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7 results (View BibTeX file of all listed publications)

2006

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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]

2006

Shin, H., Tsuda, K. Prediction of Protein Function from Networks 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)

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]

Zhou, D., Schölkopf, B. Discrete Regularization 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)

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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]

Lal, T., Chapelle, O., Schölkopf, B. Combining a Filter Method with SVMs 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)

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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]

Lal, T., Chapelle, O., Weston, J., Elisseeff, A. Embedded methods 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)

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2005

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Support Vector Machines and Kernel Algorithms

Schölkopf, B., Smola, A.

In Encyclopedia of Biostatistics (2nd edition), Vol. 8, 8, pages: 5328-5335, (Editors: P Armitage and T Colton), John Wiley & Sons, NY USA, 2005 (inbook)

[BibTex]

2005

Schölkopf, B., Smola, A. Support Vector Machines and Kernel Algorithms In Encyclopedia of Biostatistics (2nd edition), Vol. 8, 8, pages: 5328-5335, (Editors: P Armitage and T Colton), John Wiley & Sons, NY USA, 2005 (inbook)

[BibTex]

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Visual perception I: Basic principles

Wagemans, J., Wichmann, F., de Beeck, H.

In Handbook of Cognition, pages: 3-47, (Editors: Lamberts, K. , R. Goldstone), Sage, London, 2005 (inbook)

[BibTex]

Wagemans, J., Wichmann, F., de Beeck, H. Visual perception I: Basic principles In Handbook of Cognition, pages: 3-47, (Editors: Lamberts, K. , R. Goldstone), Sage, London, 2005 (inbook)

[BibTex]

2000

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An Introduction to Kernel-Based Learning Algorithms

Müller, K., Mika, S., Rätsch, G., Tsuda, K., Schölkopf, B.

In Handbook of Neural Network Signal Processing, 4, (Editors: Yu Hen Hu and Jang-Neng Hwang), CRC Press, 2000 (inbook)

[BibTex]

2000

Müller, K., Mika, S., Rätsch, G., Tsuda, K., Schölkopf, B. An Introduction to Kernel-Based Learning Algorithms In Handbook of Neural Network Signal Processing, 4, (Editors: Yu Hen Hu and Jang-Neng Hwang), CRC Press, 2000 (inbook)

[BibTex]