Publications

Empirical Inference Article Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies Fusi, N., Stegle, O., Lawrence, N. PLoS Computational Biology, 8(1):1-9, January 2012 () Web DOI BibTeX

Empirical Inference Conference Paper Personalized medicine: from genotypes and molecular phenotypes towards computed therapy Stegle, O., Roth, F., Morris, Q., Listgarten, J. In :323-326, (Editors: Altman, R.B. , A.K. Dunker, L. Hunter, T. Murray, T.E. Klein), World Scientific Publishing, Singapore, Pacific Symposium on Biocomputing (PSB 2012), January 2012 () Web DOI BibTeX

Empirical Inference Conference Paper A Blind Deconvolution Approach for Pseudo CT Prediction from MR Image Pairs Hirsch, M., Hofmann, M., Mantlik, F., Pichler, B., Schölkopf, B., Habeck, M. In 19th IEEE International Conference on Image Processing (ICIP) , :2953 -2956, IEEE, ICIP, 2012 () DOI BibTeX

Empirical Inference Conference Paper A Brain-Robot Interface for Studying Motor Learning after Stroke Meyer, T., Peters, J., Brötz, D., Zander, T., Schölkopf, B., Soekadar, S., Grosse-Wentrup, M. In IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), :4078 - 4083 , IEEE, Piscataway, NJ, USA, IROS, 2012 () PDF DOI BibTeX

Empirical Inference Conference Paper A Nonparametric Conjugate Prior Distribution for the Maximizing Argument of a Noisy Function Ortega, P., Grau-Moya, J., Genewein, T., Balduzzi, D., Braun, D. In Advances in Neural Information Processing Systems 25, :3014-3022, (Editors: P Bartlett and FCN Pereira and CJC. Burges and L Bottou and KQ Weinberger), Curran Associates Inc., 26th Annual Conference on Neural Information Processing Systems (NIPS 2012), 2012 () PDF BibTeX

Empirical Inference Conference Paper A min-cut solution to mapping phenotypes to networks of genetic markers Azencott, C., Grimm, D., Kawahara, Y., Borgwardt, K. In 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013), 2012, Submitted (Submitted) BibTeX

Empirical Inference Conference Paper A mixed model approach for joint genetic analysis of alternatively spliced transcript isoforms using RNA-Seq data Rakitsch, B., Lippert, C., Topa, H., Borgwardt, K., Honkela, A., Stegle, O. In 2012, Submitted (Submitted) Web BibTeX

Empirical Inference Conference Paper A new metric on the manifold of kernel matrices with application to matrix geometric means Sra, S. In Advances in Neural Information Processing Systems 25, :144-152, (Editors: P Bartlett and FCN Pereira and CJC. Burges and L Bottou and KQ Weinberger), Curran Associates Inc., 26th Annual Conference on Neural Information Processing Systems (NIPS 2012), 2012 () PDF BibTeX

Empirical Inference Article A sensorimotor paradigm for Bayesian model selection Genewein, T., Braun, D. Frontiers in Human Neuroscience, 6(291):1-16, October 2012 () DOI BibTeX

Empirical Inference Article Active learning for domain adaptation in the supervised classification of remote sensing images Persello, C., Bruzzone, L. IEEE Transactions on Geoscience and Remote Sensing, 50(11):4468-4483, 2012 (Published) DOI BibTeX

Empirical Inference Conference Paper Adaptive Coding of Actions and Observations Ortega, P., Braun, D. :1-4, NIPS 2012 Workshop on Information in Perception and Action, December 2012 () URL BibTeX

Empirical Inference Conference Paper Algorithms for Learning Markov Field Policies Boularias, A., Kroemer, O., Peters, J. In Advances in Neural Information Processing Systems 25, :2186-2194, (Editors: P Bartlett and FCN Pereira and CJC. Burges and L Bottou and KQ Weinberger), Curran Associates Inc., 26th Annual Conference on Neural Information Processing Systems (NIPS 2012), 2012 () PDF BibTeX

Empirical Inference Article Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis Windram, O., Madhou, P., McHattie, S., Hill, C., Hickman, R., Cooke, E., Jenkins, D., Penfold, C., Baxter, L., Breeze, E., et al. The Plant Cell Online, 24(9):3530-3557, 2012, all authors: Oliver Windram,Priyadharshini Madhou,Stuart McHattie,Claire Hill,Richard Hickman,Emma Cooke,Dafyd J. Jenkins,Christopher A. Penfold,Laura Baxter,Emily Breeze,Steven J. Kiddle,Johanna Rhodes,Susanna Atwell,Daniel J. () Web DOI BibTeX

Empirical Inference Thesis Automatische Seitenkettenzuordnung zur NMR Proteinstrukturaufklärung mittels ganzzahliger linearer Programmierung Hooge, J. University of Tübingen, Germany, 2012 () BibTeX

Empirical Inference Article Bayesian flexible fitting of biomolecular structures into EM maps Habeck, M. Biophysical journal, 2012, Submitted (Submitted) BibTeX

Empirical Inference Talk Beta oscillations propagate as traveling waves in the macaque prefrontal cortex Panagiotaropoulos, T., Besserve, M., Logothetis, N. 42nd Annual Meeting of the Society for Neuroscience (Neuroscience 2012), 2012 () BibTeX

Empirical Inference Conference Paper Blind Correction of Optical Aberrations Schuler, C., Hirsch, M., Harmeling, S., Schölkopf, B. In Computer Vision - ECCV 2012, LNCS Vol. 7574, :187-200, (Editors: A Fitzgibbon, S Lazebnik, P Perona, Y Sato, and C Schmid), Springer, Berlin, Germany, 12th IEEE European Conference on Computer Vision, ECCV, 2012 () PDF Web DOI BibTeX

Empirical Inference Ph.D. Thesis Blind Deconvolution in Scientific Imaging & Computational Photography Hirsch, M. Eberhard Karls Universität Tübingen, Germany, 2012 () Web BibTeX

Empirical Inference Conference Paper Bridging Offline and Online Social Graph Dynamics Gomez Rodriguez, M., Rogati, M. In 21st ACM Conference on Information and Knowledge Management, :2447-2450, (Editors: Chen, X., Lebanon, G., Wang, H. and Zaki, M. J.), ACM, CIKM, 2012 () PDF DOI BibTeX

Empirical Inference Article CSB: A Python framework for computational structural biology Kalev, I., Mechelke, M., Kopec, K., Holder, T., Carstens, S., Habeck, M. Bioinformatics, 28(22):2996-2997, 2012 () Web DOI BibTeX

Empirical Inference Article Calibration of Boltzmann distribution priors in Bayesian data analysis Mechelke, M., Habeck, M. Physical Review E, 86(6):066705, 2012 (Published) DOI BibTeX

Empirical Inference Conference Paper Causal discovery with scale-mixture model for spatiotemporal variance dependencies Chen, Z., Zhang, K., Chan, L. In Advances in Neural Information Processing Systems 25, :1736-1744, (Editors: P Bartlett and FCN Pereira and CJC. Burges and L Bottou and KQ Weinberger), Curran Associates Inc., 26th Annual Conference on Neural Information Processing Systems (NIPS 2012), 2012 () PDF PDF BibTeX

Empirical Inference Poster Centrality of the Mammalian Functional Brain Network Besserve, M., Bartels, A., Murayama, Y., Logothetis, N. 42nd Annual Meeting of the Society for Neuroscience (Neuroscience 2012), 2012 () BibTeX

Empirical Inference Conference Paper Clustering: Science or Art? von Luxburg, U., Williamson, R., Guyon, I. In JMLR Workshop and Conference Proceedings, Volume 27, :65-79, Workshop on Unsupervised Learning and Transfer Learning, 2012 () PDF BibTeX

Empirical Inference Ph.D. Thesis Combinatorial Problems with Submodular Coupling in Machine Learning and Computer Vision Jegelka, S. ETH Zürich, Switzerland, 2012 () BibTeX

Empirical Inference Conference Paper Computational vascular morphometry for the assessment of pulmonary vascular disease based on scale-space particles Estépar, R., Ross, J., Krissian, K., Schultz, T., Washko, G., Kindlmann, G. In :1479-1482, IEEE, 9th International Symposium on Biomedical Imaging (ISBI 2012) , 2012 () DOI BibTeX

Empirical Inference Conference Paper Conditional mean embeddings as regressors Grünewälder, S., Lever, G., Baldassarre, L., Patterson, S., Gretton, A., Pontil, M. In Proceedings of the 29th International Conference on Machine Learning, :1823-1830, (Editors: J Langford and J Pineau), Omnipress, New York, NY, USA, ICML, 2012 () PDF BibTeX

Empirical Inference Article Design of a Haptic Interface for a Gastrointestinal Endoscopy Simulation Yu, S., Woo, H. S., Son, H. I., Ahn, W., Jung, H., Lee, D. Y., Yi, S. Y. Advanced Robotics, 26(18):2115-2143, 2012 (Published) DOI BibTeX

Empirical Inference Conference Paper Distributed multisensory signals acquisition and analysis in dyadic interactions Tawari, A., Tran, C., Doshi, A., Zander, T. In Proceedings of the 2012 ACM Annual Conference on Human Factors in Computing Systems Extended Abstracts, :2261-2266, (Editors: JA Konstan and EH Chi and K Höök), ACM, New York, NY, USA, CHI, 2012 () DOI BibTeX

Empirical Inference Article Effect of MR contrast agents on quantitative accuracy of PET in combined whole-body PET/MR imaging Lois, C., Bezrukov, I., Schmidt, H., Schwenzer, N., Werner, M., Kupferschläger, J., Beyer, T. European Journal of Nuclear Medicine and Molecular Imaging, 39(11):1756-1766, 2012 () DOI BibTeX

Empirical Inference Conference Paper Efficient Training of Graph-Regularized Multitask SVMs Widmer, C., Kloft, M., Görnitz, N., Rätsch, G. In Machine Learning and Knowledge Discovery in Databases - European Conference, ECML/PKDD 2012, LNCS Vol. 7523, :633-647, (Editors: PA Flach and T De Bie and N Cristianini), Springer, Berlin, Germany, ECML, 2012 () DOI BibTeX

Empirical Inference Conference Paper Efficiently mapping phenotypes to networks of genetic loci Azencott, C., Grimm, D., Kawahara, Y., Borgwardt, K. In NIPS 2012 Workshop on Machine Learning in Computational Biology (MLCB 2012), 2012, Submitted (Submitted) BibTeX

Empirical Inference Poster Evaluation of Whole-Body MR-Based Attenuation Correction in Bone and Soft Tissue Lesions Bezrukov, I., Mantlik, F., Schmidt, H., Schwenzer, N., Brendle, C., Schölkopf, B., Pichler, B. Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC 2012), 2012 (Published) BibTeX

Empirical Inference Conference Paper Evaluation of marginal likelihoods via the density of states Habeck, M. In Journal of Machine Learning Research, Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics (AISTATS 2012) , 22:486-494, (Editors: N Lawrence and M Girolami), JMLR: W&CP 22, AISTATS, 2012 () PDF BibTeX

Empirical Inference Article Existential neuroscience: a functional magnetic resonance imaging investigation of neural responses to reminders of one’s mortality Quirin, M., Loktyushin, A., Arndt, J., Küstermann, E., Lo, Y., Kuhl, J., Eggert, L. Social Cognitive and Affective Neuroscience, 7(2):193-198, 2012 () Web DOI BibTeX

Empirical Inference Article First SN Discoveries from the Dark Energy Survey Abbott, T., Abdalla, F., Achitouv, I., Ahn, E., Aldering, G., Allam, S., Alonso, D., Amara, A., Annis, J., Antonik, M., et al. The Astronomer's Telegram, 4668:1, 2012 (Published) BibTeX

Empirical Inference Conference Paper Free Energy and the Generalized Optimality Equations for Sequential Decision Making Ortega, P., Braun, D. :1-10, 10th European Workshop on Reinforcement Learning (EWRL 2012), July 2012 () URL BibTeX

Empirical Inference Conference Paper Generalization of Human Grasping for Multi-Fingered Robot Hands Ben Amor, H., Kroemer, O., Hillenbrand, U., Neumann, G., Peters, J. In IEEE/RSJ International Conference on Intelligent Robots and Systems , :2043-2050, IROS, 2012 () PDF DOI BibTeX

Empirical Inference Conference Paper Gradient Weights help Nonparametric Regressors Kpotufe, S., Boularias, A. In Advances in Neural Information Processing Systems 25, :2870-2878, (Editors: P Bartlett and FCN Pereira and CJC. Burges and L Bottou and KQ Weinberger), 26th Annual Conference on Neural Information Processing Systems (NIPS 2012), 2012 () PDF BibTeX

Empirical Inference Book Chapter Higher-Order Tensors in Diffusion MRI Schultz, T., Fuster, A., Ghosh, A., Deriche, R., Florack, L., Lim, L. In Visualization and Processing of Tensors and Higher Order Descriptors for Multi-Valued Data, (Editors: Westin, C. F., Vilanova, A. and Burgeth, B.), Springer, 2012, Accepted (Accepted) BibTeX

Empirical Inference Conference Paper Hilbert Space Embeddings of POMDPs Nishiyama, Y., Boularias, A., Gretton, A., Fukumizu, K. In Conference on Uncertainty in Artificial Intelligence (UAI 2012), 2012 () PDF Web BibTeX

Empirical Inference Conference Paper Hilbert space embedding for Dirichlet Process mixtures Muandet, K. In NIPS 2012 Workshop on confluence between kernel methods and graphical models, 2012 (Published) arXiv BibTeX

Empirical Inference Conference Paper Hypothesis testing using pairwise distances and associated kernels Sejdinovic, D., Gretton, A., Sriperumbudur, B., Fukumizu, K. In Proceedings of the 29th International Conference on Machine Learning, :1111-1118, (Editors: J Langford and J Pineau), Omnipress, New York, NY, USA, ICML, 2012 () PDF BibTeX

Empirical Inference Poster Identifying endogenous rhythmic spatio-temporal patterns in micro-electrode array recordings Besserve, M., Panagiotaropoulos, T., Crocker, B., Kapoor, V., Tolias, A., Panzeri, S., Logothetis, N. 9th annual Computational and Systems Neuroscience meeting (Cosyne 2012), 2012 () BibTeX

Empirical Inference Article Image analysis for cosmology: results from the GREAT10 Galaxy Challenge Kitching, T. D., Balan, S. T., Bridle, S., Cantale, N., Courbin, F., Eifler, T., Gentile, M., Gill, M. S. S., Harmeling, S., Heymans, C., et al. Monthly Notices of the Royal Astronomical Society, 423(4):3163-3208, Oxford University Press, 2012 (Published) DOI BibTeX

Empirical Inference Article Image denoising with multi-layer perceptrons, part 1: comparison with existing algorithms and with bounds Burger, H., Schuler, C., Harmeling, S. 2012, Submitted (Submitted) Web BibTeX

Empirical Inference Article Image denoising with multi-layer perceptrons, part 2: training trade-offs and analysis of their mechanisms Burger, H., Schuler, C., Harmeling, S. 2012, Submitted (Submitted) Web BibTeX

Empirical Inference Article Improved Linear Mixed Models for Genome-Wide Association Studies Listgarten, J., Lippert, C., Kadie, C., Davidson, R., Eskin, E., Heckerman, D. Nature Methods, 9:525–526, 2012 () DOI BibTeX

Empirical Inference Book Chapter Inferential structure determination from NMR data Habeck, M. In Bayesian methods in structural bioinformatics, :287-312, (Editors: Hamelryck, T., Mardia, K. V. and Ferkinghoff-Borg, J.), Springer, New York, 2012 () BibTeX

Empirical Inference Talk Influence of MR-based attenuation correction on lesions within bone and susceptibility artifact regions Bezrukov, I., Schmidt, H., Mantlik, F., Schwenzer, N., Brendle, C., Pichler, B. Molekulare Bildgebung 2012 (MoBi 2012), 2012 () BibTeX

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