for Sparse Graphs
Juuso Parkkinen, Janne Sinkkonen, Adam Gyenge and Samuel Kaski
In: Proceedings of the 7th International Workshop on Mining and Learning with Graphs (MLG 2009) (2009) KU Leuven .

Bayesian Solutions to the Label Switching Problem
Kai Puolamäki and Samuel Kaski
In: Advances in Intelligent Data Analysis VIII, Proceedings of the 8th International Symposium on Intelligent Data Analysis, IDA 2009 (2009) Springer , Berlin , pp. 381-392.

An Analysis of Generalization Error in Relevant Subtask Learning
Keisuke Yamazaki and Samuel Kaski
In: Advances in Neuro-Information Processing, 15th International Conference, ICONIP 2008 (2009) Springer , Berlin , pp. 629-637.

Hierarchical generative biclustering for MicroRNA Expression Analysis
Jose Caldas and Samuel Kaski
Journal of Computational Biology pp. 251-261, 2011.

Dimensionality Reduction for Data Visualization
Samuel Kaski and Jaakko Peltonen
IEEE Signal Processing Magazine Volume 28, Number 2, pp. 100-104, 2011.

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays
Leo Lahti, Laura Elo, Tero Aittokallio and Samuel Kaski
IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 8, Number 1, pp. 217-225, 2011.

Hierarchical generative biclustering for microRNA expression analysis
Jose Caldas and Samuel Kaski
In: Research in Computational Molecular Biology, Proceedings of 14th Annual International Conference RECOMB 2010 (2010) Springer , Berlin , pp. 65-79.

Global modeling of transcriptional responses in interaction networks
Leo Lahti, Juha Knuuttila and Samuel Kaski
Bioinformatics Volume 26, pp. 2713-2720, 2010.

Inferring Object Relevance from Gaze in Dynamic Scenes
Melih Kandemir, Veli-Matti Saarinen and Samuel Kaski
In: Proceedings of ETRA 2010, ACM Symposium on Eye Tracking Research & Applications, Austin, TX, USA, March 22-24 (2010) ACM , New York, NY , pp. 105-108.

Pinview: Implicit Feedback in Content-Based Image Retrieval
Peter Auer, Zakria Hussain, Samuel Kaski, Arto Klami, Jussi Kujala, Jorma Laaksonen, Alex Leung, Kitsuchart Pasupa and John Shawe-Taylor
In: Proceedings of Workshop on Applications of Pattern Analysis JMLR Workshop and Conference Proceedings , 11 . (2010) JMLR , pp. 51-57.

Proceedings of the 2010 IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010)
Samuel Kaski, David Miller, Erkki Oja and Antti Honkela, ed. (2010) IEEE , Piscataway, NJ .

Data-Driven Information Retrieval in Heterogeneous Collections of Transcriptomics Data Links SIM2s to Malignant Pleural Mesothelioma
Jose Caldas, Nils Gehlenborg, Eeva Kettunen, Ali Faisal, Mikko Rönty, Andrew Nicholson, Sakari Knuutila, Alvis Brazma and Samuel Kaski
Bioinformatics Volume 28, pp. 246-253, 2012.

Biomarker discovery via dependency analysis of multi-view functional genomics data
Ali Faisal, Riku Louhimo, Leo Lahti, Sampsa Hautaniemi and Samuel Kaski
In: NIPS 2011 workshop From Statistical Genetics to Predictive Models in Personalized Medicine(2011).

Systematic Use of Computational Methods Allows Stratifying Treatment Responders in Glioblastoma Multiforme
Riku Louhimo, Viljami Aittomäki, Ali Faisal, Marko Laakso, Ping Chen, Kristian Ovaska, Erkka Valo, Vladimir Rogojin, Samuel Kaski and Sampsa Hautaniemi
In: Proceedings of CAMDA 2011, Critical Assessment of Massive Data Analysis(2011).

Dimensionality Reduction for Data Visualization
Samuel Kaski and Jaakko Peltonen
IEEE Signal Processing Magazine Volume 28, Number 2, pp. 100-104, 2011.

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays
Leo Lahti, Laura Elo, Tero Aittokallio and Samuel Kaski
IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 8, Number 1, pp. 217-225, 2011.

Cross-species translation of multi-way biomarkers
Tommi Suvitaival, Ilkka Huopaniemi, Matej Oresic and Samuel Kaski
In: Proc. ICANN 2011(2011).

Detecting similar high-dimensional responses to experimental factors between human and model organism
Tommi Suvitaival, Ilkka Huopaniemi, Matej Oresic and Samuel Kaski
In: NIPS 2011 workshop From Statistical Genetics to Predictive Models in Personalized Medicine(2011).

Metabolic regulation in progression to autoimmune diabetes
Marko Sysi-Aho, Andrey Ermolov, Peddinti Gopalacharyulu, Abhishek Tripathi, Tuulikki Seppänen-Laakso, Johanna Maukonen, Ismo Mattila, Suvi Ruohonen, Laura Vähätalo, Laxman Yetukuri, Taina Härkönen, Erno Lindfors, Janne Nikkilä, Jorma Ilonen, Olli Simell, Maria Saarela, Mikael Knip, Samuel Kaski, Eriika Savontaus and Matej Oresic
PLoS Computational Biology Volume 7, Number e1002257, 2011.

High Density Lipoprotein structural changes and drug response in lipidomic profiles following the long-term fenofibrate therapy in the FIELD substudy
Laxman Yetukuri, Ilkka Huopaniemi, Artturi Koivuniemi, Marianna Maranghi, Anne Hiukka, Heli Nygren, Samuel Kaski, Marja-Riitta Taskinen, Ilpo Vattulainen, Matti Jauhiainen and Matej Oresic
PLoS ONE Volume 6, Number 8, e23589, 2011.

The rocky road to personalized medicine: computational and statistical challenges
Jukka Corander, Tero Aittokallio, Samuli Ripatti and Samuel Kaski
Personalized Medicine Volume 2, Number 9, pp. 109-114, 2012.

Unsupervised inference of auditory attention from biosensors
Melih Kandemir, Arto Klami, Akos Vetek and Samuel Kaski
In: ECML PKDD 2012(2012).

Learning Relevance from Natural Eye Movements in Pervasive Interfaces
Melih Kandemir and Samuel Kaski
In: ICMI 2012(2012).

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs
Suleiman Khan, Ali Faisal, John Patrick Mpindi, Juuso Parkkinen, Tuomo Kalliokoski, Antti Poso Poso, Olli P. Kallioniemi, Krister Wennerberg and Samuel Kaski
BMC Bioinformatics Volume 13, Number 112, 2012.

Identifying fragments of natural speech from the listener's MEG signals
Miika Koskinen, Jaakko Viinikanoja, Arto Klami, Samuel Kaski and Riitta Hari
Human Brain Mapping 2012.