Journal Club

Meetings are held every Monday between 14:15 and 15:00 in room A328. We discuss recent papers on machine learning or bioinformatics topics.

2012

• 13.2.2012 (Juuso)
  Detecting novel associations in large data sets. David Reshef, ..., Pardis Sabeti. Science 16 December 2011: Vol. 334 no. 6062 pp. 1518-1524.
  and
  MINE: Maximal Information-based Nonparametric Exploration. Includes code (Java/R/Python) and data for the Science paper.


• 6.2.2012 CANCELLED (Juuso)


• 30.1.2012 (Melih)
  Quasi-Newton Methods for Markov Chain Monte Carlo. Y. Zhang and C. Sutton. NIPS, 2011.


• 16.1.2012 (Sohan)
  Kernel Bayes' rule. Kenji Fukumizu, Le Song, Arthur Gretton. NIPS, 2011.


• 9.1.2012 (Ali)
  Testing a Bayesian Measure of Representativeness Using a Large Image Database. Joshua Abbott, Katherine Heller, Zoubin Ghahramani, Tom Griffiths. NIPS, 2011.


• 2.1.2012 (Suleiman)
  Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data . Xing-Ming Zhao, Murat Iskar, Georg Zeller, Michael Kuhn, Vera van Noort and Peer Bork. PLoS CB, 2011.

2011

• 19.12.2011 (Arto)
  Riemannian manifold Langevin and Hamiltonian Monte Carlo methods . Mark Girolami and Ben Calderhead. J.R. Statist. Soc. B, 2011.


• 12.12.2011 (Elisabeth)
  Mixture models for analysis of the taxonomic composition of metagenomes . Peter Meinicke, Kathrin Asshauer, Thomas Lingner. Bioinformatics, 2011.


• 28.11.2011 (Mehmet)
  Sparse Bayesian Multi-Task Learning. Cedric Archambeau, Shengbo Guo, Onno Zoeter. NIPS, 2011.


• 21.11.2011 (Antti)
  MCMC using Hamiltonian dynamics. Radford M. Neal. Handbook of Markov Chain Monte Carlo, Chapman & Hall / CRC Press, 2011.


• 14.11.2011 (Tommi)
  Bayesian Functional ANOVA Modeling Using Gaussian Process Prior Distributions. Cari G. Kaufman and Stephan R. Sain. Bayesian Analysis, 2010.


• 07.11.2011 (Suleiman)
  Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes. Yinyin Yuan, Richard S. Savage, Florian Markowetz. PLoS CB, 2011


• 24.10.2011 (SamiK)
  One-shot learning with a hierarchical nonparametric Bayesian model. Salakhutdinov, Tenenbaum, Torralba, MIT-CSAIL-TR-2010-052.


• 17.10.2011 (Juuso)
  Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches . Yen Low, ..., Alexander Tropsha, Chemical research in toxicology.
  and
  Use of in Vitro HTS-Derived Concentration -Response Data as Biological Descriptors Improves the Accuracy of QSAR Models of in Vivo Toxicity. Alexander Sedykh, ..., Alexander Tropsha, Environmental health perspectives.


• 10.10.2011 (SamiK) [CANCELLED and moved to a later slot. Sorry! /Sami]
  One-shot learning with a hierarchical nonparametric Bayesian model. Salakhutdinov, Tenenbaum, Torralba, MIT-CSAIL-TR-2010-052.


• 3.10.2011 (Melih)
  Generalised Wishart Processes. A.G. Wilson, Z. Ghahramani. UAI, 2011.


• 26.9.2011 (Ali)
  Bayesian Hierarchical Mixture of Experts. C.M.Bishop, M. Svensen. UAI, 2003.
  and
  Mixtures of Probabilistic Principal Component Analyzers. M.E.Tipping, C.M.Bishop. Neural Computation 1999.


• 19.9.2011 (Kristian)
  http://www.sciencedirect.com/science/article/pii/S1053811911003259. Firdaus Janoos, Raghu Machirajua, Shantanu Singha and Istvan Akos Moroczb. Neuroimage, 2011.


• 12.9.2011 (Chiwei)
  Online Learning for Latent Dirichlet Allocation. M. Hoffman, D. Blei, F. Bach. NIPS2010.


• 05.9.2011 (Jaakko)
  Tree Preserving Embedding. Shieh, A., Hashimoto, T. & Airoldi, EM. ICML2011 / PNAS (In press).


• 29.8.2011 (Arto)
  Sparse additive generative models of text. J. Eisenstein, A. Ahmed, E.P. Xing. ICML 2011.


• 22.8.2011 (Elisabeth)
  Subgroup discovery meets Bayesian networks - an Exceptional Model Mining approach. W. Duivesteijn, A. Knobbe, A. Feelders, M. van Leeuwen. ICDM 2010.


• 15.8.2011 (Mehmet)
  Context relevance assessment and exploitation in mobile recommender systems. L. Baltrunas, B. Ludwig, S. Peer, and F. Ricci, Personal and Ubiquitous Computing.


• 8.8.2011 (Antti)
  Fast context-aware recommendations with factorization machines. S. Rendle, Z. Gantner, C. Freudenthaler and L. Schmidt-Thieme, SIGIR 2011.


• 1.8.2011 (Tommi)
  Learning Multi-View Neighborhood Preserving Projections. N. Quadrianto and C. Lampert, ICML 2011.


• 10.7.2011 (Juuso)
  Engineering Data Analysis (with R and ggplot2) - a Google Tech Talk given by Hadley Wickham


• 4.7.2011 (Suleiman)
  H.Rohn et al. Creating views on integrated multidomain data Bioinformatics 2011


• 27.6.2011 (Melih)
  Chen et al. The Hierarchical Beta Process for Convolutional Factor Analysis and Deep Learning ICML 2011


• 20.6.2011 (Seppo)
  Categories and Functional Units: An Infinite Hierarchical Model for Brain Activations, NIPS10


• 6.6.2011 (Juuso)
  TopicNets (submitted pdf)
  and
  Web service, using WiGI visualization tool


• 30.5.2011 (Ali)
  Survival Analysis Part II: Multivariate data analysis . an introduction to concepts and methods. M J Bradburn, T G Clark, S B Love and D G Altman, British Journal of Cancer 2003.
  and
  Survival Analysis. A self-learning text. (Chapter 1-3) Kleinbaum, D.G. and Klein, M., Springer 2005


• 23.5.2011 (Sami)
  Learning from Multiple Outlooks. Harel, Mannor, arXiv, paper with the same name accepted to ICML2011.


• 16.5.2011 (Jussi)
  A Dirty Model for Multi-task Learning. Jalali, Ravikumar, Sanghavi, Ruan, NIPS 2010.


• 11.4.2011 (Elisabeth)
  Generative Local Metric Learning for Nearest Neighbor Classification. Noh, Zhang, and Lee, NIPS 2010.


• 4.4.2011 (Mehmet)
  Bayesian Generalized Kernel Mixed Models. Z. Zhang, G. Dai, and M. I. Jordan, JMLR 2011.


• 28.3.2011 (Tommi)
  Copula Processes. A. Wilson and Z. Ghahramani, NIPS 2010.


• 21.3.2011 (Arto)
  F. Huszar and S. Lacoste-Julien, Nonparametric Bayesian density estimation via the kernel trick, arXiv 2011


• 14.3.2011 (Suleiman)
  Sandra Waaijenborg, Philip C. Verselewel de Witt Hamer, Aeilko H. Zwinderman Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis, Statistical Applications in Genetics and Molecular Biology. 2008, 7(1)
  along with
  Elena Parkhomenko, David Tritchler, Joseph Beyene Sparse Canonical Correlation Analysis with Application to Genomic Data Integration, Statistical Applications in Genetics and Molecular Biology. 2009, 8(1)


• 7.3.2011 (Juuso)
  Liat Perlman, Assaf Gottlieb, Nir Atias, Eytan Ruppin, Roded Sharan, Combining Drug and Gene Similarity Measures for Drug-Target Elucidation, Journal of Computational Biology. February 2011, 18(2)


• 28.2.2011 (Antti)
  R.W. White, P. Bennett and S.T. Dumais, Predicting short-term interests using activity-based search context, CIKM 2010


• 21.2.2011 (Ilkka)
  H.S. Le, Z. Bar-Joseph,Cross Species Expression Analysis using a Dirichlet Process Mixture Model with Latent Matchings, NIPS 2010
  Oliver Stegle, Katherine Denby, David L. Wild, Zoubin Ghahramani, Karsten M. Borgwardt, A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series, Journal of computational biology 2009


• 7.2.2011 (Melih)
  S. Nakajima, M. Sugiyama, R. Tomioka, Global Analytic Solution for Variational Bayesian Matrix Factorization, NIPS 2010


• 17.1.2011 (Ali)
  Richard S. Savage, Zoubin Ghahramani, Jim E. Griffin, Bernard J. de la Cruz and David L. Wild Discovering transcriptional modules by Bayesian data integration. ISMB (2010), doi: 10.1093/bioinformatics/btq210


• 10.1.2011 (Sami)
  C. Kemp and J. Tenenbaum The discovery of structural form. PNAS 105(31), pp. 10687-10692, 2008.


• 3.1.2011 (Maija)
  D. Lin, E. Grimson and J. Fisher. Construction of Dependent Dirichlet Processes based on Poisson Processes. NIPS, 2010.



2010

• 13.12.2010 (Maria)
  D. Calvetti, A. Kuceyeski, and E. Somersalo. Sampling-Based Analysis of a Spatially Distributed Model for Liver Metabolism at Steady State Multiscale Model. Multiscale Model. Simul. Volume 7, Issue 1, pp. 407-431 (2008)


• 22.11.2010 (Kristian)
  A. Hyvarinen, P. Ramkumar, L. Parkkonen, and R. Hari. Independent component analysis of short-time Fourier transforms for spontaneous EEG/MEG analysis. NeuroImage, 49(1):257-271, 2010.


• 8.11.2010 (Elisabeth)
  Cross-species queries of large gene expression databases. H.-S. Le, Z.N. Oltvai, Z. Bar-Joseph. Bioinformatics, 2010, 26(19): 2416-2423.
  Automated multidimensional phenotypic profiling using large public microarray repositories. M. Xu, W. Li, G.M. James, M.R. Mehan, and X.J. Zhou. PNAS, 2009, 106(30) 12323-12328.


• 25.10.2010 (JaakkoV)
  Stochastic blockmodels and community structure in networks . B. Karrer, M.E.J. Newman, 2010.


• 18.10.2010 (Seppo)
  Structured sparse principal component anal\ ysis . R. Jenatton, G. Obozinski and F. Bach AISTATS 2010.


• 11.10.2010 (Mehmet)
  Constructing Nonlinear Discriminants from Multiple Data Views. T. Diethe, D.R. Hardoon, and J. Shawe-Taylor. ECML, 2010.


• 4.10.2010 (Tommi)
  A Bayesian analysis strategy for cross-study translation of gene expression biomarkers. J.E. Lucas, C.M. Carvalho and M. West. Statistical Applications in Genetics and Molecular Biology, 8(1), Article 11, 2009.


• 27.9.2010 (Arto)
  Integrating Multiple-Study Multiple-Subject fMRI Datasets Using Canonical Correlation Analysis. I. Rustandi, M.A. Just, T.M. Mitchell. Proceedings of the MICCAI 2009 Workshop, 2009.


• 20.9.2010 (José)
  Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses. I. Amit et al., Science 326, 2009.
  
  
• 13.9.2010 (Jussi)
  The Indian Buffet Process: Scalable Inference and Extensions. F. Doshi-Velez, 2009.
  
  
• 6.9.2010 (Antti)
  Cognitive User Interfaces. S. Young, IEEE Signal Processing Magazine 27(3):128-140, 2010.
  
  
• 30.8.2010 (Juuso)
  Mixed Membership Matrix Factorization. L. Mackey, D. Weiss and M.I. Jordan, ICML, 2010.
  
  
• 23.8.2010 (Jaakko)
  On Over-fitting in Model Selection and Subsequent Selection Bias in Performance Evaluation. Gavin C. Cawley and Nicola L. C. Talbot, Journal of Machine Learning Research 11:2079-2107, 2010.
  
  
• 16.8.2010 (Ilkka)
  Cross-species common regulatory network inference without requirement for prior gene affiliation>. A Gholami and K. Fellenberg Bioinformatics, 2010, 26(8):1082-1090. See the supplement as well.
  
  
• 9.8.2010 (Melih)
  Gaussian Processes Multiple Instance Learning. M.Kim, F.De la Torre ICML 2010
  
  
• 2.8.2010 (Maria)
  Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Yishak et al.Bioinformatics, 2010, vol. 26 ISBM 2010 p.i255-i260.
  
  
• 26.7.2010 (Rony)
  Hierarchical Mixture of Classification Experts Uncovers Interactions between Brain Regions. B. Yao et al., NIPS 2009.
  
  
• 12.7.2010 (Suleiman)
  Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium.Yongxi Tan., et al.,Bioinformatics 2006 22(1):77-87.
  
  
• 28.6.2010 (Ali)
  Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework.Yamanishi Y., et al.,Bioinformatics 2010 26(12):i246-i254 (ISMB 2010).
  
  
• 21.6.2010 (JussiK)
  Not-So-Latent Dirichlet Allocation: Collapsed Gibbs Sampling Using Human Judgments. Jonathan Chang, In NAACL 2010 Workshop on Creating Speech and Language Data With Amazon's Mechanical Turk, 2010.
  
  
• 14.6.2010 (Maija)
  Combining Brain Computer Interfaces with Vision for Object Categorization A. Kapoor et al. IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 2008.
  
  
• 07.6.2010 (Kristian)
  S. A. Abdallah and M. D. Plumbley. Information Dynamics: Patterns of expectation and surprise in the perception of music. Connection Science, 21(2), 89-117, 2009.
  
  
• 24.5.2010 (Elisabeth)
  T.-R. Xu, V. Vyshemirsky, A. Gormand, A. von Kriegsheim, M. Girolami, G. S. Baillie, D. Ketley, A. J. Dunlop, G. Milligan, M. D. Houslay, W. Kolch. Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species. Sci. Signal. 3, ra20 (2010)
  
  
• 17.5.2010 (Seppo)
  J. Sui et. al. A CCA + ICA based model for multi-task brain imaging data fusion and its application to schizophrenia . Neuroimage.
  
  
• 10.5.2010 (JaakkoV)
  Lan Du et. al. The Hierarchical Local Partition Process . JMLR submitted.
  
  
• 3.5.2010 (Gayle)
  Sinead Williamson, Peter Orbanz and Zoubin Ghahramani Dependent Indian Buffet Processes. AISTATS 2010.
  
  
• 26.4.2010 (Tommi)
  Y. Shiraishi, S. Kimura and M. Okada. Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. Bioinformatics 26(8), 2010.
  
  
• 19.4.2010 (Juuso)
  Francesco Iorio, Roberto Tagliaferri and Diego di Bernardo. Identifying Network of Drug Mode of Action by Gene Expression Profiling. Journal of Computational Biology, 2009.
  
  
• 12.4.2010 (Leo)
  Jun Li and Dacheng Tao. Simple Exponential Family PCA. AISTATS 2010.
  
  
• 29.3.2010
  Cancelled.
  
  
• 22.3.2010 (Arto)
  David R. Hardoon and John Shawe-Taylor. Decomposing the Tensor Kernel Support Vector Machine for Neuroscience Data with Structure Labels. Machine Learning 2010.
  
  
• 15.3.2010 (Antti)
  F. Wood, C. Archambeau, J. Gasthaus, L. James and Y. W. Teh. A stochastic memoizer for sequence data. ICML 09.
  
  
• 8.3.2010 (JaakkoP)
  F. Wood and Y. W. Teh. A Hierarchical Nonparametric Bayesian Approach to Statistical Language Model Domain Adaptation. AISTATS'09. See also the previous paper about a similar model without domain adaptation.
  
  
• 1.3.2010 (Sami)
  E.B. Fox, E.B. Sudderth, M.I. Jordan, A.S. Willsky. Sharing Features among Dynamical Systems with Beta Processes. NIPS09.
  
  
• 22.02.2010 (José)
  H. Goodarzi, O. Elemento, S. Tavazoie. Revealing Global Regulatory Perturbations across Human Cancers. Molecular Cell 36(5), pp. 900-911, 2009.
  
  
• 15.02.2010 (Melih)
  A. Wilson, A. Fern, S. Ray, P. Tadepalli Multi-Task Reinforcement Learning: A Hierarchical Bayesian Approach. ICML, 2007. (pdf)
  
  
• 08.02.2010 (Ilkka)
  W.-J. Li D.-Y. Yeung,Z. Zhang Probabilistic Relational PCA. NIPS, 2009. (pdf)
  
  
• 01.02.2010 (Ali)
  Y. W. Teh, M. I. Jordan, M. J. Beal and D. M. Blei. Hierarchical Dirichlet processes. Journal of the American Statistical Association, 101, 1566-1581, 2006. (pdf)
  
  
• 25.01.2010 (Elisabeth)
  R. Shen, A.B. Olshen, M. Ladanyi. Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 25(22):2906-2912, 2009. (pdf)
  
  
• 18.01.2010 (JussiK)
  Bing Bai, Jason Weston, David Grangier, Ronan Collobert, Kunihiko Sadamasa, Yanjun Qi, Corinna Cortes, Mehryar Mohri Polynomial Semantic Indexing In NIPS 2009. (pdf).
  David Grangier and Samy Bengio A Discriminative Kernel-Based Model to Rank Images from Text Queries In IEEE transactions on pattern analysis and machine intelligence '08. (pdf).
  
  
• 11.01.2010 (Seppo)
  K.T. Miller, T.L. Griffits and M.I. Jordan Nonparametric latent feature models for link prediction. In NIPS 2009. (pdf).
  
  
• 4.01.2010 (Kristian)
  Vuust, P., Pallesen, K. J., Bailey, C., van Zuijen, T. L., Gjedde, A., Roepstorff, A. and ?stergaard., L. To musicians, the message is in the meter. Pre-attentive neuronal responses to incongruent rhythm are left-lateralized in musicians. NeuroImage, 24, 560--564, 2005.
  
  

2009

 
• 14.12.2009 (JaakkoV)
  Yue Guan, Jennifer Dy Sparse Probabilistic Principal Component Analysis In AISTATS 2009 . (pdf)

  Piyush Rai, Hal Daume Multi-Label Prediction via Sparse Infinite CCA In NIPS 2009 . (pdf)
  
  

• 7.12.2009 (Maija)
  R. W. Picard, E. Vyzas and J. Healey Toward Machine Emotional Intelligence: Analysis of Affective Physiological State. In IEEE Transactions on Pattern Analysis and Machine Intelligence, 23(10), 2001. (pdf).
  
  
• 30.11.2009 (Suleiman)
  Michael J. Keise et al: Predicting new molecular targets for known drugs
  In Nature 462, pp. 175-182, 2009. (pdf) Along with (pdf)
  
  
• 16.11.2009 (Gayle)
  N. Lawrence and R. Urtasun: Nonlinear matrix factorization using Gaussian processes
  In L. Bottou and M. Littman (eds) Proceedings of the International Conference in Machine Learning, Morgan Kauffman, San Francisco, CA, 2009. (pdf)
  
  
• 9.11.2009 (Tommi)
  Y. Lu, P. Huggins, Z. Bar-Joseph: Cross species analysis of microarray expression data
  In Bioinformatics, 25(12), pp. 1476-1483, 2009. (html, pdf)
  
  
• 2.11.2009 No presentation
  
  
• 26.10.2009 No presentation
  
  
• 19.10.2009 (Arto)
  Finale Doshi-Velez and Zoubin Ghahramani: Accelerated Sampling for the Indian Buffet Process
  In ICML 2009. (pdf)
  
  
• 12.10.2009 (Juuso)
  Kasper Lage et al. (Integrative systems biology group lead by Soeren Brunak) A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
  IN PNAS 2008. (html) Note! A closely related earlier paper can be found here.
  
  
• 5.10.2009 (Helena)
  Simon Lacoste-Julien, Fei Sha, and Michael Jordan: DiscLDA: Discriminative learning for dimensionality reduction and classification
  In NIPS 2008. (pdf)
  
  
• 28.9.2009 (José)
  David M. Blei, Thomas L. Griffiths, and Michael I. Jordan: The nested Chinese restaurant process and Bayesian inference of topic hierarchies.
  In Journal of the ACM, to appear. (pdf)
  
  
• 21.9.2009 (Leo)
  Elaine R. Mardis: Next-Generation DNA Sequencing Methods
  In Annual Review of Genomics and Human Genetics. (html)
  
  
• 14.9.2009 (Antti)
  Bradley Love, Matt Jones, Marc Tomlinson and Michael Howe: Learning to predict information needs: context-aware display as a cognitive aid and an assesment tool. In CHI 2009. (pdf).
  
  
• 7.9.2009 (Jaakko)
  Christian Walder and Bernhard Schölkopf: Diffeomorphic Dimensionality Reduction. In NIPS 2008. (pdf)
  
  
• 31.8.2009 (Sami)
  authors: Susan Dumais. A couple of recent talks (UMAP2009 and ACL2008), and two papers (Knoll et al, HCI2009, Viewing Personal Data over Time, and Cutrell et al, CHI2006, Fast, Flexible Filtering with Phlat - Personal Search and Organization Made Easy.)
  
  
• 24.8.2009 (Andrey, please kindly add yours here...)
  authors: title. In source. (pdf).
  
  
• 17.8.2009 (Ilkka)
  Daniela Witten, Robert Tibshirani. Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data Vol. 8 : Iss. 1, Article 28, 2009. In The Berkeley Electronic Press. (pdf).
  
  
• 20.7.2009 (Ali)
  Hanna Wallach, Iain Murray, Ruslan Salakhutdinov, and David Mimno. Evaluation Methods for Topic Models. In ICML, 2009. (pdf).
  
  
• 13.7. (Melih)
  W. Kienzle, M.O. Franz, B. Scholkopf, F.A. Wichman: Center-surround patterns emerge as optimal predictors for human saccade targets. In Journal of Vision, 9(5):7, 1-15, 2009. (pdf).
  
  
• 8.6.2009 (Gayle)
  Wu-Jun Li, zhihua zhang, Dit-Yan Yeung. Latent Wishart Processes for Relational Kernel Learning. AISTATS 2009. (pdf).
  
  
• 27.4. (Arto)
  A. Torralba, A. Oliva, M.S. Castelhano, and J.M. Henderson: Contextual guidance of eye movements and attention in real-world scenes: The role of global features on object search. In Physchological Review, 113:4, 766-786. (pdf).
  
  
• 20.4. (Jarkko)
  Field et al.: Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals. In PLoS Comput. Biol. 4(11):e1000216. (pdf).
  
  
• 6.4.2009 (Helena)
  Celine Vens et al.: Decision trees for hierarchical multi-label classification. In Machine Learning, 73(2), 2008. (link).
  
  
• 23.3.2009 (László)
  Peter Auer, Alex Leung Models of Exploration-Exploitation Trade-offs PinView Deliverable D4.1, 2009. (pdf).
  
  
• 16.3.2009 (Ali)
  Bradley PH, Brauer MJ, Rabinowitz JD, Troyanskaya OG. Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae. In PLoS Comput Biol 5(1), 2009. (pdf).
  
  
• 9.3.2009 (Hasan)
  Chen-Hsiang Yeang and Martin Vingron A joint model of regulatory and metabolic networks. In BMC Bioinformatics, 7:332, 2006. (pdf).
  
  
• 1.3.2009 (Melih)
  Kai Ni, Lawrence Carin, and David Dunson. Multi-Task Learning for Sequential Data via iHMMs and the Nested Dirichlet Process. In ICML, 689-696, 2007. (pdf).
  
  
• 23.2.2009 (Leo)
  Calin, George A. and Croce, Carlo M. MicroRNA signatures in human cancers. In Nat Rev Cancer 6, 857-866, 2006. (html).
  
  
• 16.2.2009 (Antti)
  Samantha R. Cook, Andrew Gelman, and Donald B. Rubin: Validation of Software for Bayesian Models Using Posterior Quantiles. In Journal of Computational and Graphical Statistics 15(3):675-692, 2006. (pdf).
  
  
• 9.2.2009 (José)
  J.-G. Joung and Z. Fei Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model. In Bioinformatics 25(3):387-393, 2009. (pdf).
  
  
• 2.2.2009 (Sami)
  Justin Lamb The Connectivity Map: a new tool for biomedical research. Nature Reviews Cancer 7, 54-60 (January 2007) doi:10.1038/nrc2044. (abstract). Lamb et al The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease. Science 313(5795):1929-1935. DOI: 10.1126/science.1132939 (abstract).
  
  
• 19.1.2009 (Ilkka)
  Gilles Celeux, Olivier Martin and Christian Lavergne Mixture of linear mixed models for clustering gene expression profiles from repeated microarray experiments. In Statistical Modelling 2005; 5; 243 . (pdf).
  
  
• 5.1.2009 (Jaakko)
  Yishay Mansour, Mehryar Mohri, and Afshin Rostamizadeh: Domain Adaptation with Multiple Sources. In Advances in Neural Information Processing Systems (NIPS 2008), 2009. (pdf).
  
  

2008

 
• 15.12.2008 (Abhishek)
  Novi Quadrianto, Le Song and Alex J. Smola: Kernelized Sorting. In Advances in Neural Information Processing Systems 22, 2009.. (pdf).
  
  
• 8.12.2008 (Jarkko)
  Lily Wang, Bing Zhang, Russell D. Wolfinger, and Xi Chen: An Integrated Approach for the Analysis of Biological Pathways using Mixed Models. In PLoS Genetics 4(7):e1000115. (DOI).
  
  
• 01.12.2008 (Helena)
  Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif and Eric Kolaczyk: Integration of Relational and Hierarchical Network Information for Protein Function Prediction In BMC Bioinformatics, 2008. (pdf)
  Babak Shahbaba and Radford Neal: Improving Classification When a Class Hierarchy is Available Using a Hierarchy-Based Prior In Bayesian Analysis 2(1):221-238, 2007. (pdf)
  
  
• 24.11.2008 (Arto)
  Nicolas Lartillot and Herve Philippe: Computing Bayes factors using thermodynamic integration. Systematic Biology 55(2):195-207, 2006. (pdf). See also Radford Neal's blog entry on the harmonic mean estimator.
  
  
• 17.11.2008 (László)
  Kienzle, W., B. Sch?kopf, F. Wichmann and M. O. Franz: How to Find Interesting Locations in Video: A Spatiotemporal Interest Point Detector Learned from Human Eye movements. In Pattern Recognition: 29th DAGM Symposium, 2007. (pdf).
  
  
• 10.11.2008 (Melih)
  T. Mitchell, S. Shinkareva, A. Carlson, K-M. Chang, V. Malave, R. Mason, M.A. Just Predicting Human Brain Activity Associated with the Meanings of Nouns. In Science, 2008. (pdf).
  
  
• 3.11.2008 (Ali)
  Steyvers, M. and Griffiths, T.L. Probabilistic topic models.. In Latent Semantic Analysis: A Road to Meaning (Landauer, T. et al., eds), Erlbaum (in press). (pdf).
  
  
• 27.10.2008 (Hasan)
  A.Kundaje, M.Middendorf, F.Gao, K.Wigginsa and C.Leslie: Combining sequence and time series expression data to learn transcriptional modules . In IEEE TCBB 2 194-202, 2005. (pdf).
  
  
• 20.10.2008 (Leo)
  Eran Segal et al.: Predicting expression patterns from regulatory sequence in Drosophila segmentation. In Nature 451 535--540, 2008. (pdf). See also supplementary information (pdf).
  
  
• 13.10.2008 (Antti)
  Gregory Druck, Gideon Mann, Andrew McCallum: Learning from Labeled Features using Generalized Expectation Criteria. In SIGIR 2008. (pdf).
  
  
• 6.10.2008 (Sami)
  Georg Buscher, Andreas Dengel, Ludger van Elst: Query Expansion Using Gaze-Based Feedback on the Subdocument Level. In SIGIR 2008. (pdf).
  
  
• 29/9/08 (Ilkka)
  Mike West: Bayesian Factor Regression Models in the Large p, Small n Paradigm. In Bayesian Statistics 2003. (pdf).
  
  
• 22/9/08 (Andrey)
  Ichigaku Takigawa and Hiroshi Mamitsuka: Probabilistic path rankng based on adjacent pairwise coexpression for metabolic transcripts analysis, In Bioinformatics 24 250-257, 2008. (pdf).
  
  
• 15/9/08 (José)
  A. Jaimovich, G. Elidan, H. Margalit, and N. Friedman: Towards an integrated protein-protein interaction network: a relational Markov network approach.. In Journal of Computational Biology 13 145-164, 2006. (pdf).
  
  
• 1.9.2008 (Gayle)
  G. Sanguinetti, J. Noirel, and P. C. Wright: MMG: a probabilistic tool to identify submodules of metabolic pathways. Bioinformatics, 24(8) 1078-1084, 2008. (link)
  
  
• 1.9.2008 (Jaakko)
  Jian Zhang, Zoubin Ghahramani, and Yiming Yang: Flexible latent variable models for multi-task learning. Machine Learning, "Online First" article (published online April 2, 2008). (pdf)
  
  
• 25.8.2008 (Helena)
  Yangqing Jia, Zheng Wang, and Changshui Zhang: Distortion-free nonlinear dimensionality reduction. In ECML 2008. (pdf).
  
  
• 18.8.2008 (Arto)
  Su, Zhang, Ling, and Matwin: Discriminative parameter learning for Bayesian networks. In ICML 2008. (pdf).
  
  
• 11.8.2008 (Jarkko)
  P. Liang and M.I. Jordan: An Asymptotic Analysis of Generative, Discriminative, and Pseudolikelihood Estimators. In ICML 2008. (pdf).
  
  
• 4.8.2008 (Leo)
  authors: P. Lianf, D. Klein, and M.I. Jordan Agreement-Based Learning. In NIPS 2008. (pdf).
  
  
• 28.7.2008 (László)
  authors: Benyah Shaparenko, Thorsten Joachims "Information Genealogy: Uncovering the Flow of Ideas in Non-Hyperlinked Document Databases". In KDD 2007. (pdf).
  
  
• 21.7.2008 (Antti)
  authors: Yisong Yue and T. Joachims Predicting Diverse Subsets Using Structural SVMs. In Proceedings of ICML 2008. (pdf).
  
  
• 14.7.2008 (Abhishek)
  authors: Aria Haghighi, Percy Liang, Taylor Berg-Kirkpatrick and Dan Klien Learning Bilingual Lexicons from Monolingual Corpora. In Proceedings of ACL 2008. (pdf).
  
  
• 23.6.2008 (Sami)
  authors: Kay KN, Naselaris T, Prenger RJ, Gallant JL. Identifying natural images from human brain activity. In Nature, 452:352-5, 2008. (pdf). Plus supplementary material: (pdf)
  
  
• 16.6.2008 (Ilkka)
  authors: Mattias Rantalainen et al. Statistically Integrated Metabonomic-Proteomic Studies on a Human Prostate Cancer Xenograft Model in Mice. In ACS publications. (html).
  
  
• 2.6.2008 (Eika)
  S. Ghebreab, A.W.M. Smeulders and P. Adriaans: Predictive Modeling of fMRI Brain States Using Functional Canonical Correlation Analysis. In Proceedings of Artificial Intelligence in Medicine 2007. (pdf).
  and background material:
  Guozhong He, Hans-Georg M?ler and Jane-Ling Wang: Functional canonical analysis for square integrable stochastic processes. In Journal of Multivariate Analysis,Volume 85, Issue 1, Pages 54-77,2003. (pdf).
  
  
• 12.05.2008 (Andrey)
  Theodoros Damoulas and Mark A. Girolami: Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection , In Bioinformatics 24 250-257, 2008. (pdf).
  
  
• 5.5.2008 (Sourangshu)
  D.D. Lee and H.S. Seung. Algorithms for non-negative matrix factorization. In NIPS 2000. (pdf).
  I. Dhillon and S. Sra. Generalized nonnegative matrix approximations with Bregman divergences. In NIPS 2005. (pdf).
  
  
• 28.4.2008 (Jos?
  A. Banerjee et al. Model-Based Overlapping Clustering. In KDD 2005. (pdf).
  
  
• 21.4.2008 (Antti)
  G. Buscher, A. Dengel, and L. van Elst: Eye Movements as Implicit Relevance Feedback. In CHI 2008 extended abstract. (pdf).
  C. S. Campbell and P. P. Maglio: A robust algorithm for reading detection. In Proceedings of the 2001 workshop on Perceptive user interfaces. (pdf).
  
  
• 14.4.2008 (Jarkko)
  B. Frey and D. Dueck: Clustering by Passing Messages Between Data Points. In Science, 315:972-977, 2007. (pdf).
  
  
• 7.4.2008 (Jaakko)
  Pierre Geurts, Nizar Touleimat, Marie Dutreix, and Florence d'Alch?Buc: Inferring biological networks with output kernel trees. BMC Bioinformatics, 8(Suppl 2):S4, 2007. (html).
  
  
• 31.3.2008 Algorithms and Methods seminar (Alexander)
  Leading approaches to collaborative filtering in the Netflix competition.
  
  
• 17.3.2008 (Abhishek)
  Stephane Lafon, Yosi Keller, and Ronald R. Coifman: Data Fusion and Multicue Data Matching by Diffusion Maps. In IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2006. (pdf).
  
  
• 10.3.2008 (Arto)
  A. Gretton, K. Fukumizu, C.H. Teo, L. Song, B. Sch?kopf and A.J. Smola: A kernel statistical test of independence. In Proceedings of NIPS 2007. (pdf).
  
  
• 25.2.2008 Algorithms and Methods Seminar (Leo)
  Overview of approaches to integrate network information and vector-valued data. See the list of articles.
  
  
• 18.2.2008 (Ilkka)
  Feng Tai and Wei Pan Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data. In Bioinformatics 2007. (pdf).
  
  
• 11.2.2008 (Sami)
  Xu, Tresp, Yu, Kriegel: Infinite hidden relational models. In (UAI06), (MLG07).
  
  
• 28.1.2008 (Jos?
  Katherine A. Heller and Zoubin Ghahramani: A Nonparametric Bayesian Approach to Modeling Overlapping Clusters. In AISTATS 2007. (pdf)
  
  
• 21.1.2008 (Antti)
  Jason D.R. Farquhar, David R. Hardoon, Hongying Meng, John Shawe-Taylor, Sandor Szedmak: Two view learning: SVM-2k, Theory and Practice. In NIPS 2005. (pdf).
  
  
• 14.1.2008 (Jarkko)
  A. V. Werhli, M. Grzegorczyk, and D. Husmeier Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical Gaussian models and Bayesian networks. In Bioinformatics 22(20):2523-2531, 2006. (pdf).
  (See also: Schäfer and Strimmer: An Emprical Bayes approach to inferring large-scale gene association netowrks. Bioinformatics 21(6):754-764. 2005.
  Ma, Gong, Bohnert: An arabidopsis gene network based on the graphical Gaussian model. Genome research, October 2007, 10.1101/gr.6911207)
  
  
• 7.1.2008 (Jaakko)
  A. Banerjee and H. Shan. Latent Dirichlet Conditional Naive-Bayes Models. In ICDM 2007, 2007. (pdf).
  D. M. Blei and J. D. McAuliffe. Supervised Topic Models. In NIPS 2007, 2007. (pdf).
  
  

2007

 
• 17.12.2007 Algorithms and Methods Seminar (Markus Harva)
  R. Silva, K. A. Heller, and Z. Ghahramani: Analogical Reasoning with Relational Bayesian Sets. In AISTATS'07, 2007. (pdf).
  Z. Ghahramani and K. A. Heller: Bayesian sets. In NIPS'05, 2005. (pdf).
  
  
• 9.12.2007 (Merja)
  Leek JT, Storey JD (2007) Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis. In PLoS Genet 3(9): e161.
  
  
• 26.11.2007 (Abhishek)
  Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela Kristensen, Anne-Lise B?resen-Dale, Eytan Ruppin, and Roded Sharan: A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data. In Bioinformatics. (pdf).
  
  
• 5.11.2007 (Eika)
  Christian Sigg, Bernd Fischer, Bj?n Ommer, Volker Roth and Joachim Buhmann: Nonnegative CCA for Audiovisual Source Separation. In Machine Learning for Signal Processing--MLSP 2007. (pdf).
  
  
• 29.10.2007 Algorithms and Methods Seminar (Arto)
  Li, Ogihara, Ma: On combining multiple clusterings. (pdf).
  Gionis, Mannila, Tsaparas: Clustering aggregation. (html).
  Hu, Yu, Xiong, Sung: Maximum likelihood combination of multiple clusterings. (html).
  Li, Ding, Jordan: Solving consensus and semi-supervised clustering problems using nonnegative matrix factorization. (pdf)
  
  
• 22.10.2007 (JanneN)
  Jose C. Pinheiro and Douglas M. Bates Mixed Effects Models in S and Splus (Ch 1), 2000. (an ebook at TKK library, choose "ebrary", then search for Pinheiro).
  
  
• 15.10.2007 (Ilkka)
  ?vind Langsrud: 5050 multivariate analysis of variance for collinear responses Journal of the Royal Statistical Society: Series D (The Statistician) Volume 51 Issue 3 Page 305-317, September 2002 (html).
  
  
• 7.10.2007 (Leo)
  Goeman, Jelle J. and Buhlmann, Peter: Analyzing gene expression data in terms of gene sets: methodological issues. In Bioinformatics 2007 23(8):980-987 . (pdf).
  
  

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NOTE: Previous journal clubs, Machine Learning journal club and Bioinformatics journal club were merged at October 7, 2007. See the corresponding sites for a list of previous presentations.