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2004


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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)

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PDF [BibTex]

2004


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)

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PDF [BibTex]

PDF [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.

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[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

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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)

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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)

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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.

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PDF PostScript Web [BibTex]

PDF PostScript Web [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.

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PDF [BibTex]

2001


PDF [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)

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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

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PDF [BibTex]

PDF [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)

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PDF Web [BibTex]

PDF Web [BibTex]