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2016


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Nonlinear functional causal models for distinguishing cause from effect

Zhang, K., Hyvärinen, A.

In Statistics and Causality: Methods for Applied Empirical Research, pages: 185-201, 8, 1st, (Editors: Wolfgang Wiedermann and Alexander von Eye), John Wiley & Sons, Inc., 2016 (inbook)

[BibTex]

2016

[BibTex]


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A cognitive brain–computer interface for patients with amyotrophic lateral sclerosis

Hohmann, M., Fomina, T., Jayaram, V., Widmann, N., Förster, C., Just, J., Synofzik, M., Schölkopf, B., Schöls, L., Grosse-Wentrup, M.

In Brain-Computer Interfaces: Lab Experiments to Real-World Applications, 228(Supplement C):221-239, 8, Progress in Brain Research, (Editors: Damien Coyle), Elsevier, 2016 (incollection)

DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Screening Rules for Convex Problems

Raj, A., Olbrich, J., Gärtner, B., Schölkopf, B., Jaggi, M.

2016 (unpublished) Submitted

[BibTex]

[BibTex]

2014


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Single-Source Domain Adaptation with Target and Conditional Shift

Zhang, K., Schölkopf, B., Muandet, K., Wang, Z., Zhou, Z., Persello, C.

In Regularization, Optimization, Kernels, and Support Vector Machines, pages: 427-456, 19, Chapman & Hall/CRC Machine Learning & Pattern Recognition, (Editors: Suykens, J. A. K., Signoretto, M. and Argyriou, A.), Chapman and Hall/CRC, Boca Raton, USA, 2014 (inbook)

[BibTex]

2014

[BibTex]


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Higher-Order Tensors in Diffusion Imaging

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, pages: 129-161, Mathematics + Visualization, (Editors: Westin, C.-F., Vilanova, A. and Burgeth, B.), Springer, 2014 (inbook)

[BibTex]

[BibTex]


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Fuzzy Fibers: Uncertainty in dMRI Tractography

Schultz, T., Vilanova, A., Brecheisen, R., Kindlmann, G.

In Scientific Visualization: Uncertainty, Multifield, Biomedical, and Scalable Visualization, pages: 79-92, 8, Mathematics + Visualization, (Editors: Hansen, C. D., Chen, M., Johnson, C. R., Kaufman, A. E. and Hagen, H.), Springer, 2014 (inbook)

[BibTex]

[BibTex]


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Nonconvex Proximal Splitting with Computational Errors

Sra, S.

In Regularization, Optimization, Kernels, and Support Vector Machines, pages: 83-102, 4, (Editors: Suykens, J. A. K., Signoretto, M. and Argyriou, A.), CRC Press, 2014 (inbook)

[BibTex]

[BibTex]


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Active Learning - Modern Learning Theory

Balcan, M., Urner, R.

In Encyclopedia of Algorithms, (Editors: Kao, M.-Y.), Springer Berlin Heidelberg, 2014 (incollection)

link (url) DOI [BibTex]

link (url) DOI [BibTex]

2007


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Bayesian Estimators for Robins-Ritov’s Problem

Harmeling, S., Toussaint, M.

(EDI-INF-RR-1189), School of Informatics, University of Edinburgh, October 2007 (techreport)

Abstract
Bayesian or likelihood-based approaches to data analysis became very popular in the field of Machine Learning. However, there exist theoretical results which question the general applicability of such approaches; among those a result by Robins and Ritov which introduce a specific example for which they prove that a likelihood-based estimator will fail (i.e. it does for certain cases not converge to a true parameter estimate, even given infinite data). In this paper we consider various approaches to formulate likelihood-based estimators in this example, basically by considering various extensions of the presumed generative model of the data. We can derive estimators which are very similar to the classical Horvitz-Thompson and which also account for a priori knowledge of an observation probability function.

PDF [BibTex]

2007

PDF [BibTex]


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Support Vector Machine Learning for Interdependent and Structured Output Spaces

Altun, Y., Hofmann, T., Tsochantaridis, I.

In Predicting Structured Data, pages: 85-104, Advances in neural information processing systems, (Editors: Bakir, G. H. , T. Hofmann, B. Schölkopf, A. J. Smola, B. Taskar, S. V. N. Vishwanathan), MIT Press, Cambridge, MA, USA, September 2007 (inbook)

Web [BibTex]

Web [BibTex]


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Brisk Kernel ICA

Jegelka, S., Gretton, A.

In Large Scale Kernel Machines, pages: 225-250, Neural Information Processing, (Editors: Bottou, L. , O. Chapelle, D. DeCoste, J. Weston), MIT Press, Cambridge, MA, USA, September 2007 (inbook)

Abstract
Recent approaches to independent component analysis have used kernel independence measures to obtain very good performance in ICA, particularly in areas where classical methods experience difficulty (for instance, sources with near-zero kurtosis). In this chapter, we compare two efficient extensions of these methods for large-scale problems: random subsampling of entries in the Gram matrices used in defining the independence measures, and incomplete Cholesky decomposition of these matrices. We derive closed-form, efficiently computable approximations for the gradients of these measures, and compare their performance on ICA using both artificial and music data. We show that kernel ICA can scale up to much larger problems than yet attempted, and that incomplete Cholesky decomposition performs better than random sampling.

PDF Web [BibTex]

PDF Web [BibTex]


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Training a Support Vector Machine in the Primal

Chapelle, O.

In Large Scale Kernel Machines, pages: 29-50, Neural Information Processing, (Editors: Bottou, L. , O. Chapelle, D. DeCoste, J. Weston), MIT Press, Cambridge, MA, USA, September 2007, This is a slightly updated version of the Neural Computation paper (inbook)

Abstract
Most literature on Support Vector Machines (SVMs) concentrate on the dual optimization problem. In this paper, we would like to point out that the primal problem can also be solved efficiently, both for linear and non-linear SVMs, and that there is no reason to ignore this possibility. On the contrary, from the primal point of view new families of algorithms for large scale SVM training can be investigated.

PDF Web [BibTex]

PDF Web [BibTex]


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Approximation Methods for Gaussian Process Regression

Quiñonero-Candela, J., Rasmussen, CE., Williams, CKI.

In Large-Scale Kernel Machines, pages: 203-223, Neural Information Processing, (Editors: Bottou, L. , O. Chapelle, D. DeCoste, J. Weston), MIT Press, Cambridge, MA, USA, September 2007 (inbook)

Abstract
A wealth of computationally efficient approximation methods for Gaussian process regression have been recently proposed. We give a unifying overview of sparse approximations, following Quiñonero-Candela and Rasmussen (2005), and a brief review of approximate matrix-vector multiplication methods.

PDF Web [BibTex]

PDF Web [BibTex]


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Learning with Transformation Invariant Kernels

Walder, C., Chapelle, O.

(165), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, September 2007 (techreport)

Abstract
Abstract. This paper considers kernels invariant to translation, rotation and dilation. We show that no non-trivial positive definite (p.d.) kernels exist which are radial and dilation invariant, only conditionally positive definite (c.p.d.) ones. Accordingly, we discuss the c.p.d. case and provide some novel analysis, including an elementary derivation of a c.p.d. representer theorem. On the practical side, we give a support vector machine (s.v.m.) algorithm for arbitrary c.p.d. kernels. For the thin-plate kernel this leads to a classifier with only one parameter (the amount of regularisation), which we demonstrate to be as effective as an s.v.m. with the Gaussian kernel, even though the Gaussian involves a second parameter (the length scale).

PDF [BibTex]

PDF [BibTex]


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Density Estimation of Structured Outputs in Reproducing Kernel Hilbert Spaces

Altun, Y., Smola, A.

In Predicting Structured Data, pages: 283-300, Advances in neural information processing systems, (Editors: BakIr, G. H., T. Hofmann, B. Schölkopf, A. J. Smola, B. Taskar, S. V.N. Vishwanathan), MIT Press, Cambridge, MA, USA, September 2007 (inbook)

Abstract
In this paper we study the problem of estimating conditional probability distributions for structured output prediction tasks in Reproducing Kernel Hilbert Spaces. More specically, we prove decomposition results for undirected graphical models, give constructions for kernels, and show connections to Gaussian Process classi- cation. Finally we present ecient means of solving the optimization problem and apply this to label sequence learning. Experiments on named entity recognition and pitch accent prediction tasks demonstrate the competitiveness of our approach.

Web [BibTex]

Web [BibTex]


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Trading Convexity for Scalability

Collobert, R., Sinz, F., Weston, J., Bottou, L.

In Large Scale Kernel Machines, pages: 275-300, Neural Information Processing, (Editors: Bottou, L. , O. Chapelle, D. DeCoste, J. Weston), MIT Press, Cambridge, MA, USA, September 2007 (inbook)

Abstract
Convex learning algorithms, such as Support Vector Machines (SVMs), are often seen as highly desirable because they offer strong practical properties and are amenable to theoretical analysis. However, in this work we show how nonconvexity can provide scalability advantages over convexity. We show how concave-convex programming can be applied to produce (i) faster SVMs where training errors are no longer support vectors, and (ii) much faster Transductive SVMs.

PDF Web [BibTex]

PDF Web [BibTex]


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Scalable Semidefinite Programming using Convex Perturbations

Kulis, B., Sra, S., Jegelka, S.

(TR-07-47), University of Texas, Austin, TX, USA, September 2007 (techreport)

Abstract
Several important machine learning problems can be modeled and solved via semidefinite programs. Often, researchers invoke off-the-shelf software for the associated optimization, which can be inappropriate for many applications due to computational and storage requirements. In this paper, we introduce the use of convex perturbations for semidefinite programs (SDPs). Using a particular perturbation function, we arrive at an algorithm for SDPs that has several advantages over existing techniques: a) it is simple, requiring only a few lines of MATLAB, b) it is a first-order method which makes it scalable, c) it can easily exploit the structure of a particular SDP to gain efficiency (e.g., when the constraint matrices are low-rank). We demonstrate on several machine learning applications that the proposed algorithm is effective in finding fast approximations to large-scale SDPs.

PDF [BibTex]

PDF [BibTex]


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Classifying Event-Related Desynchronization in EEG, ECoG and MEG signals

Hill, N., Lal, T., Tangermann, M., Hinterberger, T., Widman, G., Elger, C., Schölkopf, B., Birbaumer, N.

In Toward Brain-Computer Interfacing, pages: 235-260, Neural Information Processing, (Editors: G Dornhege and J del R Millán and T Hinterberger and DJ McFarland and K-R Müller), MIT Press, Cambridge, MA, USA, September 2007 (inbook)

PDF Web [BibTex]

PDF Web [BibTex]


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Joint Kernel Maps

Weston, J., Bakir, G., Bousquet, O., Mann, T., Noble, W., Schölkopf, B.

In Predicting Structured Data, pages: 67-84, Advances in neural information processing systems, (Editors: GH Bakir and T Hofmann and B Schölkopf and AJ Smola and B Taskar and SVN Vishwanathan), MIT Press, Cambridge, MA, USA, September 2007 (inbook)

Web [BibTex]

Web [BibTex]


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Brain-Computer Interfaces for Communication in Paralysis: A Clinical Experimental Approach

Hinterberger, T., Nijboer, F., Kübler, A., Matuz, T., Furdea, A., Mochty, U., Jordan, M., Lal, T., Hill, J., Mellinger, J., Bensch, M., Tangermann, M., Widman, G., Elger, C., Rosenstiel, W., Schölkopf, B., Birbaumer, N.

In Toward Brain-Computer Interfacing, pages: 43-64, Neural Information Processing, (Editors: G. Dornhege and J del R Millán and T Hinterberger and DJ McFarland and K-R Müller), MIT Press, Cambridge, MA, USA, September 2007 (inbook)

PDF Web [BibTex]

PDF Web [BibTex]


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Sparse Multiscale Gaussian Process Regression

Walder, C., Kim, K., Schölkopf, B.

(162), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, August 2007 (techreport)

Abstract
Most existing sparse Gaussian process (g.p.) models seek computational advantages by basing their computations on a set of m basis functions that are the covariance function of the g.p. with one of its two inputs fixed. We generalise this for the case of Gaussian covariance function, by basing our computations on m Gaussian basis functions with arbitrary diagonal covariance matrices (or length scales). For a fixed number of basis functions and any given criteria, this additional flexibility permits approximations no worse and typically better than was previously possible. Although we focus on g.p. regression, the central idea is applicable to all kernel based algorithms, such as the support vector machine. We perform gradient based optimisation of the marginal likelihood, which costs O(m2n) time where n is the number of data points, and compare the method to various other sparse g.p. methods. Our approach outperforms the other methods, particularly for the case of very few basis functions, i.e. a very high sparsity ratio.

PDF [BibTex]

PDF [BibTex]


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Efficient Subwindow Search for Object Localization

Blaschko, M., Hofmann, T., Lampert, C.

(164), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, August 2007 (techreport)

Abstract
Recent years have seen huge advances in object recognition from images. Recognition rates beyond 95% are the rule rather than the exception on many datasets. However, most state-of-the-art methods can only decide if an object is present or not. They are not able to provide information on the object location or extent within in the image. We report on a simple yet powerful scheme that extends many existing recognition methods to also perform localization of object bounding boxes. This is achieved by maximizing the classification score over all possible subrectangles in the image. Despite the impression that this would be computationally intractable, we show that in many situations efficient algorithms exist which solve a generalized maximum subrectangle problem. We show how our method is applicable to a variety object detection frameworks and demonstrate its performance by applying it to the popular bag of visual words model, achieving competitive results on the PASCAL VOC 2006 dataset.

PDF [BibTex]

PDF [BibTex]


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Cluster Identification in Nearest-Neighbor Graphs

Maier, M., Hein, M., von Luxburg, U.

(163), Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany, May 2007 (techreport)

Abstract
Assume we are given a sample of points from some underlying distribution which contains several distinct clusters. Our goal is to construct a neighborhood graph on the sample points such that clusters are ``identified‘‘: that is, the subgraph induced by points from the same cluster is connected, while subgraphs corresponding to different clusters are not connected to each other. We derive bounds on the probability that cluster identification is successful, and use them to predict ``optimal‘‘ values of k for the mutual and symmetric k-nearest-neighbor graphs. We point out different properties of the mutual and symmetric nearest-neighbor graphs related to the cluster identification problem.

PDF [BibTex]

PDF [BibTex]


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Exploring model selection techniques for nonlinear dimensionality reduction

Harmeling, S.

(EDI-INF-RR-0960), School of Informatics, University of Edinburgh, March 2007 (techreport)

Abstract
Nonlinear dimensionality reduction (NLDR) methods have become useful tools for practitioners who are faced with the analysis of high-dimensional data. Of course, not all NLDR methods are equally applicable to a particular dataset at hand. Thus it would be useful to come up with model selection criteria that help to choose among different NLDR algorithms. This paper explores various approaches to this problem and evaluates them on controlled data sets. Comprehensive experiments will show that model selection scores based on stability are not useful, while scores based on Gaussian processes are helpful for the NLDR problem.

PDF Web [BibTex]

PDF Web [BibTex]


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Probabilistic Structure Calculation

Rieping, W., Habeck, M., Nilges, M.

In Structure and Biophysics: New Technologies for Current Challenges in Biology and Beyond, pages: 81-98, NATO Security through Science Series, (Editors: Puglisi, J. D.), Springer, Berlin, Germany, March 2007 (inbook)

Web DOI [BibTex]

Web DOI [BibTex]


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Dirichlet Mixtures of Bayesian Linear Gaussian State-Space Models: a Variational Approach

Chiappa, S., Barber, D.

(161), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, March 2007 (techreport)

Abstract
We describe two related models to cluster multidimensional time-series under the assumption of an underlying linear Gaussian dynamical process. In the first model, times-series are assigned to the same cluster when they show global similarity in their dynamics, while in the second model times-series are assigned to the same cluster when they show simultaneous similarity. Both models are based on Dirichlet Mixtures of Bayesian Linear Gaussian State-Space Models in order to (semi) automatically determine an appropriate number of components in the mixture, and to additionally bias the components to a parsimonious parameterization. The resulting models are formally intractable and to deal with this we describe a deterministic approximation based on a novel implementation of Variational Bayes.

PDF [BibTex]

PDF [BibTex]


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Modeling data using directional distributions: Part II

Sra, S., Jain, P., Dhillon, I.

(TR-07-05), University of Texas, Austin, TX, USA, February 2007 (techreport)

Abstract
High-dimensional data is central to most data mining applications, and only recently has it been modeled via directional distributions. In [Banerjee et al., 2003] the authors introduced the use of the von Mises-Fisher (vMF) distribution for modeling high-dimensional directional data, particularly for text and gene expression analysis. The vMF distribution is one of the simplest directional distributions. TheWatson, Bingham, and Fisher-Bingham distributions provide distri- butions with an increasing number of parameters and thereby commensurately increased modeling power. This report provides a followup study to the initial development in [Banerjee et al., 2003] by presenting Expectation Maximization (EM) procedures for estimating parameters of a mixture of Watson (moW) distributions. The numerical challenges associated with parameter estimation for both of these distributions are significantly more difficult than for the vMF distribution. We develop new numerical approximations for estimating the parameters permitting us to model real- life data more accurately. Our experimental results establish that for certain data sets improved modeling power translates into better results.

PDF [BibTex]

PDF [BibTex]


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Automatic 3D Face Reconstruction from Single Images or Video

Breuer, P., Kim, K., Kienzle, W., Blanz, V., Schölkopf, B.

(160), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, February 2007 (techreport)

Abstract
This paper presents a fully automated algorithm for reconstructing a textured 3D model of a face from a single photograph or a raw video stream. The algorithm is based on a combination of Support Vector Machines (SVMs) and a Morphable Model of 3D faces. After SVM face detection, individual facial features are detected using a novel regression-and classification-based approach, and probabilistically plausible configurations of features are selected to produce a list of candidates for several facial feature positions. In the next step, the configurations of feature points are evaluated using a novel criterion that is based on a Morphable Model and a combination of linear projections. Finally, the feature points initialize a model-fitting procedure of the Morphable Model. The result is a high-resolution 3D surface model.

PDF [BibTex]

PDF [BibTex]


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On the Pre-Image Problem in Kernel Methods

BakIr, G., Schölkopf, B., Weston, J.

In Kernel Methods in Bioengineering, Signal and Image Processing, pages: 284-302, (Editors: G Camps-Valls and JL Rojo-Álvarez and M Martínez-Ramón), Idea Group Publishing, Hershey, PA, USA, January 2007 (inbook)

Abstract
In this chapter we are concerned with the problem of reconstructing patterns from their representation in feature space, known as the pre-image problem. We review existing algorithms and propose a learning based approach. All algorithms are discussed regarding their usability and complexity and evaluated on an image denoising application.

DOI [BibTex]

DOI [BibTex]


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Some comments on ν-SVM

Dinuzzo, F., De Nicolao, G.

In A tribute to Antonio Lepschy, pages: -, (Editors: Picci, G. , M. E. Valcher), Edizione Libreria Progetto, Padova, Italy, 2007 (inbook)

[BibTex]

[BibTex]


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Relative Entropy Policy Search

Peters, J.

CLMC Technical Report: TR-CLMC-2007-2, Computational Learning and Motor Control Lab, Los Angeles, CA, 2007, clmc (techreport)

Abstract
This technical report describes a cute idea of how to create new policy search approaches. It directly relates to the Natural Actor-Critic methods but allows the derivation of one shot solutions. Future work may include the application to interesting problems.

PDF link (url) [BibTex]

PDF link (url) [BibTex]

2006


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A New Projected Quasi-Newton Approach for the Nonnegative Least Squares Problem

Kim, D., Sra, S., Dhillon, I.

(TR-06-54), Univ. of Texas, Austin, December 2006 (techreport)

PDF [BibTex]

2006

PDF [BibTex]


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Probabilistic inference for solving (PO)MDPs

Toussaint, M., Harmeling, S., Storkey, A.

(934), School of Informatics, University of Edinburgh, December 2006 (techreport)

PDF [BibTex]

PDF [BibTex]


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Minimal Logical Constraint Covering Sets

Sinz, F., Schölkopf, B.

(155), Max Planck Institute for Biological Cybernetics, Tübingen, December 2006 (techreport)

Abstract
We propose a general framework for computing minimal set covers under class of certain logical constraints. The underlying idea is to transform the problem into a mathematical programm under linear constraints. In this sense it can be seen as a natural extension of the vector quantization algorithm proposed by Tipping and Schoelkopf. We show which class of logical constraints can be cast and relaxed into linear constraints and give an algorithm for the transformation.

PDF [BibTex]

PDF [BibTex]


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Prediction of Protein Function from Networks

Shin, H., Tsuda, K.

In Semi-Supervised Learning, pages: 361-376, Adaptive Computation and Machine Learning, (Editors: Chapelle, O. , B. Schölkopf, A. Zien), MIT Press, Cambridge, MA, USA, November 2006 (inbook)

Abstract
In computational biology, it is common to represent domain knowledge using graphs. Frequently there exist multiple graphs for the same set of nodes, representing information from different sources, and no single graph is sufficient to predict class labels of unlabelled nodes reliably. One way to enhance reliability is to integrate multiple graphs, since individual graphs are partly independent and partly complementary to each other for prediction. In this chapter, we describe an algorithm to assign weights to multiple graphs within graph-based semi-supervised learning. Both predicting class labels and searching for weights for combining multiple graphs are formulated into one convex optimization problem. The graph-combining method is applied to functional class prediction of yeast proteins.When compared with individual graphs, the combined graph with optimized weights performs significantly better than any single graph.When compared with the semidefinite programming-based support vector machine (SDP/SVM), it shows comparable accuracy in a remarkably short time. Compared with a combined graph with equal-valued weights, our method could select important graphs without loss of accuracy, which implies the desirable property of integration with selectivity.

Web [BibTex]

Web [BibTex]


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Discrete Regularization

Zhou, D., Schölkopf, B.

In Semi-supervised Learning, pages: 237-250, Adaptive computation and machine learning, (Editors: O Chapelle and B Schölkopf and A Zien), MIT Press, Cambridge, MA, USA, November 2006 (inbook)

Abstract
Many real-world machine learning problems are situated on finite discrete sets, including dimensionality reduction, clustering, and transductive inference. A variety of approaches for learning from finite sets has been proposed from different motivations and for different problems. In most of those approaches, a finite set is modeled as a graph, in which the edges encode pairwise relationships among the objects in the set. Consequently many concepts and methods from graph theory are adopted. In particular, the graph Laplacian is widely used. In this chapter we present a systemic framework for learning from a finite set represented as a graph. We develop discrete analogues of a number of differential operators, and then construct a discrete analogue of classical regularization theory based on those discrete differential operators. The graph Laplacian based approaches are special cases of this general discrete regularization framework. An important thing implied in this framework is that we have a wide choices of regularization on graph in addition to the widely-used graph Laplacian based one.

PDF Web [BibTex]

PDF Web [BibTex]


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New Methods for the P300 Visual Speller

Biessmann, F.

(1), (Editors: Hill, J. ), Max-Planck Institute for Biological Cybernetics, Tübingen, Germany, November 2006 (techreport)

PDF [BibTex]

PDF [BibTex]


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Geometric Analysis of Hilbert Schmidt Independence criterion based ICA contrast function

Shen, H., Jegelka, S., Gretton, A.

(PA006080), National ICT Australia, Canberra, Australia, October 2006 (techreport)

Web [BibTex]

Web [BibTex]


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A tutorial on spectral clustering

von Luxburg, U.

(149), Max Planck Institute for Biological Cybernetics, Tübingen, August 2006 (techreport)

Abstract
In recent years, spectral clustering has become one of the most popular modern clustering algorithms. It is simple to implement, can be solved efficiently by standard linear algebra software, and very often outperforms traditional clustering algorithms such as the k-means algorithm. Nevertheless, on the first glance spectral clustering looks a bit mysterious, and it is not obvious to see why it works at all and what it really does. This article is a tutorial introduction to spectral clustering. We describe different graph Laplacians and their basic properties, present the most common spectral clustering algorithms, and derive those algorithms from scratch by several different approaches. Advantages and disadvantages of the different spectral clustering algorithms are discussed.

PDF [BibTex]

PDF [BibTex]


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Towards the Inference of Graphs on Ordered Vertexes

Zien, A., Raetsch, G., Ong, C.

(150), Max Planck Institute for Biological Cybernetics, Tübingen, August 2006 (techreport)

Abstract
We propose novel methods for machine learning of structured output spaces. Specifically, we consider outputs which are graphs with vertices that have a natural order. We consider the usual adjacency matrix representation of graphs, as well as two other representations for such a graph: (a) decomposing the graph into a set of paths, (b) converting the graph into a single sequence of nodes with labeled edges. For each of the three representations, we propose an encoding and decoding scheme. We also propose an evaluation measure for comparing two graphs.

PDF [BibTex]

PDF [BibTex]


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Nonnegative Matrix Approximation: Algorithms and Applications

Sra, S., Dhillon, I.

Univ. of Texas, Austin, May 2006 (techreport)

[BibTex]

[BibTex]


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An Automated Combination of Sequence Motif Kernels for Predicting Protein Subcellular Localization

Zien, A., Ong, C.

(146), Max Planck Institute for Biological Cybernetics, Tübingen, April 2006 (techreport)

Abstract
Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions. While many predictive computational tools have been proposed, they tend to have complicated architectures and require many design decisions from the developer. We propose an elegant and fully automated approach to building a prediction system for protein subcellular localization. We propose a new class of protein sequence kernels which considers all motifs including motifs with gaps. This class of kernels allows the inclusion of pairwise amino acid distances into their computation. We further propose a multiclass support vector machine method which directly solves protein subcellular localization without resorting to the common approach of splitting the problem into several binary classification problems. To automatically search over families of possible amino acid motifs, we generalize our method to optimize over multiple kernels at the same time. We compare our automated approach to four other predictors on three different datasets.

PDF Web [BibTex]

PDF Web [BibTex]


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Training a Support Vector Machine in the Primal

Chapelle, O.

(147), Max Planck Institute for Biological Cybernetics, Tübingen, April 2006, The version in the "Large Scale Kernel Machines" book is more up to date. (techreport)

Abstract
Most literature on Support Vector Machines (SVMs) concentrate on the dual optimization problem. In this paper, we would like to point out that the primal problem can also be solved efficiently, both for linear and non-linear SVMs, and there is no reason for ignoring it. Moreover, from the primal point of view, new families of algorithms for large scale SVM training can be investigated.

PDF [BibTex]

PDF [BibTex]


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Cross-Validation Optimization for Structured Hessian Kernel Methods

Seeger, M., Chapelle, O.

Max-Planck Institute for Biological Cybernetics, Tübingen, Germany, February 2006 (techreport)

Abstract
We address the problem of learning hyperparameters in kernel methods for which the Hessian of the objective is structured. We propose an approximation to the cross-validation log likelihood whose gradient can be computed analytically, solving the hyperparameter learning problem efficiently through nonlinear optimization. Crucially, our learning method is based entirely on matrix-vector multiplication primitives with the kernel matrices and their derivatives, allowing straightforward specialization to new kernels or to large datasets. When applied to the problem of multi-way classification, our method scales linearly in the number of classes and gives rise to state-of-the-art results on a remote imaging task.

PDF Web [BibTex]

PDF Web [BibTex]


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Combining a Filter Method with SVMs

Lal, T., Chapelle, O., Schölkopf, B.

In Feature Extraction: Foundations and Applications, Studies in Fuzziness and Soft Computing, Vol. 207, pages: 439-446, Studies in Fuzziness and Soft Computing ; 207, (Editors: I Guyon and M Nikravesh and S Gunn and LA Zadeh), Springer, Berlin, Germany, 2006 (inbook)

Abstract
Our goal for the competition (feature selection competition NIPS 2003) was to evaluate the usefulness of simple machine learning techniques. We decided to use the correlation criteria as a feature selection method and Support Vector Machines for the classification part. Here we explain how we chose the regularization parameter C of the SVM, how we determined the kernel parameter and how we estimated the number of features used for each data set. All analyzes were carried out on the training sets of the competition data. We choose the data set Arcene as an example to explain the approach step by step. In our view the point of this competition was the construction of a well performing classifier rather than the systematic analysis of a specific approach. This is why our search for the best classifier was only guided by the described methods and that we deviated from the road map at several occasions. All calculations were done with the software Spider [2004].

PDF DOI [BibTex]

PDF DOI [BibTex]


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Embedded methods

Lal, T., Chapelle, O., Weston, J., Elisseeff, A.

In Feature Extraction: Foundations and Applications, pages: 137-165, Studies in Fuzziness and Soft Computing ; 207, (Editors: Guyon, I. , S. Gunn, M. Nikravesh, L. A. Zadeh), Springer, Berlin, Germany, 2006 (inbook)

Abstract
Embedded methods are a relatively new approach to feature selection. Unlike filter methods, which do not incorporate learning, and wrapper approaches, which can be used with arbitrary classifiers, in embedded methods the features selection part can not be separated from the learning part. Existing embedded methods are reviewed based on a unifying mathematical framework.

PDF Web [BibTex]

PDF Web [BibTex]


Thumb xl screen shot 2012 06 06 at 11.31.38 am
Implicit Wiener Series, Part II: Regularised estimation

Gehler, P., Franz, M.

(148), Max Planck Institute, 2006 (techreport)

pdf [BibTex]

2003


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Support Vector Channel Selection in BCI

Lal, T., Schröder, M., Hinterberger, T., Weston, J., Bogdan, M., Birbaumer, N., Schölkopf, B.

(120), Max Planck Institute for Biological Cybernetics, Tuebingen, Germany, December 2003 (techreport)

Abstract
Designing a Brain Computer Interface (BCI) system one can choose from a variety of features that may be useful for classifying brain activity during a mental task. For the special case of classifying EEG signals we propose the usage of the state of the art feature selection algorithms Recursive Feature Elimination [3] and Zero-Norm Optimization [13] which are based on the training of Support Vector Machines (SVM) [11]. These algorithms can provide more accurate solutions than standard filter methods for feature selection [14]. We adapt the methods for the purpose of selecting EEG channels. For a motor imagery paradigm we show that the number of used channels can be reduced significantly without increasing the classification error. The resulting best channels agree well with the expected underlying cortical activity patterns during the mental tasks. Furthermore we show how time dependent task specific information can be visualized.

PDF Web [BibTex]

2003

PDF Web [BibTex]


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Technical report on Separation methods for nonlinear mixtures

Jutten, C., Karhunen, J., Almeida, L., Harmeling, S.

(D29), EU-Project BLISS, October 2003 (techreport)

PDF [BibTex]

PDF [BibTex]


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Image Reconstruction by Linear Programming

Tsuda, K., Rätsch, G.

(118), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, October 2003 (techreport)

PDF [BibTex]

PDF [BibTex]