Journal Club

We discuss recent papers and other topics related to probabilistic machine learning. Meetings take place on every Tuesday starting at 12:15, excluding the first Tuesday of each Month when there is no journal club. During the semester, the meetings are held in T4, but during the summer time (until 16.10) they are in T3.

This page lists the confirmed papers and topics.

















  • 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).


  • 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).


  • 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).