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33 results (View BibTeX file of all listed publications)
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Causal Inference for Empirical Time Series Based on the Postulate of Independence of Cause and Mechanism

Besserve, M.

53rd Annual Allerton Conference on Communication, Control, and Computing, September 2015 (talk)

ei

[BibTex]

ei Besserve, M. Causal Inference for Empirical Time Series Based on the Postulate of Independence of Cause and Mechanism 53rd Annual Allerton Conference on Communication, Control, and Computing, September 2015 (talk)

[BibTex]

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Methods of forming dry adhesive structures

Sitti, M., Murphy, M., Aksak, B.

September 2015, US Patent 9,120,953 (patent)

Abstract
Methods of forming dry adhesives including a method of making a dry adhesive including applying a liquid polymer to the second end of the stem, molding the liquid polymer on the stem in a mold, wherein the mold includes a recess having a cross-sectional area that is less than a cross-sectional area of the second end of the stem, curing the liquid polymer in the mold to form a tip at the second end of the stem, wherein the tip includes a second layer stem; corresponding to the recess in the mold, and removing the tip from the mold after the liquid polymer cures.

pi

[BibTex]

pi Sitti, M., Murphy, M., Aksak, B. Methods of forming dry adhesive structures September 2015, US Patent 9,120,953 (patent)

[BibTex]

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Micro-fiber arrays with tip coating and transfer method for preparing same

Sitti, M., Washburn, N. R., Glass, P. S., Chung, H.

July 2015, US Patent 9,079,215 (patent)

Abstract
Present invention describes a patterned and coated micro- and nano-scale fibers elastomeric material for enhanced adhesion in wet or dry environments. A multi-step fabrication process including optical lithography, micromolding, polymer synthesis, dipping, stamping, and photopolymerization is described to produce uniform arrays of micron-scale fibers with mushroom-shaped tips coated with a thin layer of an intrinsically adhesive synthetic polymer, such as lightly crosslinked p(DMA-co-MEA).

pi

[BibTex]

pi Sitti, M., Washburn, N. R., Glass, P. S., Chung, H. Micro-fiber arrays with tip coating and transfer method for preparing same July 2015, US Patent 9,079,215 (patent)

[BibTex]

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Independence of cause and mechanism in brain networks

Besserve, M.

DALI workshop on Networks: Processes and Causality, April 2015 (talk)

ei

[BibTex]

ei Besserve, M. Independence of cause and mechanism in brain networks DALI workshop on Networks: Processes and Causality, April 2015 (talk)

[BibTex]

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Dry adhesives and methods for making dry adhesives

Sitti, M., Murphy, M., Aksak, B.

March 2015, US Patent App. 14/625,162 (patent)

Abstract
Dry adhesives and methods for forming dry adhesives. A method of forming a dry adhesive structure on a substrate, comprises: forming a template backing layer of energy sensitive material on the substrate; forming a template layer of energy sensitive material on the template backing layer; exposing the template layer to a predetermined pattern of energy; removing a portion of the template layer related to the predetermined pattern of energy, and leaving a template structure formed from energy sensitive material and connected to the substrate via the template backing layer.

pi

[BibTex]

pi Sitti, M., Murphy, M., Aksak, B. Dry adhesives and methods for making dry adhesives March 2015, US Patent App. 14/625,162 (patent)

[BibTex]

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Information-Theoretic Implications of Classical and Quantum Causal Structures

Chaves, R., Majenz, C., Luft, L., Maciel, T., Janzing, D., Schölkopf, B., Gross, D.

18th Conference on Quantum Information Processing (QIP), 2015 (talk)

ei

Web link (url) [BibTex]

ei Chaves, R., Majenz, C., Luft, L., Maciel, T., Janzing, D., Schölkopf, B., Gross, D. Information-Theoretic Implications of Classical and Quantum Causal Structures 18th Conference on Quantum Information Processing (QIP), 2015 (talk)

Web link (url) [BibTex]

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The search for single exoplanet transits in the Kepler light curves

Foreman-Mackey, D., Hogg, D. W., Schölkopf, B.

IAU General Assembly, 22, pages: 2258352, 2015 (talk)

ei

link (url) [BibTex]

ei Foreman-Mackey, D., Hogg, D. W., Schölkopf, B. The search for single exoplanet transits in the Kepler light curves IAU General Assembly, 22, pages: 2258352, 2015 (talk)

link (url) [BibTex]

2006

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A Kernel Method for the Two-Sample-Problem

Gretton, A., Borgwardt, K., Rasch, M., Schölkopf, B., Smola, A.

20th Annual Conference on Neural Information Processing Systems (NIPS), December 2006 (talk)

Abstract
We propose two statistical tests to determine if two samples are from different distributions. Our test statistic is in both cases the distance between the means of the two samples mapped into a reproducing kernel Hilbert space (RKHS). The first test is based on a large deviation bound for the test statistic, while the second is based on the asymptotic distribution of this statistic. We show that the test statistic can be computed in $O(m^2)$ time. We apply our approach to a variety of problems, including attribute matching for databases using the Hungarian marriage method, where our test performs strongly. We also demonstrate excellent performance when comparing distributions over graphs, for which no alternative tests currently exist.

ei

PDF [BibTex]

2006

ei Gretton, A., Borgwardt, K., Rasch, M., Schölkopf, B., Smola, A. A Kernel Method for the Two-Sample-Problem 20th Annual Conference on Neural Information Processing Systems (NIPS), December 2006 (talk)

PDF [BibTex]

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Ab-initio gene finding using machine learning

Schweikert, G., Zeller, G., Zien, A., Ong, C., de Bona, F., Sonnenburg, S., Phillips, P., Rätsch, G.

NIPS Workshop on New Problems and Methods in Computational Biology, December 2006 (talk)

ei

Web [BibTex]

ei Schweikert, G., Zeller, G., Zien, A., Ong, C., de Bona, F., Sonnenburg, S., Phillips, P., Rätsch, G. Ab-initio gene finding using machine learning NIPS Workshop on New Problems and Methods in Computational Biology, December 2006 (talk)

Web [BibTex]

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Graph boosting for molecular QSAR analysis

Saigo, H., Kadowaki, T., Kudo, T., Tsuda, K.

NIPS Workshop on New Problems and Methods in Computational Biology, December 2006 (talk)

Abstract
We propose a new boosting method that systematically combines graph mining and mathematical programming-based machine learning. Informative and interpretable subgraph features are greedily found by a series of graph mining calls. Due to our mathematical programming formulation, subgraph features and pre-calculated real-valued features are seemlessly integrated. We tested our algorithm on a quantitative structure-activity relationship (QSAR) problem, which is basically a regression problem when given a set of chemical compounds. In benchmark experiments, the prediction accuracy of our method favorably compared with the best results reported on each dataset.

ei

Web [BibTex]

ei Saigo, H., Kadowaki, T., Kudo, T., Tsuda, K. Graph boosting for molecular QSAR analysis NIPS Workshop on New Problems and Methods in Computational Biology, December 2006 (talk)

Web [BibTex]

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Inferring Causal Directions by Evaluating the Complexity of Conditional Distributions

Sun, X., Janzing, D., Schölkopf, B.

NIPS Workshop on Causality and Feature Selection, December 2006 (talk)

Abstract
We propose a new approach to infer the causal structure that has generated the observed statistical dependences among n random variables. The idea is that the factorization of the joint measure of cause and effect into P(cause)P(effect|cause) leads typically to simpler conditionals than non-causal factorizations. To evaluate the complexity of the conditionals we have tried two methods. First, we have compared them to those which maximize the conditional entropy subject to the observed first and second moments since we consider the latter as the simplest conditionals. Second, we have fitted the data with conditional probability measures being exponents of functions in an RKHS space and defined the complexity by a Hilbert-space semi-norm. Such a complexity measure has several properties that are useful for our purpose. We describe some encouraging results with both methods applied to real-world data. Moreover, we have combined constraint-based approaches to causal discovery (i.e., methods using only information on conditional statistical dependences) with our method in order to distinguish between causal hypotheses which are equivalent with respect to the imposed independences. Furthermore, we compare the performance to Bayesian approaches to causal inference.

ei

Web [BibTex]

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Learning Optimal EEG Features Across Time, Frequency and Space

Farquhar, J., Hill, J., Schölkopf, B.

NIPS Workshop on Current Trends in Brain-Computer Interfacing, December 2006 (talk)

ei

PDF Web [BibTex]

ei Farquhar, J., Hill, J., Schölkopf, B. Learning Optimal EEG Features Across Time, Frequency and Space NIPS Workshop on Current Trends in Brain-Computer Interfacing, December 2006 (talk)

PDF Web [BibTex]

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Semi-Supervised Learning

Zien, A.

Advanced Methods in Sequence Analysis Lectures, November 2006 (talk)

ei

Web [BibTex]

ei Zien, A. Semi-Supervised Learning Advanced Methods in Sequence Analysis Lectures, November 2006 (talk)

Web [BibTex]

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A Machine Learning Approach for Determining the PET Attenuation Map from Magnetic Resonance Images

Hofmann, M., Steinke, F., Judenhofer, M., Claussen, C., Schölkopf, B., Pichler, B.

IEEE Medical Imaging Conference, November 2006 (talk)

Abstract
A promising new combination in multimodality imaging is MR-PET, where the high soft tissue contrast of Magnetic Resonance Imaging (MRI) and the functional information of Positron Emission Tomography (PET) are combined. Although many technical problems have recently been solved, it is still an open problem to determine the attenuation map from the available MR scan, as the MR intensities are not directly related to the attenuation values. One standard approach is an atlas registration where the atlas MR image is aligned with the patient MR thus also yielding an attenuation image for the patient. We also propose another approach, which to our knowledge has not been tried before: Using Support Vector Machines we predict the attenuation value directly from the local image information. We train this well-established machine learning algorithm using small image patches. Although both approaches sometimes yielded acceptable results, they also showed their specific shortcomings: The registration often fails with large deformations whereas the prediction approach is problematic when the local image structure is not characteristic enough. However, the failures often do not coincide and integration of both information sources is promising. We therefore developed a combination method extending Support Vector Machines to use not only local image structure but also atlas registered coordinates. We demonstrate the strength of this combination approach on a number of examples.

ei

[BibTex]

ei Hofmann, M., Steinke, F., Judenhofer, M., Claussen, C., Schölkopf, B., Pichler, B. A Machine Learning Approach for Determining the PET Attenuation Map from Magnetic Resonance Images IEEE Medical Imaging Conference, November 2006 (talk)

[BibTex]

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Semi-Supervised Support Vector Machines and Application to Spam Filtering

Zien, A.

ECML Discovery Challenge Workshop, September 2006 (talk)

Abstract
After introducing the semi-supervised support vector machine (aka TSVM for "transductive SVM"), a few popular training strategies are briefly presented. Then the assumptions underlying semi-supervised learning are reviewed. Finally, two modern TSVM optimization techniques are applied to the spam filtering data sets of the workshop; it is shown that they can achieve excellent results, if the problem of the data being non-iid can be handled properly.

ei

PDF Web [BibTex]

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Semi-Supervised Learning

Chapelle, O., Schölkopf, B., Zien, A.

pages: 508, Adaptive computation and machine learning, MIT Press, Cambridge, MA, USA, September 2006 (book)

Abstract
In the field of machine learning, semi-supervised learning (SSL) occupies the middle ground, between supervised learning (in which all training examples are labeled) and unsupervised learning (in which no label data are given). Interest in SSL has increased in recent years, particularly because of application domains in which unlabeled data are plentiful, such as images, text, and bioinformatics. This first comprehensive overview of SSL presents state-of-the-art algorithms, a taxonomy of the field, selected applications, benchmark experiments, and perspectives on ongoing and future research. Semi-Supervised Learning first presents the key assumptions and ideas underlying the field: smoothness, cluster or low-density separation, manifold structure, and transduction. The core of the book is the presentation of SSL methods, organized according to algorithmic strategies. After an examination of generative models, the book describes algorithms that implement the low-density separation assumption, graph-based methods, and algorithms that perform two-step learning. The book then discusses SSL applications and offers guidelines for SSL practitioners by analyzing the results of extensive benchmark experiments. Finally, the book looks at interesting directions for SSL research. The book closes with a discussion of the relationship between semi-supervised learning and transduction.

ei

Web [BibTex]

ei Chapelle, O., Schölkopf, B., Zien, A. Semi-Supervised Learning pages: 508, Adaptive computation and machine learning, MIT Press, Cambridge, MA, USA, September 2006 (book)

Web [BibTex]

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Inferential Structure Determination: Probabilistic determination and validation of NMR structures

Habeck, M.

Gordon Research Conference on Computational Aspects of Biomolecular NMR, September 2006 (talk)

ei

Web [BibTex]

ei Habeck, M. Inferential Structure Determination: Probabilistic determination and validation of NMR structures Gordon Research Conference on Computational Aspects of Biomolecular NMR, September 2006 (talk)

Web [BibTex]

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Machine Learning Algorithms for Polymorphism Detection

Schweikert, G., Zeller, G., Clark, R., Ossowski, S., Warthmann, N., Shinn, P., Frazer, K., Ecker, J., Huson, D., Weigel, D., Schölkopf, B., Rätsch, G.

2nd ISCB Student Council Symposium, August 2006 (talk)

Abstract
Analyzing resequencing array data using machine learning, we obtain a genome-wide inventory of polymorphisms in 20 wild strains of Arabidopsis thaliana, including 750,000 single nucleotide poly- morphisms (SNPs) and thousands of highly polymorphic regions and deletions. We thus provide an unprecedented resource for the study of natural variation in plants.

ei

Web [BibTex]

ei Schweikert, G., Zeller, G., Clark, R., Ossowski, S., Warthmann, N., Shinn, P., Frazer, K., Ecker, J., Huson, D., Weigel, D., Schölkopf, B., Rätsch, G. Machine Learning Algorithms for Polymorphism Detection 2nd ISCB Student Council Symposium, August 2006 (talk)

Web [BibTex]

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Inferential structure determination: Overview and new developments

Habeck, M.

Sixth CCPN Annual Conference: Efficient and Rapid Structure Determination by NMR, July 2006 (talk)

ei

Web [BibTex]

ei Habeck, M. Inferential structure determination: Overview and new developments Sixth CCPN Annual Conference: Efficient and Rapid Structure Determination by NMR, July 2006 (talk)

Web [BibTex]

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MR/PET Attenuation Correction

Hofmann, M., Schölkopf, B., Steinke, F., Pichler, B.

Max-Planck-Gesellschaft, Biologische Kybernetik, July 2006 (patent)

ei

[BibTex]

ei Hofmann, M., Schölkopf, B., Steinke, F., Pichler, B. MR/PET Attenuation Correction Max-Planck-Gesellschaft, Biologische Kybernetik, July 2006 (patent)

[BibTex]

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MCMC inference in (Conditionally) Conjugate Dirichlet Process Gaussian Mixture Models

Rasmussen, C., Görür, D.

ICML Workshop on Learning with Nonparametric Bayesian Methods, June 2006 (talk)

Abstract
We compare the predictive accuracy of the Dirichlet Process Gaussian mixture models using conjugate and conditionally conjugate priors and show that better density models result from using the wider class of priors. We explore several MCMC schemes exploiting conditional conjugacy and show their computational merits on several multidimensional density estimation problems.

ei

Web [BibTex]

ei Rasmussen, C., Görür, D. MCMC inference in (Conditionally) Conjugate Dirichlet Process Gaussian Mixture Models ICML Workshop on Learning with Nonparametric Bayesian Methods, June 2006 (talk)

Web [BibTex]

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Sampling for non-conjugate infinite latent feature models

Görür, D., Rasmussen, C.

(Editors: Bernardo, J. M.), 8th Valencia International Meeting on Bayesian Statistics (ISBA), June 2006 (talk)

Abstract
Latent variable models are powerful tools to model the underlying structure in data. Infinite latent variable models can be defined using Bayesian nonparametrics. Dirichlet process (DP) models constitute an example of infinite latent class models in which each object is assumed to belong to one of the, mutually exclusive, infinitely many classes. Recently, the Indian buffet process (IBP) has been defined as an extension of the DP. IBP is a distribution over sparse binary matrices with infinitely many columns which can be used as a distribution for non-exclusive features. Inference using Markov chain Monte Carlo (MCMC) in conjugate IBP models has been previously described, however requiring conjugacy restricts the use of IBP. We describe an MCMC algorithm for non-conjugate IBP models. Modelling the choice behaviour is an important topic in psychology, economics and related fields. Elimination by Aspects (EBA) is a choice model that assumes each alternative has latent features with associated weights that lead to the observed choice outcomes. We formulate a non-parametric version of EBA by using IBP as the prior over the latent binary features. We infer the features of objects that lead to the choice data by using our sampling scheme for inference.

ei

PDF [BibTex]

ei Görür, D., Rasmussen, C. Sampling for non-conjugate infinite latent feature models (Editors: Bernardo, J. M.), 8th Valencia International Meeting on Bayesian Statistics (ISBA), June 2006 (talk)

PDF [BibTex]

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An Inventory of Sequence Polymorphisms For Arabidopsis

Clark, R., Ossowski, S., Schweikert, G., Rätsch, G., Shinn, P., Zeller, G., Warthmann, N., Fu, G., Hinds, D., Chen, H., Frazer, K., Huson, D., Schölkopf, B., Nordborg, M., Ecker, J., Weigel, D.

17th International Conference on Arabidopsis Research, April 2006 (talk)

Abstract
We have used high-density oligonucleotide arrays to characterize common sequence variation in 20 wild strains of Arabidopsis thaliana that were chosen for maximal genetic diversity. Both strands of each possible SNP of the 119 Mb reference genome were represented on the arrays, which were hybridized with whole genome, isothermally amplified DNA to minimize ascertainment biases. Using two complementary approaches, a model based algorithm, and a newly developed machine learning method, we identified over 550,000 SNPs with a false discovery rate of ~ 0.03 (average of 1 SNP for every 216 bp of the genome). A heuristic algorithm predicted in addition ~700 highly polymorphic or deleted regions per accession. Over 700 predicted polymorphisms with major functional effects (e.g., premature stop codons, or deletions of coding sequence) were validated by dideoxy sequencing. Using this data set, we provide the first systematic description of the types of genes that harbor major effect polymorphisms in natural populations at moderate allele frequencies. The data also provide an unprecedented resource for the study of genetic variation in an experimentally tractable, multicellular model organism.

ei

[BibTex]

ei Clark, R., Ossowski, S., Schweikert, G., Rätsch, G., Shinn, P., Zeller, G., Warthmann, N., Fu, G., Hinds, D., Chen, H., Frazer, K., Huson, D., Schölkopf, B., Nordborg, M., Ecker, J., Weigel, D. An Inventory of Sequence Polymorphisms For Arabidopsis 17th International Conference on Arabidopsis Research, April 2006 (talk)

[BibTex]

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Gaussian Processes for Machine Learning

Rasmussen, CE., Williams, CKI.

pages: 248, Adaptive Computation and Machine Learning, MIT Press, Cambridge, MA, USA, January 2006 (book)

Abstract
Gaussian processes (GPs) provide a principled, practical, probabilistic approach to learning in kernel machines. GPs have received increased attention in the machine-learning community over the past decade, and this book provides a long-needed systematic and unified treatment of theoretical and practical aspects of GPs in machine learning. The treatment is comprehensive and self-contained, targeted at researchers and students in machine learning and applied statistics. The book deals with the supervised-learning problem for both regression and classification, and includes detailed algorithms. A wide variety of covariance (kernel) functions are presented and their properties discussed. Model selection is discussed both from a Bayesian and a classical perspective. Many connections to other well-known techniques from machine learning and statistics are discussed, including support-vector machines, neural networks, splines, regularization networks, relevance vector machines and others. Theoretical issues including learning curves and the PAC-Bayesian framework are treated, and several approximation methods for learning with large datasets are discussed. The book contains illustrative examples and exercises, and code and datasets are available on the Web. Appendixes provide mathematical background and a discussion of Gaussian Markov processes.

ei

Web [BibTex]

ei Rasmussen, CE., Williams, CKI. Gaussian Processes for Machine Learning pages: 248, Adaptive Computation and Machine Learning, MIT Press, Cambridge, MA, USA, January 2006 (book)

Web [BibTex]

2003

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Statistical Learning Theory

Bousquet, O.

Machine Learning Summer School, August 2003 (talk)

ei

PDF [BibTex]

2003

ei Bousquet, O. Statistical Learning Theory Machine Learning Summer School, August 2003 (talk)

PDF [BibTex]

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Remarks on Statistical Learning Theory

Bousquet, O.

Machine Learning Summer School, August 2003 (talk)

ei

PDF [BibTex]

ei Bousquet, O. Remarks on Statistical Learning Theory Machine Learning Summer School, August 2003 (talk)

PDF [BibTex]

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Rademacher and Gaussian averages in Learning Theory

Bousquet, O.

Universite de Marne-la-Vallee, March 2003 (talk)

ei

PDF [BibTex]

ei Bousquet, O. Rademacher and Gaussian averages in Learning Theory Universite de Marne-la-Vallee, March 2003 (talk)

PDF [BibTex]

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Introduction: Robots with Cognition?

Franz, MO.

6, pages: 38, (Editors: H.H. Bülthoff, K.R. Gegenfurtner, H.A. Mallot, R. Ulrich, F.A. Wichmann), 6. T{\"u}binger Wahrnehmungskonferenz (TWK), February 2003 (talk)

Abstract
Using robots as models of cognitive behaviour has a long tradition in robotics. Parallel to the historical development in cognitive science, one observes two major, subsequent waves in cognitive robotics. The first is based on ideas of classical, cognitivist Artificial Intelligence (AI). According to the AI view of cognition as rule-based symbol manipulation, these robots typically try to extract symbolic descriptions of the environment from their sensors that are used to update a common, global world representation from which, in turn, the next action of the robot is derived. The AI approach has been successful in strongly restricted and controlled environments requiring well-defined tasks, e.g. in industrial assembly lines. AI-based robots mostly failed, however, in the unpredictable and unstructured environments that have to be faced by mobile robots. This has provoked the second wave in cognitive robotics which tries to achieve cognitive behaviour as an emergent property from the interaction of simple, low-level modules. Robots of the second wave are called animats as their architecture is designed to closely model aspects of real animals. Using only simple reactive mechanisms and Hebbian-type or evolutionary learning, the resulting animats often outperformed the highly complex AI-based robots in tasks such as obstacle avoidance, corridor following etc. While successful in generating robust, insect-like behaviour, typical animats are limited to stereotyped, fixed stimulus-response associations. If one adopts the view that cognition requires a flexible, goal-dependent choice of behaviours and planning capabilities (H.A. Mallot, Kognitionswissenschaft, 1999, 40-48) then it appears that cognitive behaviour cannot emerge from a collection of purely reactive modules. It rather requires environmentally decoupled structures that work without directly engaging the actions that it is concerned with. This poses the current challenge to cognitive robotics: How can we build cognitive robots that show the robustness and the learning capabilities of animats without falling back into the representational paradigm of AI? The speakers of the symposium present their approaches to this question in the context of robot navigation and sensorimotor learning. In the first talk, Prof. Helge Ritter introduces a robot system for imitation learning capable of exploring various alternatives in simulation before actually performing a task. The second speaker, Angelo Arleo, develops a model of spatial memory in rat navigation based on his electrophysiological experiments. He validates the model on a mobile robot which, in some navigation tasks, shows a performance comparable to that of the real rat. A similar model of spatial memory is used to investigate the mechanisms of territory formation in a series of robot experiments presented by Prof. Hanspeter Mallot. In the last talk, we return to the domain of sensorimotor learning where Ralf M{\"o}ller introduces his approach to generate anticipatory behaviour by learning forward models of sensorimotor relationships.

ei

Web [BibTex]

ei Franz, MO. Introduction: Robots with Cognition? 6, pages: 38, (Editors: H.H. Bülthoff, K.R. Gegenfurtner, H.A. Mallot, R. Ulrich, F.A. Wichmann), 6. T{\"u}binger Wahrnehmungskonferenz (TWK), February 2003 (talk)

Web [BibTex]

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Magnetism and the Microstructure of Ferromagnetic Solids

Kronmüller, H., Fähnle, M.

pages: 432 p., 1st ed., Cambridge University Press, Cambridge, 2003 (book)

mms

[BibTex]

mms Kronmüller, H., Fähnle, M. Magnetism and the Microstructure of Ferromagnetic Solids pages: 432 p., 1st ed., Cambridge University Press, Cambridge, 2003 (book)

[BibTex]