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2009


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PAC-Bayesian Generalization Bound for Density Estimation with Application to Co-clustering

Seldin, Y., Tishby, N.

In JMLR Workshop and Conference Proceedings Volume 5: AISTATS 2009, pages: 472-479, MIT Press, Cambridge, MA, USA, 12th International Conference on Artificial Intelligence and Statistics, April 2009 (inproceedings)

Abstract
We derive a PAC-Bayesian generalization bound for density estimation. Similar to the PAC-Bayesian generalization bound for classification, the result has the appealingly simple form of a tradeoff between empirical performance and the KL-divergence of the posterior from the prior. Moreover, the PAC-Bayesian generalization bound for classification can be derived as a special case of the bound for density estimation. To illustrate a possible application of our bound we derive a generalization bound for co-clustering. The bound provides a criterion to evaluate the ability of co-clustering to predict new co-occurrences, thus introducing a supervised flavor to this traditionally unsupervised task.

ei

PDF Web [BibTex]

2009


PDF Web [BibTex]


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Kernel Methods in Computer Vision:Object Localization, Clustering,and Taxonomy Discovery

Blaschko, MB.

Biologische Kybernetik, Technische Universität Berlin, Berlin, Germany, March 2009 (phdthesis)

ei

PDF PDF [BibTex]

PDF PDF [BibTex]


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Nearest Neighbor Clustering: A Baseline Method for Consistent Clustering with Arbitrary Objective Functions

Bubeck, S., von Luxburg, U.

Journal of Machine Learning Research, 10, pages: 657-698, March 2009 (article)

Abstract
Clustering is often formulated as a discrete optimization problem. The objective is to find, among all partitions of the data set, the best one according to some quality measure. However, in the statistical setting where we assume that the finite data set has been sampled from some underlying space, the goal is not to find the best partition of the given sample, but to approximate the true partition of the underlying space. We argue that the discrete optimization approach usually does not achieve this goal, and instead can lead to inconsistency. We construct examples which provably have this behavior. As in the case of supervised learning, the cure is to restrict the size of the function classes under consideration. For appropriate “small” function classes we can prove very general consistency theorems for clustering optimization schemes. As one particular algorithm for clustering with a restricted function space we introduce “nearest neighbor clustering”. Similar to the k-nearest neighbor classifier in supervised learning, this algorithm can be seen as a general baseline algorithm to minimize arbitrary clustering objective functions. We prove that it is statistically consistent for all commonly used clustering objective functions.

ei

PDF Web [BibTex]


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Protein Functional Class Prediction With a Combined Graph

Shin, H., Tsuda, K., Schölkopf, B.

Expert Systems with Applications, 36(2):3284-3292, March 2009 (article)

Abstract
In bioinformatics, there exist multiple descriptions of graphs for the same set of genes or proteins. For instance, in yeast systems, graph edges can represent different relationships such as protein–protein interactions, genetic interactions, or co-participation in a protein complex, etc. Relying on similarities between nodes, each graph can be used independently for prediction of protein function. However, since different graphs contain partly independent and partly complementary information about the problem at hand, one can enhance the total information extracted by combining all graphs. In this paper, we propose a method for integrating multiple graphs within a framework of semi-supervised learning. The method alternates between minimizing the objective function with respect to network output and with respect to combining weights. We apply the method to the task of protein functional class prediction in yeast. The proposed method performs significantly better than the same algorithm trained on any singl e graph.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Gaussian Process Dynamic Programming

Deisenroth, M., Rasmussen, C., Peters, J.

Neurocomputing, 72(7-9):1508-1524, March 2009 (article)

Abstract
Reinforcement learning (RL) and optimal control of systems with contin- uous states and actions require approximation techniques in most interesting cases. In this article, we introduce Gaussian process dynamic programming (GPDP), an approximate value-function based RL algorithm. We consider both a classic optimal control problem, where problem-specific prior knowl- edge is available, and a classic RL problem, where only very general priors can be used. For the classic optimal control problem, GPDP models the unknown value functions with Gaussian processes and generalizes dynamic programming to continuous-valued states and actions. For the RL problem, GPDP starts from a given initial state and explores the state space using Bayesian active learning. To design a fast learner, available data has to be used efficiently. Hence, we propose to learn probabilistic models of the a priori unknown transition dynamics and the value functions on the fly. In both cases, we successfully apply the resulting continuous-valued controllers to the under-actuated pendulum swing up and analyze the performances of the suggested algorithms. It turns out that GPDP uses data very efficiently and can be applied to problems, where classic dynamic programming would be cumbersome.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Towards quantitative PET/MRI: a review of MR-based attenuation correction techniques

Hofmann, M., Pichler, B., Schölkopf, B., Beyer, T.

European Journal of Nuclear Medicine and Molecular Imaging, 36(Supplement 1):93-104, March 2009 (article)

Abstract
Introduction Positron emission tomography (PET) is a fully quantitative technology for imaging metabolic pathways and dynamic processes in vivo. Attenuation correction of raw PET data is a prerequisite for quantification and is typically based on separate transmission measurements. In PET/CT attenuation correction, however, is performed routinely based on the available CT transmission data. Objective Recently, combined PET/magnetic resonance (MR) has been proposed as a viable alternative to PET/CT. Current concepts of PET/MRI do not include CT-like transmission sources and, therefore, alternative methods of PET attenuation correction must be found. This article reviews existing approaches to MR-based attenuation correction (MR-AC). Most groups have proposed MR-AC algorithms for brain PET studies and more recently also for torso PET/MR imaging. Most MR-AC strategies require the use of complementary MR and transmission images, or morphology templates generated from transmission images. We review and discuss these algorithms and point out challenges for using MR-AC in clinical routine. Discussion MR-AC is work-in-progress with potentially promising results from a template-based approach applicable to both brain and torso imaging. While efforts are ongoing in making clinically viable MR-AC fully automatic, further studies are required to realize the potential benefits of MR-based motion compensation and partial volume correction of the PET data.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Generating Spike Trains with Specified Correlation Coefficients

Macke, J., Berens, P., Ecker, A., Tolias, A., Bethge, M.

Neural Computation, 21(2):397-423, February 2009 (article)

Abstract
Spike trains recorded from populations of neurons can exhibit substantial pairwise correlations between neurons and rich temporal structure. Thus, for the realistic simulation and analysis of neural systems, it is essential to have efficient methods for generating artificial spike trains with specified correlation structure. Here we show how correlated binary spike trains can be simulated by means of a latent multivariate gaussian model. Sampling from the model is computationally very efficient and, in particular, feasible even for large populations of neurons. The entropy of the model is close to the theoretical maximum for a wide range of parameters. In addition, this framework naturally extends to correlations over time and offers an elegant way to model correlated neural spike counts with arbitrary marginal distributions.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Automatic detection of preclinical neurodegeneration: Presymptomatic Huntington disease

Klöppel, S., Chu, C., Tan, G., Draganski, B., Johnson, H., Paulsen, J., Kienzle, W., Tabrizi, S., Ashburner, J., Frackowiak, R.

Neurology, 72(5):426-431, February 2009 (article)

Abstract
Background: Treatment of neurodegenerative diseases is likely to be most beneficial in the very early, possibly preclinical stages of degeneration. We explored the usefulness of fully automatic structural MRI classification methods for detecting subtle degenerative change. The availability of a definitive genetic test for Huntington disease (HD) provides an excellent metric for judging the performance of such methods in gene mutation carriers who are free of symptoms. Methods: Using the gray matter segment of MRI scans, this study explored the usefulness of a multivariate support vector machine to automatically identify presymptomatic HD gene mutation carriers (PSCs) in the absence of any a priori information. A multicenter data set of 96 PSCs and 95 age- and sex-matched controls was studied. The PSC group was subclassified into three groups based on time from predicted clinical onset, an estimate that is a function of DNA mutation size and age. Results: Subjects with at least a 33% chance of developing unequivocal signs of HD in 5 years were correctly assigned to the PSC group 69% of the time. Accuracy improved to 83% when regions affected by the disease were selected a priori for analysis. Performance was at chance when the probability of developing symptoms in 5 years was less than 10%. Conclusions: Presymptomatic Huntington disease gene mutation carriers close to estimated diagnostic onset were successfully separated from controls on the basis of single anatomic scans, without additional a priori information. Prior information is required to allow separation when degenerative changes are either subtle or variable.

ei

Web [BibTex]

Web [BibTex]


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Enumeration of condition-dependent dense modules in protein interaction networks

Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K.

Bioinformatics, 25(7):933-940, February 2009 (article)

Abstract
Motivation: Modern systems biology aims at understanding how the different molecular components of a biological cell interact. Often, cellular functions are performed by complexes consisting of many different proteins. The composition of these complexes may change according to the cellular environment, and one protein may be involved in several different processes. The automatic discovery of functional complexes from protein interaction data is challenging. While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration. Furthermore, constraints from additional information sources such as gene expression and phenotype data can be integrated, so we can systematically mine for dense modules with interesting profiles. Results: Given a weighted protein interaction network, our method discovers all protein sets that satisfy a user-defined minimum density threshold. We employ a reverse search strategy, which allows us to exploit the density criterion in an efficient way. Our experiments show that the novel approach is feasible and produces biologically meaningful results. In comparative validation studies using yeast data, the method achieved the best overall prediction performance with respect to confirmed complexes. Moreover, by enhancing the yeast network with phenotypic and phylogenetic profiles and the human network with tissue-specific expression data, we identified condition-dependent complex variants.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Prototype Classification: Insights from Machine Learning

Graf, A., Bousquet, O., Rätsch, G., Schölkopf, B.

Neural Computation, 21(1):272-300, January 2009 (article)

Abstract
We shed light on the discrimination between patterns belonging to two different classes by casting this decoding problem into a generalized prototype framework. The discrimination process is then separated into two stages: a projection stage that reduces the dimensionality of the data by projecting it on a line and a threshold stage where the distributions of the projected patterns of both classes are separated. For this, we extend the popular mean-of-class prototype classification using algorithms from machine learning that satisfy a set of invariance properties. We report a simple yet general approach to express different types of linear classification algorithms in an identical and easy-to-visualize formal framework using generalized prototypes where these prototypes are used to express the normal vector and offset of the hyperplane. We investigate nonmargin classifiers such as the classical prototype classifier, the Fisher classifier, and the relevance vector machine. We then study hard and soft margin cl assifiers such as the support vector machine and a boosted version of the prototype classifier. Subsequently, we relate mean-of-class prototype classification to other classification algorithms by showing that the prototype classifier is a limit of any soft margin classifier and that boosting a prototype classifier yields the support vector machine. While giving novel insights into classification per se by presenting a common and unified formalism, our generalized prototype framework also provides an efficient visualization and a principled comparison of machine learning classification.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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The DICS repository: module-assisted analysis of disease-related gene lists

Dietmann, S., Georgii, E., Antonov, A., Tsuda, K., Mewes, H.

Bioinformatics, 25(6):830-831, January 2009 (article)

Abstract
The DICS database is a dynamic web repository of computationally predicted functional modules from the human protein–protein interaction network. It provides references to the CORUM, DrugBank, KEGG and Reactome pathway databases. DICS can be accessed for retrieving sets of overlapping modules and protein complexes that are significantly enriched in a gene list, thereby providing valuable information about the functional context.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Large Margin Methods for Part of Speech Tagging

Altun, Y.

In Automatic Speech and Speaker Recognition: Large Margin and Kernel Methods, pages: 141-160, (Editors: Keshet, J. and Bengio, S.), Wiley, Hoboken, NJ, USA, January 2009 (inbook)

ei

Web [BibTex]

Web [BibTex]


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Motor Control and Learning in Table Tennis

Mülling, K.

Eberhard Karls Universität Tübingen, Gerrmany, 2009 (diplomathesis)

ei

[BibTex]

[BibTex]


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Hierarchical Clustering and Density Estimation Based on k-nearest-neighbor graphs

Drewe, P.

Eberhard Karls Universität Tübingen, Germany, 2009 (diplomathesis)

ei

[BibTex]

[BibTex]


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mGene: accurate SVM-based gene finding with an application to nematode genomes

Schweikert, G., Zien, A., Zeller, G., Behr, J., Dieterich, C., Ong, C., Philips, P., De Bona, F., Hartmann, L., Bohlen, A., Krüger, N., Sonnenburg, S., Rätsch, G.

Genome Research, 19(11):2133-43, 2009 (article)

Abstract
We present a highly accurate gene-prediction system for eukaryotic genomes, called mGene. It combines in an unprecedented manner the flexibility of generalized hidden Markov models (gHMMs) with the predictive power of modern machine learning methods, such as Support Vector Machines (SVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. Considering the average of sensitivity and specificity, the developmental version of mGene exhibited the best prediction performance on nucleotide, exon, and transcript level for ab initio and multiple-genome gene-prediction tasks. The fully developed version shows superior performance in 10 out of 12 evaluation criteria compared with the other participating gene finders, including Fgenesh++ and Augustus. An in-depth analysis of mGene's genome-wide predictions revealed that approximately 2200 predicted genes were not contained in the current genome annotation. Testing a subset of 57 of these genes by RT-PCR and sequencing, we confirmed expression for 24 (42%) of them. mGene missed 300 annotated genes, out of which 205 were unconfirmed. RT-PCR testing of 24 of these genes resulted in a success rate of merely 8%. These findings suggest that even the gene catalog of a well-studied organism such as C. elegans can be substantially improved by mGene's predictions. We also provide gene predictions for the four nematodes C. briggsae, C. brenneri, C. japonica, and C. remanei. Comparing the resulting proteomes among these organisms and to the known protein universe, we identified many species-specific gene inventions. In a quality assessment of several available annotations for these genomes, we find that mGene's predictions are most accurate.

ei

DOI [BibTex]

DOI [BibTex]


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Efficient Bregman Range Search

Cayton, L.

In Advances in Neural Information Processing Systems 22, pages: 243-251, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
We develop an algorithm for efficient range search when the notion of dissimilarity is given by a Bregman divergence. The range search task is to return all points in a potentially large database that are within some specified distance of a query. It arises in many learning algorithms such as locally-weighted regression, kernel density estimation, neighborhood graph-based algorithms, and in tasks like outlier detection and information retrieval. In metric spaces, efficient range search-like algorithms based on spatial data structures have been deployed on a variety of statistical tasks. Here we describe an algorithm for range search for an arbitrary Bregman divergence. This broad class of dissimilarity measures includes the relative entropy, Mahalanobis distance, Itakura-Saito divergence, and a variety of matrix divergences. Metric methods cannot be directly applied since Bregman divergences do not in general satisfy the triangle inequality. We derive geometric properties of Bregman divergences that yield an efficient algorithm for range search based on a recently proposed space decomposition for Bregman divergences.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Learning with Structured Data: Applications to Computer Vision

Nowozin, S.

Technische Universität Berlin, Germany, 2009 (phdthesis)

ei

PDF [BibTex]

PDF [BibTex]


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Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases

Djuranovic, S., Hartmann, MD., Habeck, M., Ursinus, A., Zwickl, P., Martin, J., Lupas, AN., Zeth, K.

Molecular Cell, 34(5):580-590, 2009 (article)

Abstract
The proteasome forms the core of the protein quality control system in archaea and eukaryotes and also occurs in one bacterial lineage, the Actinobacteria. Access to its proteolytic compartment is controlled by AAA ATPases, whose N-terminal domains (N domains) are thought to mediate substrate recognition. The N domains of an archaeal proteasomal ATPase, Archaeoglobus fulgidus PAN, and of its actinobacterial homolog, Rhodococcus erythropolis ARC, form hexameric rings, whose subunits consist of an N-terminal coiled coil and a C-terminal OB domain. In ARC-N, the OB domains are duplicated and form separate rings. PAN-N and ARC-N can act as chaperones, preventing the aggregation of heterologous proteins in vitro, and this activity is preserved in various chimeras, even when these include coiled coils and OB domains from unrelated proteins. The structures suggest a molecular mechanism for substrate processing based on concerted radial motions of the coiled coils relative to the OB rings.

ei

DOI [BibTex]

DOI [BibTex]


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Discussion of: Brownian Distance Covariance

Gretton, A., Fukumizu, K., Sriperumbudur, B.

The Annals of Applied Statistics, 3(4):1285-1294, 2009 (article)

ei

[BibTex]

[BibTex]


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Covariate shift and local learning by distribution matching

Gretton, A., Smola, A., Huang, J., Schmittfull, M., Borgwardt, K., Schölkopf, B.

In Dataset Shift in Machine Learning, pages: 131-160, (Editors: Quiñonero-Candela, J., Sugiyama, M., Schwaighofer, A. and Lawrence, N. D.), MIT Press, Cambridge, MA, USA, 2009 (inbook)

Abstract
Given sets of observations of training and test data, we consider the problem of re-weighting the training data such that its distribution more closely matches that of the test data. We achieve this goal by matching covariate distributions between training and test sets in a high dimensional feature space (specifically, a reproducing kernel Hilbert space). This approach does not require distribution estimation. Instead, the sample weights are obtained by a simple quadratic programming procedure. We provide a uniform convergence bound on the distance between the reweighted training feature mean and the test feature mean, a transductive bound on the expected loss of an algorithm trained on the reweighted data, and a connection to single class SVMs. While our method is designed to deal with the case of simple covariate shift (in the sense of Chapter ??), we have also found benefits for sample selection bias on the labels. Our correction procedure yields its greatest and most consistent advantages when the learning algorithm returns a classifier/regressor that is simpler" than the data might suggest.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Kernel Choice and Classifiability for RKHS Embeddings of Probability Distributions

Sriperumbudur, B., Fukumizu, K., Gretton, A., Lanckriet, G., Schölkopf, B.

In Advances in Neural Information Processing Systems 22, pages: 1750-1758, (Editors: Y Bengio and D Schuurmans and J Lafferty and C Williams and A Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
Embeddings of probability measures into reproducing kernel Hilbert spaces have been proposed as a straightforward and practical means of representing and comparing probabilities. In particular, the distance between embeddings (the maximum mean discrepancy, or MMD) has several key advantages over many classical metrics on distributions, namely easy computability, fast convergence and low bias of finite sample estimates. An important requirement of the embedding RKHS is that it be characteristic: in this case, the MMD between two distributions is zero if and only if the distributions coincide. Three new results on the MMD are introduced in the present study. First, it is established that MMD corresponds to the optimal risk of a kernel classifier, thus forming a natural link between the distance between distributions and their ease of classification. An important consequence is that a kernel must be characteristic to guarantee classifiability between distributions in the RKHS. Second, the class of characteristic kernels is broadened to incorporate all strictly positive definite kernels: these include non-translation invariant kernels and kernels on non-compact domains. Third, a generalization of the MMD is proposed for families of kernels, as the supremum over MMDs on a class of kernels (for instance the Gaussian kernels with different bandwidths). This extension is necessary to obtain a single distance measure if a large selection or class of characteristic kernels is potentially appropriate. This generalization is reasonable, given that it corresponds to the problem of learning the kernel by minimizing the risk of the corresponding kernel classifier. The generalized MMD is shown to have consistent finite sample estimates, and its performance is demonstrated on a homogeneity testing example.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Nonlinear directed acyclic structure learning with weakly additive noise models

Tillman, R., Gretton, A., Spirtes, P.

In Advances in Neural Information Processing Systems 22, pages: 1847-1855, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
The recently proposed emph{additive noise model} has advantages over previous structure learning algorithms, when attempting to recover some true data generating mechanism, since it (i) does not assume linearity or Gaussianity and (ii) can recover a unique DAG rather than an equivalence class. However, its original extension to the multivariate case required enumerating all possible DAGs, and for some special distributions, e.g. linear Gaussian, the model is invertible and thus cannot be used for structure learning. We present a new approach which combines a PC style search using recent advances in kernel measures of conditional dependence with local searches for additive noise models in substructures of the equivalence class. This results in a more computationally efficient approach that is useful for arbitrary distributions even when additive noise models are invertible. Experiments with synthetic and real data show that this method is more accurate than previous methods when data are nonlinear and/or non-Gaussian.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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From Differential Equations to Differential Geometry: Aspects of Regularisation in Machine Learning

Steinke, F.

Universität des Saarlandes, Saarbrücken, Germany, 2009 (phdthesis)

ei

PDF [BibTex]


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Graphical models for decoding in BCI visual speller systems

Martens, S., Farquhar, J., Hill, J., Schölkopf, B.

In pages: 470-473, IEEE, 4th International IEEE EMBS Conference on Neural Engineering (NER), 2009 (inproceedings)

ei

DOI [BibTex]

DOI [BibTex]


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A Fast, Consistent Kernel Two-Sample Test

Gretton, A., Fukumizu, K., Harchaoui, Z., Sriperumbudur, B.

In Advances in Neural Information Processing Systems 22, pages: 673-681, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
A kernel embedding of probability distributions into reproducing kernel Hilbert spaces (RKHS) has recently been proposed, which allows the comparison of two probability measures P and Q based on the distance between their respective embeddings: for a sufficiently rich RKHS, this distance is zero if and only if P and Q coincide. In using this distance as a statistic for a test of whether two samples are from different distributions, a major difficulty arises in computing the significance threshold, since the empirical statistic has as its null distribution (where P = Q) an infinite weighted sum of x2 random variables. Prior finite sample approximations to the null distribution include using bootstrap resampling, which yields a consistent estimate but is computationally costly; and fitting a parametric model with the low order moments of the test statistic, which can work well in practice but has no consistency or accuracy guarantees. The main result of the present work is a novel estimate of the null distribution, computed from the eigenspectrum of the Gram matrix on the aggregate sample from P and Q, and having lower computational cost than the bootstrap. A proof of consistency of this estimate is provided. The performance of the null distribution estimate is compared with the bootstrap and parametric approaches on an artificial example, high dimensional multivariate data, and text.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Augmenting Feature-driven fMRI Analyses: Semi-supervised learning and resting state activity

Blaschko, M., Shelton, J., Bartels, A.

In Advances in Neural Information Processing Systems 22, pages: 126-134, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
Resting state activity is brain activation that arises in the absence of any task, and is usually measured in awake subjects during prolonged fMRI scanning sessions where the only instruction given is to close the eyes and do nothing. It has been recognized in recent years that resting state activity is implicated in a wide variety of brain function. While certain networks of brain areas have different levels of activation at rest and during a task, there is nevertheless significant similarity between activations in the two cases. This suggests that recordings of resting state activity can be used as a source of unlabeled data to augment discriminative regression techniques in a semi-supervised setting. We evaluate this setting empirically yielding three main results: (i) regression tends to be improved by the use of Laplacian regularization even when no additional unlabeled data are available, (ii) resting state data seem to have a similar marginal distribution to that recorded during the execution of a visual processing task implying largely similar types of activation, and (iii) this source of information can be broadly exploited to improve the robustness of empirical inference in fMRI studies, an inherently data poor domain.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Non-linear System Identification: Visual Saliency Inferred from Eye-Movement Data

Wichmann, F., Kienzle, W., Schölkopf, B., Franz, M.

Journal of Vision, 9(8):article 32, 2009 (article)

Abstract
For simple visual patterns under the experimenter's control we impose which information, or features, an observer can use to solve a given perceptual task. For natural vision tasks, however, there are typically a multitude of potential features in a given visual scene which the visual system may be exploiting when analyzing it: edges, corners, contours, etc. Here we describe a novel non-linear system identification technique based on modern machine learning methods that allows the critical features an observer uses to be inferred directly from the observer's data. The method neither requires stimuli to be embedded in noise nor is it limited to linear perceptive fields (classification images). We demonstrate our technique by deriving the critical image features observers fixate in natural scenes (bottom-up visual saliency). Unlike previous studies where the relevant structure is determined manually—e.g. by selecting Gabors as visual filters—we do not make any assumptions in this regard, but numerically infer number and properties them from the eye-movement data. We show that center-surround patterns emerge as the optimal solution for predicting saccade targets from local image structure. The resulting model, a one-layer feed-forward network with contrast gain-control, is surprisingly simple compared to previously suggested saliency models. Nevertheless, our model is equally predictive. Furthermore, our findings are consistent with neurophysiological hardware in the superior colliculus. Bottom-up visual saliency may thus not be computed cortically as has been thought previously.

ei

Web DOI [BibTex]


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mGene.web: a web service for accurate computational gene finding

Schweikert, G., Behr, J., Zien, A., Zeller, G., Ong, C., Sonnenburg, S., Rätsch, G.

Nucleic Acids Research, 37, pages: W312-6, 2009 (article)

Abstract
We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to train the system with their own data for other organisms on the push of a button, a functionality that will greatly accelerate the annotation of newly sequenced genomes. The system is built in a highly modular way, such that individual components of the framework, like the promoter prediction tool or the splice site predictor, can be used autonomously. The underlying gene finding system mGene is based on discriminative machine learning techniques and its high accuracy has been demonstrated in an international competition on nematode genomes. mGene.web is available at http://www.mgene.org/web, it is free of charge and can be used for eukaryotic genomes of small to moderate size (several hundred Mbp).

ei

DOI [BibTex]

DOI [BibTex]


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Fast subtree kernels on graphs

Shervashidze, N., Borgwardt, K.

In Advances in Neural Information Processing Systems 22, pages: 1660-1668, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
In this article, we propose fast subtree kernels on graphs. On graphs with n nodes and m edges and maximum degree d, these kernels comparing subtrees of height h can be computed in O(mh), whereas the classic subtree kernel by Ramon & G{\"a}rtner scales as O(n24dh). Key to this efficiency is the observation that the Weisfeiler-Lehman test of isomorphism from graph theory elegantly computes a subtree kernel as a byproduct. Our fast subtree kernels can deal with labeled graphs, scale up easily to large graphs and outperform state-of-the-art graph kernels on several classification benchmark datasets in terms of accuracy and runtime.

ei

PDF Web [BibTex]

PDF Web [BibTex]

2006


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Conformal Multi-Instance Kernels

Blaschko, M., Hofmann, T.

In NIPS 2006 Workshop on Learning to Compare Examples, pages: 1-6, NIPS Workshop on Learning to Compare Examples, December 2006 (inproceedings)

Abstract
In the multiple instance learning setting, each observation is a bag of feature vectors of which one or more vectors indicates membership in a class. The primary task is to identify if any vectors in the bag indicate class membership while ignoring vectors that do not. We describe here a kernel-based technique that defines a parametric family of kernels via conformal transformations and jointly learns a discriminant function over bags together with the optimal parameter settings of the kernel. Learning a conformal transformation effectively amounts to weighting regions in the feature space according to their contribution to classification accuracy; regions that are discriminative will be weighted higher than regions that are not. This allows the classifier to focus on regions contributing to classification accuracy while ignoring regions that correspond to vectors found both in positive and in negative bags. We show how parameters of this transformation can be learned for support vector machines by posing the problem as a multiple kernel learning problem. The resulting multiple instance classifier gives competitive accuracy for several multi-instance benchmark datasets from different domains.

ei

PDF Web [BibTex]

2006


PDF Web [BibTex]


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Some observations on the pedestal effect or dipper function

Henning, B., Wichmann, F.

Journal of Vision, 6(13):50, 2006 Fall Vision Meeting of the Optical Society of America, December 2006 (poster)

Abstract
The pedestal effect is the large improvement in the detectabilty of a sinusoidal “signal” grating observed when the signal is added to a masking or “pedestal” grating of the same spatial frequency, orientation, and phase. We measured the pedestal effect in both broadband and notched noise - noise from which a 1.5-octave band centred on the signal frequency had been removed. Although the pedestal effect persists in broadband noise, it almost disappears in the notched noise. Furthermore, the pedestal effect is substantial when either high- or low-pass masking noise is used. We conclude that the pedestal effect in the absence of notched noise results principally from the use of information derived from channels with peak sensitivities at spatial frequencies different from that of the signal and pedestal. The spatial-frequency components of the notched noise above and below the spatial frequency of the signal and pedestal prevent the use of information about changes in contrast carried in channels tuned to spatial frequencies that are very much different from that of the signal and pedestal. Thus the pedestal or dipper effect measured without notched noise is not a characteristic of individual spatial-frequency tuned channels.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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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]

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]

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]

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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Structure validation of the Josephin domain of ataxin-3: Conclusive evidence for an open conformation

Nicastro, G., Habeck, M., Masino, L., Svergun, DI., Pastore, A.

Journal of Biomolecular NMR, 36(4):267-277, December 2006 (article)

Abstract
The availability of new and fast tools in structure determination has led to a more than exponential growth of the number of structures solved per year. It is therefore increasingly essential to assess the accuracy of the new structures by reliable approaches able to assist validation. Here, we discuss a specific example in which the use of different complementary techniques, which include Bayesian methods and small angle scattering, resulted essential for validating the two currently available structures of the Josephin domain of ataxin-3, a protein involved in the ubiquitin/proteasome pathway and responsible for neurodegenerative spinocerebellar ataxia of type 3. Taken together, our results demonstrate that only one of the two structures is compatible with the experimental information. Based on the high precision of our refined structure, we show that Josephin contains an open cleft which could be directly implicated in the interaction with polyubiquitin chains and other partners.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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A Unifying View of Wiener and Volterra Theory and Polynomial Kernel Regression

Franz, M., Schölkopf, B.

Neural Computation, 18(12):3097-3118, December 2006 (article)

Abstract
Volterra and Wiener series are perhaps the best understood nonlinear system representations in signal processing. Although both approaches have enjoyed a certain popularity in the past, their application has been limited to rather low-dimensional and weakly nonlinear systems due to the exponential growth of the number of terms that have to be estimated. We show that Volterra and Wiener series can be represented implicitly as elements of a reproducing kernel Hilbert space by utilizing polynomial kernels. The estimation complexity of the implicit representation is linear in the input dimensionality and independent of the degree of nonlinearity. Experiments show performance advantages in terms of convergence, interpretability, and system sizes that can be handled.

ei

PDF Web DOI [BibTex]

PDF Web DOI [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.

ei

PDF [BibTex]

PDF [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]

PDF Web [BibTex]


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Semi-Supervised Learning

Zien, A.

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

ei

Web [BibTex]

Web [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.

ei

Web [BibTex]

Web [BibTex]


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Adapting Spatial Filter Methods for Nonstationary BCIs

Tomioka, R., Hill, J., Blankertz, B., Aihara, K.

In IBIS 2006, pages: 65-70, 2006 Workshop on Information-Based Induction Sciences, November 2006 (inproceedings)

Abstract
A major challenge in applying machine learning methods to Brain-Computer Interfaces (BCIs) is to overcome the possible nonstationarity in the data from the datablock the method is trained on and that the method is applied to. Assuming the joint distributions of the whitened signal and the class label to be identical in two blocks, where the whitening is done in each block independently, we propose a simple adaptation formula that is applicable to a broad class of spatial filtering methods including ICA, CSP, and logistic regression classifiers. We characterize the class of linear transformations for which the above assumption holds. Experimental results on 60 BCI datasets show improved classification accuracy compared to (a) fixed spatial filter approach (no adaptation) and (b) fixed spatial pattern approach (proposed by Hill et al., 2006 [1]).

ei

PDF [BibTex]

PDF [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.

ei

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)

ei

PDF [BibTex]

PDF [BibTex]


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Statistical Analysis of Slow Crack Growth Experiments

Pfingsten, T., Glien, K.

Journal of the European Ceramic Society, 26(15):3061-3065, November 2006 (article)

Abstract
A common approach for the determination of Slow Crack Growth (SCG) parameters are the static and dynamic loading method. Since materials with small Weibull module show a large variability in strength, a correct statistical analysis of the data is indispensable. In this work we propose the use of the Maximum Likelihood method and a Baysian analysis, which, in contrast to the standard procedures, take into account that failure strengths are Weibull distributed. The analysis provides estimates for the SCG parameters, the Weibull module, and the corresponding confidence intervals and overcomes the necessity of manual differentiation between inert and fatigue strength data. We compare the methods to a Least Squares approach, which can be considered the standard procedure. The results for dynamic loading data from the glass sealing of MEMS devices show that the assumptions inherent to the standard approach lead to significantly different estimates.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Optimizing Spatial Filters for BCI: Margin- and Evidence-Maximization Approaches

Farquhar, J., Hill, N., Schölkopf, B.

Challenging Brain-Computer Interfaces: MAIA Workshop 2006, pages: 1, November 2006 (poster)

Abstract
We present easy-to-use alternatives to the often-used two-stage Common Spatial Pattern + classifier approach for spatial filtering and classification of Event-Related Desychnronization signals in BCI. We report two algorithms that aim to optimize the spatial filters according to a criterion more directly related to the ability of the algorithms to generalize to unseen data. Both are based upon the idea of treating the spatial filter coefficients as hyperparameters of a kernel or covariance function. We then optimize these hyper-parameters directly along side the normal classifier parameters with respect to our chosen learning objective function. The two objectives considered are margin maximization as used in Support-Vector Machines and the evidence maximization framework used in Gaussian Processes. Our experiments assessed generalization error as a function of the number of training points used, on 9 BCI competition data sets and 5 offline motor imagery data sets measured in Tubingen. Both our approaches sho w consistent improvements relative to the commonly used CSP+linear classifier combination. Strikingly, the improvement is most significant in the higher noise cases, when either few trails are used for training, or with the most poorly performing subjects. This a reversal of the usual "rich get richer" effect in the development of CSP extensions, which tend to perform best when the signal is strong enough to accurately find their additional parameters. This makes our approach particularly suitable for clinical application where high levels of noise are to be expected.

ei

PDF PDF [BibTex]

PDF PDF [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]

[BibTex]


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Mining frequent stem patterns from unaligned RNA sequences

Hamada, M., Tsuda, K., Kudo, T., Kin, T., Asai, K.

Bioinformatics, 22(20):2480-2487, October 2006 (article)

Abstract
Motivation: In detection of non-coding RNAs, it is often necessary to identify the secondary structure motifs from a set of putative RNA sequences. Most of the existing algorithms aim to provide the best motif or few good motifs, but biologists often need to inspect all the possible motifs thoroughly. Results: Our method RNAmine employs a graph theoretic representation of RNA sequences, and detects all the possible motifs exhaustively using a graph mining algorithm. The motif detection problem boils down to finding frequently appearing patterns in a set of directed and labeled graphs. In the tasks of common secondary structure prediction and local motif detection from long sequences, our method performed favorably both in accuracy and in efficiency with the state-of-the-art methods such as CMFinder.

ei

PDF Web DOI [BibTex]

PDF Web DOI [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)

ei

Web [BibTex]

Web [BibTex]