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2004


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A kernel view of the dimensionality reduction of manifolds

Ham, J., Lee, D., Mika, S., Schölkopf, B.

In Proceedings of the Twenty-First International Conference on Machine Learning, pages: 369-376, (Editors: CE Brodley), ACM, New York, NY, USA, ICML, 2004, also appeared as MPI-TR 110 (inproceedings)

Abstract
We interpret several well-known algorithms for dimensionality reduction of manifolds as kernel methods. Isomap, graph Laplacian eigenmap, and locally linear embedding (LLE) all utilize local neighborhood information to construct a global embedding of the manifold. We show how all three algorithms can be described as kernel PCA on specially constructed Gram matrices, and illustrate the similarities and differences between the algorithms with representative examples.

PDF [BibTex]

2004

PDF [BibTex]


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Protein Functional Class Prediction with a Combined Graph

Shin, H., Tsuda, K., Schölkopf, B.

In Proceedings of the Korean Data Mining Conference, pages: 200-219, Proceedings of the Korean Data Mining Conference, 2004 (inproceedings)

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 single graph.

PDF [BibTex]

PDF [BibTex]


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Learning from Labeled and Unlabeled Data Using Random Walks

Zhou, D., Schölkopf, B.

In Pattern Recognition, Proceedings of the 26th DAGM Symposium, pages: 237-244, (Editors: Rasmussen, C.E., H.H. Bülthoff, M.A. Giese and B. Schölkopf), Pattern Recognition, Proceedings of the 26th DAGM Symposium, 2004 (inproceedings)

Abstract
We consider the general problem of learning from labeled and unlabeled data. Given a set of points, some of them are labeled, and the remaining points are unlabeled. The goal is to predict the labels of the unlabeled points. Any supervised learning algorithm can be applied to this problem, for instance, Support Vector Machines (SVMs). The problem of our interest is if we can implement a classifier which uses the unlabeled data information in some way and has higher accuracy than the classifiers which use the labeled data only. Recently we proposed a simple algorithm, which can substantially benefit from large amounts of unlabeled data and demonstrates clear superiority to supervised learning methods. In this paper we further investigate the algorithm using random walks and spectral graph theory, which shed light on the key steps in this algorithm.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Learning from Labeled and Unlabeled Data Using Random Walks

Zhou, D., Schölkopf, B.

Max Planck Institute for Biological Cybernetics, 2004 (techreport)

Abstract
We consider the general problem of learning from labeled and unlabeled data. Given a set of points, some of them are labeled, and the remaining points are unlabeled. The goal is to predict the labels of the unlabeled points. Any supervised learning algorithm can be applied to this problem, for instance, Support Vector Machines (SVMs). The problem of our interest is if we can implement a classifier which uses the unlabeled data information in some way and has higher accuracy than the classifiers which use the labeled data only. Recently we proposed a simple algorithm, which can substantially benefit from large amounts of unlabeled data and demonstrates clear superiority to supervised learning methods. In this paper we further investigate the algorithm using random walks and spectral graph theory, which shed light on the key steps in this algorithm.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Masking by plaid patterns revisited

Wichmann, F.

Experimentelle Psychologie. Beitr{\"a}ge zur 46. Tagung experimentell arbeitender Psychologen, 46, pages: 285, 2004 (poster)

[BibTex]

[BibTex]


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Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data

Tsuda, K., Uda, S., Kin, T., Asai, K.

Neural Processing Letters, 19, pages: 63-72, 2004 (article)

PDF [BibTex]

PDF [BibTex]


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A Tutorial on Support Vector Regression

Smola, A., Schölkopf, B.

Statistics and Computing, 14(3):199-222, 2004 (article)

Web [BibTex]

Web [BibTex]


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Multivariate Regression via Stiefel Manifold Constraints

BakIr, G., Gretton, A., Franz, M., Schölkopf, B.

In Lecture Notes in Computer Science, Vol. 3175, pages: 262-269, (Editors: CE Rasmussen and HH Bülthoff and B Schölkopf and MA Giese), Springer, Berlin, Germany, Pattern Recognition, Proceedings of the 26th DAGM Symposium, 2004 (inproceedings)

Abstract
We introduce a learning technique for regression between high-dimensional spaces. Standard methods typically reduce this task to many one-dimensional problems, with each output dimension considered independently. By contrast, in our approach the feature construction and the regression estimation are performed jointly, directly minimizing a loss function that we specify, subject to a rank constraint. A major advantage of this approach is that the loss is no longer chosen according to the algorithmic requirements, but can be tailored to the characteristics of the task at hand; the features will then be optimal with respect to this objective, and dependence between the outputs can be exploited.

PostScript [BibTex]

PostScript [BibTex]


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Implicit estimation of Wiener series

Franz, M., Schölkopf, B.

In Machine Learning for Signal Processing XIV, Proc. 2004 IEEE Signal Processing Society Workshop, pages: 735-744, (Editors: A Barros and J Principe and J Larsen and T Adali and S Douglas), IEEE, New York, Machine Learning for Signal Processing XIV, Proc. IEEE Signal Processing Society Workshop, 2004 (inproceedings)

Abstract
The Wiener series is one of the standard methods to systematically characterize the nonlinearity of a system. The classical estimation method of the expansion coefficients via cross-correlation suffers from severe problems that prevent its application to high-dimensional and strongly nonlinear systems. We propose an implicit estimation method based on regression in a reproducing kernel Hilbert space that alleviates these problems. Experiments show performance advantages in terms of convergence, interpretability, and system sizes that can be handled.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Hilbertian Metrics on Probability Measures and their Application in SVM’s

Hein, H., Lal, T., Bousquet, O.

In Pattern Recognition, Proceedings of th 26th DAGM Symposium, 3175, pages: 270-277, Lecture Notes in Computer Science, (Editors: Rasmussen, C. E., H. H. Bülthoff, M. Giese and B. Schölkopf), Pattern Recognition, Proceedings of th 26th DAGM Symposium, 2004 (inproceedings)

Abstract
The goal of this article is to investigate the field of Hilbertian metrics on probability measures. Since they are very versatile and can therefore be applied in various problems they are of great interest in kernel methods. Quit recently Tops{o}e and Fuglede introduced a family of Hilbertian metrics on probability measures. We give basic properties of the Hilbertian metrics of this family and other used metrics in the literature. Then we propose an extension of the considered metrics which incorporates structural information of the probability space into the Hilbertian metric. Finally we compare all proposed metrics in an image and text classification problem using histogram data.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Gasussian process model based predictive control

Kocijan, J., Murray-Smith, R., Rasmussen, CE., Girard, A.

In Proceedings of the ACC 2004, pages: 2214-2219, Proceedings of the ACC, 2004 (inproceedings)

Abstract
Gaussian process models provide a probabilistic non-parametric modelling approach for black-box identi cation of non-linear dynamic systems. The Gaussian processes can highlight areas of the input space where prediction quality is poor, due to the lack of data or its complexity, by indicating the higher variance around the predicted mean. Gaussian process models contain noticeably less coef cients to be optimised. This paper illustrates possible application of Gaussian process models within model-based predictive control. The extra information provided within Gaussian process model is used in predictive control, where optimisation of control signal takes the variance information into account. The predictive control principle is demonstrated on control of pH process benchmark.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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A New Variational Framework for Rigid-Body Alignment

Kato, T., Tsuda, K., Tomii, K., Asai, K.

In Joint IAPR International Workshops on Syntactical and Structural Pattern Recognition (SSPR 2004) and Statistical Pattern Recognition (SPR 2004), pages: 171-179, (Editors: Fred, A.,T. Caelli, R.P.W. Duin, A. Campilho and D. de Ridder), Joint IAPR International Workshops on Syntactical and Structural Pattern Recognition (SSPR) and Statistical Pattern Recognition (SPR), 2004 (inproceedings)

PDF [BibTex]

PDF [BibTex]


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Protein Classification via Kernel Matrix Completion

Kin, T., Kato, T., Tsuda, K.

In pages: 261-274, (Editors: Schoelkopf, B., K. Tsuda and J.P. Vert), MIT Press, Cambridge, MA; USA, 2004 (inbook)

PDF [BibTex]

PDF [BibTex]


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Behaviour and Convergence of the Constrained Covariance

Gretton, A., Smola, A., Bousquet, O., Herbrich, R., Schölkopf, B., Logothetis, N.

(130), MPI for Biological Cybernetics, 2004 (techreport)

Abstract
We discuss reproducing kernel Hilbert space (RKHS)-based measures of statistical dependence, with emphasis on constrained covariance (COCO), a novel criterion to test dependence of random variables. We show that COCO is a test for independence if and only if the associated RKHSs are universal. That said, no independence test exists that can distinguish dependent and independent random variables in all circumstances. Dependent random variables can result in a COCO which is arbitrarily close to zero when the source densities are highly non-smooth, which can make dependence hard to detect empirically. All current kernel-based independence tests share this behaviour. Finally, we demonstrate exponential convergence between the population and empirical COCO, which implies that COCO does not suffer from slow learning rates when used as a dependence test.

PDF [BibTex]

PDF [BibTex]


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Early visual processing—data, theory, models

Wichmann, F.

Experimentelle Psychologie. Beitr{\"a}ge zur 46. Tagung experimentell arbeitender Psychologen, 46, pages: 24, 2004 (poster)

[BibTex]

[BibTex]


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Statistical Learning with Similarity and Dissimilarity Functions

von Luxburg, U.

pages: 1-166, Technische Universität Berlin, Germany, Technische Universität Berlin, Germany, 2004 (phdthesis)

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Statistische Lerntheorie und Empirische Inferenz

Schölkopf, B.

Jahrbuch der Max-Planck-Gesellschaft, 2004, pages: 377-382, 2004 (misc)

Abstract
Statistical learning theory studies the process of inferring regularities from empirical data. The fundamental problem is what is called generalization: how it is possible to infer a law which will be valid for an infinite number of future observations, given only a finite amount of data? This problem hinges upon fundamental issues of statistics and science in general, such as the problems of complexity of explanations, a priori knowledge, and representation of data.

PDF Web [BibTex]

PDF Web [BibTex]


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Bayesian analysis of the Scatterometer Wind Retrieval Inverse Problem: Some New Approaches

Cornford, D., Csato, L., Evans, D., Opper, M.

Journal of the Royal Statistical Society B, 66, pages: 1-17, 3, 2004 (article)

Abstract
The retrieval of wind vectors from satellite scatterometer observations is a non-linear inverse problem.A common approach to solving inverse problems is to adopt a Bayesian framework and to infer the posterior distribution of the parameters of interest given the observations by using a likelihood model relating the observations to the parameters, and a prior distribution over the parameters.We show how Gaussian process priors can be used efficiently with a variety of likelihood models, using local forward (observation) models and direct inverse models for the scatterometer.We present an enhanced Markov chain Monte Carlo method to sample from the resulting multimodal posterior distribution.We go on to show how the computational complexity of the inference can be controlled by using a sparse, sequential Bayes algorithm for estimation with Gaussian processes.This helps to overcome the most serious barrier to the use of probabilistic, Gaussian process methods in remote sensing inverse problems, which is the prohibitively large size of the data sets.We contrast the sampling results with the approximations that are found by using the sparse, sequential Bayes algorithm.

PDF [BibTex]

PDF [BibTex]


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Feature Selection for Support Vector Machines Using Genetic Algorithms

Fröhlich, H., Chapelle, O., Schölkopf, B.

International Journal on Artificial Intelligence Tools (Special Issue on Selected Papers from the 15th IEEE International Conference on Tools with Artificial Intelligence 2003), 13(4):791-800, 2004 (article)

Web [BibTex]

Web [BibTex]


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Semi-supervised kernel regression using whitened function classes

Franz, M., Kwon, Y., Rasmussen, C., Schölkopf, B.

In Pattern Recognition, Proceedings of the 26th DAGM Symposium, Lecture Notes in Computer Science, Vol. 3175, LNCS 3175, pages: 18-26, (Editors: CE Rasmussen and HH Bülthoff and MA Giese and B Schölkopf), Springer, Berlin, Gerrmany, 26th DAGM Symposium, 2004 (inproceedings)

Abstract
The use of non-orthonormal basis functions in ridge regression leads to an often undesired non-isotropic prior in function space. In this study, we investigate an alternative regularization technique that results in an implicit whitening of the basis functions by penalizing directions in function space with a large prior variance. The regularization term is computed from unlabelled input data that characterizes the input distribution. Tests on two datasets using polynomial basis functions showed an improved average performance compared to standard ridge regression.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Maximal Margin Classification for Metric Spaces

Hein, M., Bousquet, O.

In Learning Theory and Kernel Machines, pages: 72-86, (Editors: Schölkopf, B. and Warmuth, M. K.), Springer, Heidelberg, Germany, 16. Annual Conference on Computational Learning Theory / COLT Kernel, 2004 (inproceedings)

Abstract
In this article we construct a maximal margin classification algorithm for arbitrary metric spaces. At first we show that the Support Vector Machine (SVM) is a maximal margin algorithm for the class of metric spaces where the negative squared distance is conditionally positive definite (CPD). This means that the metric space can be isometrically embedded into a Hilbert space, where one performs linear maximal margin separation. We will show that the solution only depends on the metric, but not on the kernel. Following the framework we develop for the SVM, we construct an algorithm for maximal margin classification in arbitrary metric spaces. The main difference compared with SVM is that we no longer embed isometrically into a Hilbert space, but a Banach space. We further give an estimate of the capacity of the function class involved in this algorithm via Rademacher averages. We recover an algorithm of Graepel et al. [6].

PDF PostScript PDF DOI [BibTex]

PDF PostScript PDF DOI [BibTex]


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On the Convergence of Spectral Clustering on Random Samples: The Normalized Case

von Luxburg, U., Bousquet, O., Belkin, M.

In Proceedings of the 17th Annual Conference on Learning Theory, pages: 457-471, Proceedings of the 17th Annual Conference on Learning Theory, 2004 (inproceedings)

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Introduction to Statistical Learning Theory

Bousquet, O., Boucheron, S., Lugosi, G.

In Lecture Notes in Artificial Intelligence 3176, pages: 169-207, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, Germany, 2004 (inbook)

PDF [BibTex]

PDF [BibTex]


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A Primer on Kernel Methods

Vert, J., Tsuda, K., Schölkopf, B.

In Kernel Methods in Computational Biology, pages: 35-70, (Editors: B Schölkopf and K Tsuda and JP Vert), MIT Press, Cambridge, MA, USA, 2004 (inbook)

PDF [BibTex]

PDF [BibTex]


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Confidence Sets for Ratios: A Purely Geometric Approach To Fieller’s Theorem

von Luxburg, U., Franz, V.

(133), Max Planck Institute for Biological Cybernetics, 2004 (techreport)

Abstract
We present a simple, geometric method to construct Fieller's exact confidence sets for ratios of jointly normally distributed random variables. Contrary to previous geometric approaches in the literature, our method is valid in the general case where both sample mean and covariance are unknown. Moreover, not only the construction but also its proof are purely geometric and elementary, thus giving intuition into the nature of the confidence sets.

PDF [BibTex]

PDF [BibTex]


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Transductive Inference with Graphs

Zhou, D., Schölkopf, B.

Max Planck Institute for Biological Cybernetics, 2004, See the improved version Regularization on Discrete Spaces. (techreport)

Abstract
We propose a general regularization framework for transductive inference. The given data are thought of as a graph, where the edges encode the pairwise relationships among data. We develop discrete analysis and geometry on graphs, and then naturally adapt the classical regularization in the continuous case to the graph situation. A new and effective algorithm is derived from this general framework, as well as an approach we developed before.

[BibTex]

[BibTex]


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Classification and Feature Extraction in Man and Machine

Graf, AAB.

Biologische Kybernetik, University of Tübingen, Germany, 2004, online publication (phdthesis)

[BibTex]

[BibTex]


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Phenotypic Characterization of Human Chondrocyte Cell Line C-20/A4: A Comparison between Monolayer and Alginate Suspension Culture

Finger, F., Schorle, C., Söder, S., Zien, A., Goldring, M., Aigner, T.

Cells Tissues Organs, 178(2):65-77, 2004 (article)

Abstract
DNA microarray analysis was used to investigate the molecular phenotype of one of the first human chondrocyte cell lines, C-20/A4, derived from juvenile costal chondrocytes by immortalization with origin-defective simian virus 40 large T antigen. Clontech Human Cancer Arrays 1.2 and quantitative PCR were used to examine gene expression profiles of C-20/A4 cells cultured in the presence of serum in monolayer and alginate beads. In monolayer cultures, genes involved in cell proliferation were strongly upregulated compared to those expressed by human adult articular chondrocytes in primary culture. Of the cell cycle-regulated genes, only two, the CDK regulatory subunit and histone H4, were downregulated after culture in alginate beads, consistent with the ability of these cells to proliferate in suspension culture. In contrast, the expression of several genes that are involved in pericellular matrix formation, including MMP-14, COL6A1, fibronectin, biglycan and decorin, was upregulated when the C-20/A4 cells were transferred to suspension culture in alginate. Also, nexin-1, vimentin, and IGFBP-3, which are known to be expressed by primary chondrocytes, were differentially expressed in our study. Consistent with the proliferative phenotype of this cell line, few genes involved in matrix synthesis and turnover were highly expressed in the presence of serum. These results indicate that immortalized chondrocyte cell lines, rather than substituting for primary chondrocytes, may serve as models for extending findings on chondrocyte function not achievable by the use of primary chondrocytes.

[BibTex]

[BibTex]


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Kernel Methods and their Potential Use in Signal Processing

Perez-Cruz, F., Bousquet, O.

IEEE Signal Processing Magazine, (Special issue on Signal Processing for Mining), 2004 (article) Accepted

PostScript [BibTex]

PostScript [BibTex]


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Concentration Inequalities

Boucheron, S., Lugosi, G., Bousquet, O.

In Lecture Notes in Artificial Intelligence 3176, pages: 208-240, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, Germany, 2004 (inbook)

PDF [BibTex]

PDF [BibTex]


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Kernels for graphs

Kashima, H., Tsuda, K., Inokuchi, A.

In pages: 155-170, (Editors: Schoelkopf, B., K. Tsuda and J.P. Vert), MIT Press, Cambridge, MA; USA, 2004 (inbook)

PDF [BibTex]

PDF [BibTex]


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A primer on molecular biology

Zien, A.

In pages: 3-34, (Editors: Schoelkopf, B., K. Tsuda and J. P. Vert), MIT Press, Cambridge, MA, USA, 2004 (inbook)

Abstract
Modern molecular biology provides a rich source of challenging machine learning problems. This tutorial chapter aims to provide the necessary biological background knowledge required to communicate with biologists and to understand and properly formalize a number of most interesting problems in this application domain. The largest part of the chapter (its first section) is devoted to the cell as the basic unit of life. Four aspects of cells are reviewed in sequence: (1) the molecules that cells make use of (above all, proteins, RNA, and DNA); (2) the spatial organization of cells (``compartmentalization''); (3) the way cells produce proteins (``protein expression''); and (4) cellular communication and evolution (of cells and organisms). In the second section, an overview is provided of the most frequent measurement technologies, data types, and data sources. Finally, important open problems in the analysis of these data (bioinformatics challenges) are briefly outlined.

PDF PostScript Web [BibTex]

PDF PostScript Web [BibTex]


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Implicit Wiener series for capturing higher-order interactions in images

Franz, M., Schölkopf, B.

Sensory coding and the natural environment, (Editors: Olshausen, B.A. and M. Lewicki), 2004 (poster)

Abstract
The information about the objects in an image is almost exclusively described by the higher-order interactions of its pixels. The Wiener series is one of the standard methods to systematically characterize these interactions. However, the classical estimation method of the Wiener expansion coefficients via cross-correlation suffers from severe problems that prevent its application to high-dimensional and strongly nonlinear signals such as images. We propose an estimation method based on regression in a reproducing kernel Hilbert space that overcomes these problems using polynomial kernels as known from Support Vector Machines and other kernel-based methods. Numerical experiments show performance advantages in terms of convergence, interpretability and system sizes that can be handled. By the time of the conference, we will be able to present first results on the higher-order structure of natural images.

[BibTex]

[BibTex]


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Classification and Memory Behaviour of Man Revisited by Machine

Graf, A., Wichmann, F., Bülthoff, H., Schölkopf, B.

CSHL Meeting on Computational & Systems Neuroscience (COSYNE), 2004 (poster)

[BibTex]

[BibTex]


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Advanced Statistical Learning Theory

Bousquet, O.

Machine Learning Summer School, 2004 (talk)

PDF [BibTex]

PDF [BibTex]

2001


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Regularized principal manifolds

Smola, A., Mika, S., Schölkopf, B., Williamson, R.

Journal of Machine Learning Research, 1, pages: 179-209, June 2001 (article)

Abstract
Many settings of unsupervised learning can be viewed as quantization problems - the minimization of the expected quantization error subject to some restrictions. This allows the use of tools such as regularization from the theory of (supervised) risk minimization for unsupervised learning. This setting turns out to be closely related to principal curves, the generative topographic map, and robust coding. We explore this connection in two ways: (1) we propose an algorithm for finding principal manifolds that can be regularized in a variety of ways; and (2) we derive uniform convergence bounds and hence bounds on the learning rates of the algorithm. In particular, we give bounds on the covering numbers which allows us to obtain nearly optimal learning rates for certain types of regularization operators. Experimental results demonstrate the feasibility of the approach.

PDF [BibTex]

2001

PDF [BibTex]


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Variationsverfahren zur Untersuchung von Grundzustandseigenschaften des Ein-Band Hubbard-Modells

Eichhorn, J.

Biologische Kybernetik, Technische Universität Dresden, Dresden/Germany, May 2001 (diplomathesis)

Abstract
Using different modifications of a new variational approach, statical groundstate properties of the one-band Hubbard model such as energy and staggered magnetisation are calculated. By taking into account additional fluctuations, the method ist gradually improved so that a very good description of the energy in one and two dimensions can be achieved. After a detailed discussion of the application in one dimension, extensions for two dimensions are introduced. By use of a modified version of the variational ansatz in particular a description of the quantum phase transition for the magnetisation should be possible.

PostScript [BibTex]

PostScript [BibTex]


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The psychometric function: II. Bootstrap-based confidence intervals and sampling

Wichmann, F., Hill, N.

Perception and Psychophysics, 63 (8), pages: 1314-1329, 2001 (article)

PDF [BibTex]

PDF [BibTex]


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The psychometric function: I. Fitting, sampling and goodness-of-fit

Wichmann, F., Hill, N.

Perception and Psychophysics, 63 (8), pages: 1293-1313, 2001 (article)

Abstract
The psychometric function relates an observer'sperformance to an independent variable, usually some physical quantity of a stimulus in a psychophysical task. This paper, together with its companion paper (Wichmann & Hill, 2001), describes an integrated approach to (1) fitting psychometric functions, (2) assessing the goodness of fit, and (3) providing confidence intervals for the function'sparameters and other estimates derived from them, for the purposes of hypothesis testing. The present paper deals with the first two topics, describing a constrained maximum-likelihood method of parameter estimation and developing several goodness-of-fit tests. Using Monte Carlo simulations, we deal with two specific difficulties that arise when fitting functions to psychophysical data. First, we note that human observers are prone to stimulus-independent errors (or lapses ). We show that failure to account for this can lead to serious biases in estimates of the psychometric function'sparameters and illustrate how the problem may be overcome. Second, we note that psychophysical data sets are usually rather small by the standards required by most of the commonly applied statistical tests. We demonstrate the potential errors of applying traditional X^2 methods to psychophysical data and advocate use of Monte Carlo resampling techniques that do not rely on asymptotic theory. We have made available the software to implement our methods

PDF [BibTex]

PDF [BibTex]


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Unsupervised Segmentation and Classification of Mixtures of Markovian Sources

Seldin, Y., Bejerano, G., Tishby, N.

In The 33rd Symposium on the Interface of Computing Science and Statistics (Interface 2001 - Frontiers in Data Mining and Bioinformatics), pages: 1-15, 33rd Symposium on the Interface of Computing Science and Statistics (Interface - Frontiers in Data Mining and Bioinformatics), 2001 (inproceedings)

Abstract
We describe a novel algorithm for unsupervised segmentation of sequences into alternating Variable Memory Markov sources, first presented in [SBT01]. The algorithm is based on competitive learning between Markov models, when implemented as Prediction Suffix Trees [RST96] using the MDL principle. By applying a model clustering procedure, based on rate distortion theory combined with deterministic annealing, we obtain a hierarchical segmentation of sequences between alternating Markov sources. The method is applied successfully to unsupervised segmentation of multilingual texts into languages where it is able to infer correctly both the number of languages and the language switching points. When applied to protein sequence families (results of the [BSMT01] work), we demonstrate the method‘s ability to identify biologically meaningful sub-sequences within the proteins, which correspond to signatures of important functional sub-units called domains. Our approach to proteins classification (through the obtained signatures) is shown to have both conceptual and practical advantages over the currently used methods.

PDF Web [BibTex]

PDF Web [BibTex]


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Markovian domain fingerprinting: statistical segmentation of protein sequences

Bejerano, G., Seldin, Y., Margalit, H., Tishby, N.

Bioinformatics, 17(10):927-934, 2001 (article)

PDF Web [BibTex]

PDF Web [BibTex]


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Unsupervised Sequence Segmentation by a Mixture of Switching Variable Memory Markov Sources

Seldin, Y., Bejerano, G., Tishby, N.

In In the proceeding of the 18th International Conference on Machine Learning (ICML 2001), pages: 513-520, 18th International Conference on Machine Learning (ICML), 2001 (inproceedings)

Abstract
We present a novel information theoretic algorithm for unsupervised segmentation of sequences into alternating Variable Memory Markov sources. The algorithm is based on competitive learning between Markov models, when implemented as Prediction Suffix Trees (Ron et al., 1996) using the MDL principle. By applying a model clustering procedure, based on rate distortion theory combined with deterministic annealing, we obtain a hierarchical segmentation of sequences between alternating Markov sources. The algorithm seems to be self regulated and automatically avoids over segmentation. The method is applied successfully to unsupervised segmentation of multilingual texts into languages where it is able to infer correctly both the number of languages and the language switching points. When applied to protein sequence families, we demonstrate the method‘s ability to identify biologically meaningful sub-sequences within the proteins, which correspond to important functional sub-units called domains.

PDF [BibTex]

PDF [BibTex]


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Inference Principles and Model Selection

Buhmann, J., Schölkopf, B.

(01301), Dagstuhl Seminar, 2001 (techreport)

Web [BibTex]

Web [BibTex]