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2011


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Projected Newton-type methods in machine learning

Schmidt, M., Kim, D., Sra, S.

In Optimization for Machine Learning, pages: 305-330, (Editors: Sra, S., Nowozin, S. and Wright, S. J.), MIT Press, Cambridge, MA, USA, December 2011 (inbook)

Abstract
We consider projected Newton-type methods for solving large-scale optimization problems arising in machine learning and related fields. We first introduce an algorithmic framework for projected Newton-type methods by reviewing a canonical projected (quasi-)Newton method. This method, while conceptually pleasing, has a high computation cost per iteration. Thus, we discuss two variants that are more scalable, namely, two-metric projection and inexact projection methods. Finally, we show how to apply the Newton-type framework to handle non-smooth objectives. Examples are provided throughout the chapter to illustrate machine learning applications of our framework.

PDF Web [BibTex]

2011

PDF Web [BibTex]


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Spatiotemporal mapping of rhythmic activity in the inferior convexity of the macaque prefrontal cortex

Panagiotaropoulos, T., Besserve, M., Crocker, B., Kapoor, V., Tolias, A., Panzeri, S., Logothetis, N.

41(239.15), 41st Annual Meeting of the Society for Neuroscience (Neuroscience), November 2011 (poster)

Abstract
The inferior convexity of the macaque prefrontal cortex (icPFC) is known to be involved in higher order processing of sensory information mediating stimulus selection, attention and working memory. Until now, the vast majority of electrophysiological investigations of the icPFC employed single electrode recordings. As a result, relatively little is known about the spatiotemporal structure of neuronal activity in this cortical area. Here we study in detail the spatiotemporal properties of local field potentials (LFP's) in the icPFC using multi electrode recordings during anesthesia. We computed the LFP-LFP coherence as a function of frequency for thousands of pairs of simultaneously recorded sites anterior to the arcuate and inferior to the principal sulcus. We observed two distinct peaks of coherent oscillatory activity between approximately 4-10 and 15-25 Hz. We then quantified the instantaneous phase of these frequency bands using the Hilbert transform and found robust phase gradients across recording sites. The dependency of the phase on the spatial location reflects the existence of traveling waves of electrical activity in the icPFC. The dominant axis of these traveling waves roughly followed the ventral-dorsal plane. Preliminary results show that repeated visual stimulation with a 10s movie had no dramatic effect on the spatial structure of the traveling waves. Traveling waves of electrical activity in the icPFC could reflect highly organized cortical processing in this area of prefrontal cortex.

Web [BibTex]

Web [BibTex]


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Evaluation and Optimization of MR-Based Attenuation Correction Methods in Combined Brain PET/MR

Mantlik, F., Hofmann, M., Bezrukov, I., Schmidt, H., Kolb, A., Beyer, T., Reimold, M., Schölkopf, B., Pichler, B.

2011(MIC18.M-96), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (poster)

Abstract
Combined PET/MR provides simultaneous molecular and functional information in an anatomical context with unique soft tissue contrast. However, PET/MR does not support direct derivation of attenuation maps of objects and tissues within the measured PET field-of-view. Valid attenuation maps are required for quantitative PET imaging, specifically for scientific brain studies. Therefore, several methods have been proposed for MR-based attenuation correction (MR-AC). Last year, we performed an evaluation of different MR-AC methods, including simple MR thresholding, atlas- and machine learning-based MR-AC. CT-based AC served as gold standard reference. RoIs from 2 anatomic brain atlases with different levels of detail were used for evaluation of correction accuracy. We now extend our evaluation of different MR-AC methods by using an enlarged dataset of 23 patients from the integrated BrainPET/MR (Siemens Healthcare). Further, we analyze options for improving the MR-AC performance in terms of speed and accuracy. Finally, we assess the impact of ignoring BrainPET positioning aids during the course of MR-AC. This extended study confirms the overall prediction accuracy evaluation results of the first evaluation in a larger patient population. Removing datasets affected by metal artifacts from the Atlas-Patch database helped to improve prediction accuracy, although the size of the database was reduced by one half. Significant improvement in prediction speed can be gained at a cost of only slightly reduced accuracy, while further optimizations are still possible.

Web [BibTex]

Web [BibTex]


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Atlas- and Pattern Recognition Based Attenuation Correction on Simultaneous Whole-Body PET/MR

Bezrukov, I., Schmidt, H., Mantlik, F., Schwenzer, N., Hofmann, M., Schölkopf, B., Pichler, B.

2011(MIC18.M-116), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (poster)

Abstract
With the recent availability of clinical whole-body PET/MRI it is possible to evaluate and further develop MR-based attenuation correction methods using simultaneously acquired PET/MR data. We present first results for MRAC on patient data acquired on a fully integrated whole-body PET/MRI (Biograph mMR, Siemens) using our method that applies atlas registration and pattern recognition (ATPR) and compare them to the segmentation-based (SEG) method provided by the manufacturer. The ATPR method makes use of a database of previously aligned pairs of MR-CT volumes to predict attenuation values on a continuous scale. The robustness of the method in presence of MR artifacts was improved by location and size based detection. Lesion to liver and lesion to blood ratios (LLR and LBR) were compared for both methods on 29 iso-contour ROIs in 4 patients. ATPR showed >20% higher LBR and LLR for ROIs in and >7% near osseous tissue. For ROIs in soft tissue, both methods yielded similar ratios with max. differences <6% . For ROIs located within metal artifacts in the MR image, ATPR showed >190% higher LLR and LBR than SEG, where ratios <0.1 occured. For lesions in the neighborhood of artifacts, both ratios were >15% higher for ATPR. If artifacts in MR volumes caused by metal implants are not accounted for in the computation of attenuation maps, they can lead to a strong decrease of lesion to background ratios, even to disappearance of hot spots. Metal implants are likely to occur in the patient collective receiving combined PET/MR scans, of our first 10 patients, 3 had metal implants. Our method is currently able to account for artifacts in the pelvis caused by prostheses. The ability of the ATPR method to account for bone leads to a significant increase of LLR and LBR in osseous tissue, which supports our previous evaluations with combined PET/CT and PET/MR data. For lesions within soft tissue, lesion to background ratios of ATPR and SEG were comparable.

Web [BibTex]

Web [BibTex]


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Retrospective blind motion correction of MR images

Loktyushin, A., Nickisch, H., Pohmann, R.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):498, 28th Annual Scientific Meeting ESMRMB, October 2011 (poster)

Abstract
We present a retrospective method, which significantly reduces ghosting and blurring artifacts due to subject motion. No modifications to the sequence (as in [2, 3]), or the use of additional equipment (as in [1]) are required. Our method iteratively searches for the transformation, that applied to the lines in k-space -- yields the sparsest Laplacian filter output in the spatial domain.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Model based reconstruction for GRE EPI

Blecher, W., Pohmann, R., Schölkopf, B., Seeger, M.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):493-494, 28th Annual Scientific Meeting ESMRMB, October 2011 (poster)

Abstract
Model based nonlinear image reconstruction methods for MRI [3] are at the heart of modern reconstruction techniques (e.g.compressed sensing [6]). In general, models are expressed as a matrix equation where y and u are column vectors of k-space and image data, X model matrix and e independent noise. However, solving the corresponding linear system is not tractable. Therefore fast nonlinear algorithms that minimize a function wrt.the unknown image are the method of choice: In this work a model for gradient echo EPI, is proposed that incorporates N/2 Ghost correction and correction for field inhomogeneities. In addition to reconstruction from full data, the model allows for sparse reconstruction, joint estimation of image, field-, and relaxation-map (like [5,8] for spiral imaging), and improved N/2 ghost correction.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Simultaneous multimodal imaging of patients with bronchial carcinoma in a whole body MR/PET system

Brendle, C., Sauter, A., Schmidt, H., Schraml, C., Bezrukov, I., Martirosian, P., Hetzel, J., Müller, M., Claussen, C., Schwenzer, N., Pfannenberg, C.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):141, 28th annual scientific meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRB), October 2011 (poster)

Abstract
Purpose/Introduction: Lung cancer is among the most frequent cancers (1). Exact determination of tumour extent and viability is crucial for adequate therapy guidance. [18F]-FDG-PET allows accurate staging and the evaluation of therapy response based on glucose metabolism. Diffusion weighted MRI (DWI) is another promising tool for the evaluation of tumour viability (2,3). The aim of the study was the simultaneous PET-MR acquisition in lung cancer patients and correlation of PET and MR data. Subjects and Methods: Seven patients (age 38-73 years, mean 61 years) with highly suspected or known bronchial carcinoma were examined. First, a [18F]-FDG-PET/CT was performed (injected dose: 332-380 MBq). Subsequently, patients were examined at the whole-body MR/PET (Siemens Biograph mMR). The MRI is a modified 3T Verio whole body system with a magnet bore of 60 cm (max. amplitude gradients 45 mT/m, max. slew rate 200 T/m/s). Concerning the PET, the whole-body MR/PET system comprises 56 detector cassettes with a 59.4 cm transaxial and 25.8 cm axial FoV. The following parameters for PET acquisition were applied: 2 bed positions, 6 min/bed with an average uptake time of 124 min after injection (range: 110-143 min). The attenuation correction of PET data was conducted with a segmentation-based method provided by the manufacturer. Acquired PET data were reconstructed with an iterative 3D OSEM algorithm using 3 iterations and 21 subsets, Gaussian filter of 3 mm. DWI MR images were recorded simultaneously for each bed using two b-values (0/800 s/mm2). SUVmax and ADCmin were assessed in a ROI analysis. The following ratios were calculated: SUVmax(tumor)/SUVmean(liver) and ADCmin(tumor)/ADCmean(muscle). Correlation between SUV and ADC was analyzed (Pearson’s correlation). Results: Diagnostic scans could be obtained in all patients with good tumour delineation. The spatial matching of PET and DWI data was very exact. Most tumours showed a pronounced FDG-uptake in combination with decreased ADC values. Significant correlation was found between SUV and ADC ratios (r = -0.87, p = 0.0118). Discussion/Conclusion: Simultaneous MR/PET imaging of lung cancer is feasible. The whole-body MR/PET system can provide complementary information regarding tumour viability and cellularity which could facilitate a more profound tumour characterization. Further studies have to be done to evaluate the importance of these parameters for therapy decisions and monitoring

Web DOI [BibTex]

Web DOI [BibTex]


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JMLR Workshop and Conference Proceedings Volume 19: COLT 2011

Kakade, S., von Luxburg, U.

pages: 834, MIT Press, Cambridge, MA, USA, 24th Annual Conference on Learning Theory , June 2011 (proceedings)

Web [BibTex]

Web [BibTex]


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Statistical Learning Theory: Models, Concepts, and Results

von Luxburg, U., Schölkopf, B.

In Handbook of the History of Logic, Vol. 10: Inductive Logic, 10, pages: 651-706, (Editors: Gabbay, D. M., Hartmann, S. and Woods, J. H.), Elsevier North Holland, Amsterdam, Netherlands, May 2011 (inbook)

Abstract
Statistical learning theory provides the theoretical basis for many of today's machine learning algorithms and is arguably one of the most beautifully developed branches of artificial intelligence in general. It originated in Russia in the 1960s and gained wide popularity in the 1990s following the development of the so-called Support Vector Machine (SVM), which has become a standard tool for pattern recognition in a variety of domains ranging from computer vision to computational biology. Providing the basis of new learning algorithms, however, was not the only motivation for developing statistical learning theory. It was just as much a philosophical one, attempting to answer the question of what it is that allows us to draw valid conclusions from empirical data. In this article we attempt to give a gentle, non-technical overview over the key ideas and insights of statistical learning theory. We do not assume that the reader has a deep background in mathematics, statistics, or computer science. Given the nature of the subject matter, however, some familiarity with mathematical concepts and notations and some intuitive understanding of basic probability is required. There exist many excellent references to more technical surveys of the mathematics of statistical learning theory: the monographs by one of the founders of statistical learning theory ([Vapnik, 1995], [Vapnik, 1998]), a brief overview over statistical learning theory in Section 5 of [Sch{\"o}lkopf and Smola, 2002], more technical overview papers such as [Bousquet et al., 2003], [Mendelson, 2003], [Boucheron et al., 2005], [Herbrich and Williamson, 2002], and the monograph [Devroye et al., 1996].

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Robot Learning

Peters, J., Tedrake, R., Roy, N., Morimoto, J.

In Encyclopedia of Machine Learning, pages: 865-869, Encyclopedia of machine learning, (Editors: Sammut, C. and Webb, G. I.), Springer, New York, NY, USA, January 2011 (inbook)

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Support Vector Machines for finding deletions and short insertions using paired-end short reads

Grimm, D., Hagmann, J., König, D., Weigel, D., Borgwardt, KM.

International Conference on Intelligent Systems for Molecular Biology (ISMB), 2011 (poster)

Web [BibTex]

Web [BibTex]


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What You Expect Is What You Get? Potential Use of Contingent Negative Variation for Passive BCI Systems in Gaze-Based HCI

Ihme, K., Zander, TO.

In Affective Computing and Intelligent Interaction, 6975, pages: 447-456, Lecture Notes in Computer Science, (Editors: D’Mello, S., Graesser, A., Schuller, B. and Martin, J.-C.), Springer, Berlin, Germany, 2011 (inbook)

Abstract
When using eye movements for cursor control in human-computer interaction (HCI), it may be difficult to find an appropriate substitute for the click operation. Most approaches make use of dwell times. However, in this context the so-called Midas-Touch-Problem occurs which means that the system wrongly interprets fixations due to long processing times or spontaneous dwellings of the user as command. Lately it has been shown that brain-computer interface (BCI) input bears good prospects to overcome this problem using imagined hand movements to elicit a selection. The current approach tries to develop this idea further by exploring potential signals for the use in a passive BCI, which would have the advantage that the brain signals used as input are generated automatically without conscious effort of the user. To explore event-related potentials (ERPs) giving information about the user’s intention to select an object, 32-channel electroencephalography (EEG) was recorded from ten participants interacting with a dwell-time-based system. Comparing ERP signals during the dwell time with those occurring during fixations on a neutral cross hair, a sustained negative slow cortical potential at central electrode sites was revealed. This negativity might be a contingent negative variation (CNV) reflecting the participants’ anticipation of the upcoming selection. Offline classification suggests that the CNV is detectable in single trial (mean accuracy 74.9 %). In future, research on the CNV should be accomplished to ensure its stable occurence in human-computer interaction and render possible its use as a potential substitue for the click operation.

DOI [BibTex]

DOI [BibTex]


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Kernel Methods in Bioinformatics

Borgwardt, KM.

In Handbook of Statistical Bioinformatics, pages: 317-334, Springer Handbooks of Computational Statistics ; 3, (Editors: Lu, H.H.-S., Schölkopf, B. and Zhao, H.), Springer, Berlin, Germany, 2011 (inbook)

Abstract
Kernel methods have now witnessed more than a decade of increasing popularity in the bioinformatics community. In this article, we will compactly review this development, examining the areas in which kernel methods have contributed to computational biology and describing the reasons for their success.

PDF DOI [BibTex]

PDF DOI [BibTex]


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Statistical estimation for optimization problems on graphs

Langovoy, M., Sra, S.

Empirical Inference Symposium, 2011 (poster)

[BibTex]


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Cue Combination: Beyond Optimality

Rosas, P., Wichmann, F.

In Sensory Cue Integration, pages: 144-152, (Editors: Trommershäuser, J., Körding, K. and Landy, M. S.), Oxford University Press, 2011 (inbook)

[BibTex]

[BibTex]


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Transfer Learning with Copulas

Lopez-Paz, D., Hernandez-Lobato, J.

Neural Information Processing Systems (NIPS), 2011 (poster)

PDF [BibTex]

PDF [BibTex]

2009


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Clinical PET/MRI-System and Its Applications with MRI Based Attenuation Correction

Kolb, A., Hofmann, M., Sossi, V., Wehrl, H., Sauter, A., Schmid, A., Schlemmer, H., Claussen, C., Pichler, B.

IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC 2009), 2009, pages: 1, October 2009 (poster)

Abstract
Clinical PET/MRI is an emerging new hybrid imaging modality. In addition to provide an unique possibility for multifunctional imaging with temporally and spatially matched data, it also provides anatomical information that can also be used for attenuation correction with no radiation exposure to the subjects. A plus of combined compared to sequential PET and MR imaging is the reduction of total scan time. Here we present our initial experience with a hybrid brain PET/MRI system. Due to the ethical approval patient scans could only be performed after a diagnostic PET/CT. We estimate that in approximately 50% of the cases PET/MRI was of superior diagnostic value compared to PET/CT and was able to provide additional information, such as DTI, spectroscopy and Time Of Flight (TOF) angiography. Here we present 3 patient cases in oncology, a retropharyngeal carcinoma in neurooncology, a relapsing meningioma and in neurology a pharyngeal carcinoma in addition to an infraction of the right hemisphere. For quantitative PET imaging attenuation correction is obligatory. In current PET/MRI setup we used our MRI based atlas method for calculating the mu-map for attenuation correction. MR-based attenuation correction accuracy was quantitatively compared to CT-based PET attenuation correction. Extensive studies to assess potential mutual interferences between PET and MR imaging modalities as well as NEMA measurements have been performed. The first patient studies as well as the phantom tests clearly demonstrated the overall good imaging performance of this first human PET/MRI system. Ongoing work concentrates on advanced normalization and reconstruction methods incorporating count-rate based algorithms.

Web [BibTex]

2009

Web [BibTex]


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A flowering-time gene network model for association analysis in Arabidopsis thaliana

Klotzbücher, K., Kobayashi, Y., Shervashidze, N., Borgwardt, K., Weigel, D.

2009(39):95-96, German Conference on Bioinformatics (GCB '09), September 2009 (poster)

Abstract
In our project we want to determine a set of single nucleotide polymorphisms (SNPs), which have a major effect on the flowering time of Arabidopsis thaliana. Instead of performing a genome-wide association study on all SNPs in the genome of Arabidopsis thaliana, we examine the subset of SNPs from the flowering-time gene network model. We are interested in how the results of the association study vary when using only the ascertained subset of SNPs from the flowering network model, and when additionally using the information encoded by the structure of the network model. The network model is compiled from the literature by manual analysis and contains genes which have been found to affect the flowering time of Arabidopsis thaliana [Far+08; KW07]. The genes in this model are annotated with the SNPs that are located in these genes, or in near proximity to them. In a baseline comparison between the subset of SNPs from the graph and the set of all SNPs, we omit the structural information and calculate the correlation between the individual SNPs and the flowering time phenotype by use of statistical methods. Through this we can determine the subset of SNPs with the highest correlation to the flowering time. In order to further refine this subset, we include the additional information provided by the network structure by conducting a graph-based feature pre-selection. In the further course of this project we want to validate and examine the resulting set of SNPs and their corresponding genes with experimental methods.

PDF Web [BibTex]

PDF Web [BibTex]


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Initial Data from a first PET/MRI-System and its Applications in Clinical Studies Using MRI Based Attenuation Correction

Kolb, A., Hofmann, M., Sossi, V., Wehrl, H., Sauter, A., Schmid, A., Judenhofer, M., Schlemmer, H., Claussen, C., Pichler, B.

2009 World Molecular Imaging Congress, 2009, pages: 1200, September 2009 (poster)

Web [BibTex]

Web [BibTex]


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A High-Speed Object Tracker from Off-the-Shelf Components

Lampert, C., Peters, J.

First IEEE Workshop on Computer Vision for Humanoid Robots in Real Environments at ICCV 2009, 1, pages: 1, September 2009 (poster)

Abstract
We introduce RTblob, an open-source real-time vision system for 3D object detection that achieves over 200 Hz tracking speed with only off-the-shelf hardware component. It allows fast and accurate tracking of colored objects in 3D without expensive and often custom-built hardware, instead making use of the PC graphics cards for the necessary image processing operations.

PDF Web [BibTex]

PDF Web [BibTex]


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Estimating Critical Stimulus Features from Psychophysical Data: The Decision-Image Technique Applied to Human Faces

Macke, J., Wichmann, F.

Journal of Vision, 9(8):31, 9th Annual Meeting of the Vision Sciences Society (VSS), August 2009 (poster)

Abstract
One of the main challenges in the sensory sciences is to identify the stimulus features on which the sensory systems base their computations: they are a pre-requisite for computational models of perception. We describe a technique---decision-images--- for extracting critical stimulus features based on logistic regression. Rather than embedding the stimuli in noise, as is done in classification image analysis, we want to infer the important features directly from physically heterogeneous stimuli. A Decision-image not only defines the critical region-of-interest within a stimulus but is a quantitative template which defines a direction in stimulus space. Decision-images thus enable the development of predictive models, as well as the generation of optimized stimuli for subsequent psychophysical investigations. Here we describe our method and apply it to data from a human face discrimination experiment. We show that decision-images are able to predict human responses not only in terms of overall percent correct but are able to predict, for individual observers, the probabilities with which individual faces are (mis-) classified. We then test the predictions of the models using optimized stimuli. Finally, we discuss possible generalizations of the approach and its relationships with other models.

Web DOI [BibTex]

Web DOI [BibTex]


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Semi-supervised Analysis of Human fMRI Data

Shelton, JA., Blaschko, MB., Lampert, CH., Bartels, A.

Berlin Brain Computer Interface Workshop on Advances in Neurotechnology, 2009, pages: 1, July 2009 (poster)

Abstract
Kernel Canonical Correlation Analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, CCA learns representations tied more closely to underlying process generating the the data and can ignore high-variance noise directions. However, for data where acquisition in a given modality is expensive or otherwise limited, CCA may suffer from small sample effects. We propose to use semisupervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of CCA on human fMRI data, with regression to single and multivariate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of CCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing.

PDF Web [BibTex]

PDF Web [BibTex]


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Text Clustering with Mixture of von Mises-Fisher Distributions

Sra, S., Banerjee, A., Ghosh, J., Dhillon, I.

In Text mining: classification, clustering, and applications, pages: 121-161, Chapman & Hall/CRC data mining and knowledge discovery series, (Editors: Srivastava, A. N. and Sahami, M.), CRC Press, Boca Raton, FL, USA, June 2009 (inbook)

Web DOI [BibTex]

Web DOI [BibTex]


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Data Mining for Biologists

Tsuda, K.

In Biological Data Mining in Protein Interaction Networks, pages: 14-27, (Editors: Li, X. and Ng, S.-K.), Medical Information Science Reference, Hershey, PA, USA, May 2009 (inbook)

Abstract
In this tutorial chapter, we review basics about frequent pattern mining algorithms, including itemset mining, association rule mining and graph mining. These algorithms can find frequently appearing substructures in discrete data. They can discover structural motifs, for example, from mutation data, protein structures and chemical compounds. As they have been primarily used for business data, biological applications are not so common yet, but their potential impact would be large. Recent advances in computers including multicore machines and ever increasing memory capacity support the application of such methods to larger datasets. We explain technical aspects of the algorithms, but do not go into details. Current biological applications are summarized and possible future directions are given.

Web [BibTex]

Web [BibTex]


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Optimization of k-Space Trajectories by Bayesian Experimental Design

Seeger, M., Nickisch, H., Pohmann, R., Schölkopf, B.

17(2627), 17th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2009 (poster)

Abstract
MR image reconstruction from undersampled k-space can be improved by nonlinear denoising estimators since they incorporate statistical prior knowledge about image sparsity. Reconstruction quality depends crucially on the undersampling design (k-space trajectory), in a manner complicated by the nonlinear and signal-dependent characteristics of these methods. We propose an algorithm to assess and optimize k-space trajectories for sparse MRI reconstruction, based on Bayesian experimental design, which is scaled up to full MR images by a novel variational relaxation to iteratively reweighted FFT or gridding computations. Designs are built sequentially by adding phase encodes predicted to be most informative, given the combination of previous measurements with image prior information.

PDF Web [BibTex]

PDF Web [BibTex]


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MR-Based Attenuation Correction for PET/MR

Hofmann, M., Steinke, F., Bezrukov, I., Kolb, A., Aschoff, P., Lichy, M., Erb, M., Nägele, T., Brady, M., Schölkopf, B., Pichler, B.

17(260), 17th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2009 (poster)

Abstract
There has recently been a growing interest in combining PET and MR. Attenuation correction (AC), which accounts for radiation attenuation properties of the tissue, is mandatory for quantitative PET. In the case of PET/MR the attenuation map needs to be determined from the MR image. This is intrinsically difficult as MR intensities are not related to the electron density information of the attenuation map. Using ultra-short echo (UTE) acquisition, atlas registration and machine learning, we present methods that allow prediction of the attenuation map based on the MR image both for brain and whole body imaging.

PDF Web [BibTex]

PDF Web [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)

Web [BibTex]

Web [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.

PDF Web [BibTex]

PDF Web [BibTex]

2004


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S-cones contribute to flicker brightness in human vision

Wehrhahn, C., Hill, NJ., Dillenburger, B.

34(174.12), 34th Annual Meeting of the Society for Neuroscience (Neuroscience), October 2004 (poster)

Abstract
In the retina of primates three cone types sensitive to short, middle and long wavelengths of light convert photons into electrical signals. Many investigators have presented evidence that, in color normal observers, the signals of cones sensitive to short wavelengths of light (S-cones) do not contribute to the perception of brightness of a colored surface when this is alternated with an achromatic reference (flicker brightness). Other studies indicate that humans do use S-cone signals when performing this task. Common to all these studies is the small number of observers, whose performance data are reported. Considerable variability in the occurrence of cone types across observers has been found, but, to our knowledge, no cone counts exist from larger populations of humans. We reinvestigated how much the S-cones contribute to flicker brightness. 76 color normal observers were tested in a simple psychophysical procedure neutral to the cone type occurence (Teufel & Wehrhahn (2000), JOSA A 17: 994 - 1006). The data show that, in the majority of our observers, S-cones provide input with a negative sign - relative to L- and M-cone contribution - in the task in question. There is indeed considerable between-subject variability such that for 20 out of 76 observers the magnitude of this input does not differ significantly from 0. Finally, we argue that the sign of S-cone contribution to flicker brightness perception by an observer cannot be used to infer the relative sign their contributions to the neuronal signals carrying the information leading to the perception of flicker brightness. We conclude that studies which use only a small number of observers may easily fail to find significant evidence for the small but significant population tendency for the S-cones to contribute to flicker brightness. Our results confirm all earlier results and reconcile their contradictory interpretations.

Web [BibTex]

2004

Web [BibTex]


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Advanced Lectures on Machine Learning

Bousquet, O., von Luxburg, U., Rätsch, G.

ML Summer Schools 2003, LNAI 3176, pages: 240, Springer, Berlin, Germany, ML Summer Schools, September 2004 (proceedings)

Abstract
Machine Learning has become a key enabling technology for many engineering applications, investigating scientific questions and theoretical problems alike. To stimulate discussions and to disseminate new results, a summer school series was started in February 2002, the documentation of which is published as LNAI 2600. This book presents revised lectures of two subsequent summer schools held in 2003 in Canberra, Australia, and in T{\"u}bingen, Germany. The tutorial lectures included are devoted to statistical learning theory, unsupervised learning, Bayesian inference, and applications in pattern recognition; they provide in-depth overviews of exciting new developments and contain a large number of references. Graduate students, lecturers, researchers and professionals alike will find this book a useful resource in learning and teaching machine learning.

Web [BibTex]

Web [BibTex]


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Pattern Recognition: 26th DAGM Symposium, LNCS, Vol. 3175

Rasmussen, C., Bülthoff, H., Giese, M., Schölkopf, B.

Proceedings of the 26th Pattern Recognition Symposium (DAGM‘04), pages: 581, Springer, Berlin, Germany, 26th Pattern Recognition Symposium, August 2004 (proceedings)

Web DOI [BibTex]

Web DOI [BibTex]


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Advances in Neural Information Processing Systems 16: Proceedings of the 2003 Conference

Thrun, S., Saul, L., Schölkopf, B.

Proceedings of the Seventeenth Annual Conference on Neural Information Processing Systems (NIPS 2003), pages: 1621, MIT Press, Cambridge, MA, USA, 17th Annual Conference on Neural Information Processing Systems (NIPS), June 2004 (proceedings)

Abstract
The annual Neural Information Processing (NIPS) conference is the flagship meeting on neural computation. It draws a diverse group of attendees—physicists, neuroscientists, mathematicians, statisticians, and computer scientists. The presentations are interdisciplinary, with contributions in algorithms, learning theory, cognitive science, neuroscience, brain imaging, vision, speech and signal processing, reinforcement learning and control, emerging technologies, and applications. Only thirty percent of the papers submitted are accepted for presentation at NIPS, so the quality is exceptionally high. This volume contains all the papers presented at the 2003 conference.

Web [BibTex]

Web [BibTex]


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Distributed Command Execution

Stark, S., Berlin, M.

In BSD Hacks: 100 industrial-strength tips & tools, pages: 152-152, (Editors: Lavigne, Dru), O’Reilly, Beijing, May 2004 (inbook)

Abstract
Often you want to execute a command not only on one computer, but on several at once. For example, you might want to report the current statistics on a group of managed servers or update all of your web servers at once.

[BibTex]

[BibTex]


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Human Classification Behaviour Revisited by Machine Learning

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

7, pages: 134, (Editors: Bülthoff, H.H., H.A. Mallot, R. Ulrich and F.A. Wichmann), 7th T{\"u}bingen Perception Conference (TWK), Febuary 2004 (poster)

Abstract
We attempt to understand visual classication in humans using both psychophysical and machine learning techniques. Frontal views of human faces were used for a gender classication task. Human subjects classied the faces and their gender judgment, reaction time (RT) and condence rating (CR) were recorded for each face. RTs are longer for incorrect answers than for correct ones, high CRs are correlated with low classication errors and RTs decrease as the CRs increase. This results suggest that patterns difcult to classify need more computation by the brain than patterns easy to classify. Hyperplane learning algorithms such as Support Vector Machines (SVM), Relevance Vector Machines (RVM), Prototype learners (Prot) and K-means learners (Kmean) were used on the same classication task using the Principal Components of the texture and oweld representation of the faces. The classication performance of the learning algorithms was estimated using the face database with the true gender of the faces as labels, and also with the gender estimated by the subjects. Kmean yield a classication performance close to humans while SVM and RVM are much better. This surprising behaviour may be due to the fact that humans are trained on real faces during their lifetime while they were here tested on articial ones, while the algorithms were trained and tested on the same set of stimuli. We then correlated the human responses to the distance of the stimuli to the separating hyperplane (SH) of the learning algorithms. On the whole stimuli far from the SH are classied more accurately, faster and with higher condence than those near to the SH if we pool data across all our subjects and stimuli. We also nd three noteworthy results. First, SVMs and RVMs can learn to classify faces using the subjects' labels but perform much better when using the true labels. Second, correlating the average response of humans (classication error, RT or CR) with the distance to the SH on a face-by-face basis using Spearman's rank correlation coefcients shows that RVMs recreate human performance most closely in every respect. Third, the mean-of-class prototype, its popularity in neuroscience notwithstanding, is the least human-like classier in all cases examined.

Web [BibTex]

Web [BibTex]


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m-Alternative-Forced-Choice: Improving the Efficiency of the Method of Constant Stimuli

Jäkel, F., Hill, J., Wichmann, F.

7, pages: 118, 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
We explored several ways to improve the efficiency of measuring psychometric functions without resorting to adaptive procedures. a) The number m of alternatives in an m-alternative-forced-choice (m-AFC) task improves the efficiency of the method of constant stimuli. b) When alternatives are presented simultaneously on different positions on a screen rather than sequentially time can be saved and memory load for the subject can be reduced. c) A touch-screen can further help to make the experimental procedure more intuitive. We tested these ideas in the measurement of contrast sensitivity and compared them to results obtained by sequential presentation in two-interval-forced-choice (2-IFC). Qualitatively all methods (m-AFC and 2-IFC) recovered the characterictic shape of the contrast sensitivity function in three subjects. The m-AFC paradigm only took about 60% of the time of the 2-IFC task. We tried m=2,4,8 and found 4-AFC to give the best model fits and 2-AFC to have the least bias.

Web [BibTex]

Web [BibTex]


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Efficient Approximations for Support Vector Classifiers

Kienzle, W., Franz, M.

7, pages: 68, 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
In face detection, support vector machines (SVM) and neural networks (NN) have been shown to outperform most other classication methods. While both approaches are learning-based, there are distinct advantages and drawbacks to each method: NNs are difcult to design and train but can lead to very small and efcient classiers. In comparison, SVM model selection and training is rather straightforward, and, more importantly, guaranteed to converge to a globally optimal (in the sense of training errors) solution. Unfortunately, SVM classiers tend to have large representations which are inappropriate for time-critical image processing applications. In this work, we examine various existing and new methods for simplifying support vector decision rules. Our goal is to obtain efcient classiers (as with NNs) while keeping the numerical and statistical advantages of SVMs. For a given SVM solution, we compute a cascade of approximations with increasing complexities. Each classier is tuned so that the detection rate is near 100%. At run-time, the rst (simplest) detector is evaluated on the whole image. Then, any subsequent classier is applied only to those positions that have been classied as positive throughout all previous stages. The false positive rate at the end equals that of the last (i.e. most complex) detector. In contrast, since many image positions are discarded by lower-complexity classiers, the average computation time per patch decreases signicantly compared to the time needed for evaluating the highest-complexity classier alone.

Web [BibTex]

Web [BibTex]


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Efficient Approximations for Support Vector Classiers

Kienzle, W., Franz, M.

7, pages: 68, 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
In face detection, support vector machines (SVM) and neural networks (NN) have been shown to outperform most other classication methods. While both approaches are learning-based, there are distinct advantages and drawbacks to each method: NNs are difcult to design and train but can lead to very small and efcient classiers. In comparison, SVM model selection and training is rather straightforward, and, more importantly, guaranteed to converge to a globally optimal (in the sense of training errors) solution. Unfortunately, SVM classiers tend to have large representations which are inappropriate for time-critical image processing applications. In this work, we examine various existing and new methods for simplifying support vector decision rules. Our goal is to obtain efcient classiers (as with NNs) while keeping the numerical and statistical advantages of SVMs. For a given SVM solution, we compute a cascade of approximations with increasing complexities. Each classier is tuned so that the detection rate is near 100%. At run-time, the rst (simplest) detector is evaluated on the whole image. Then, any subsequent classier is applied only to those positions that have been classied as positive throughout all previous stages. The false positive rate at the end equals that of the last (i.e. most complex) detector. In contrast, since many image positions are discarded by lower-complexity classiers, the average computation time per patch decreases signicantly compared to the time needed for evaluating the highest-complexity classier alone.

Web [BibTex]

Web [BibTex]


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Selective Attention to Auditory Stimuli: A Brain-Computer Interface Paradigm

Hill, N., Lal, T., Schröder, M., Hinterberger, T., Birbaumer, N., Schölkopf, B.

7, pages: 102, (Editors: Bülthoff, H.H., H.A. Mallot, R. Ulrich and F.A. Wichmann), 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
During the last 20 years several paradigms for Brain Computer Interfaces have been proposed— see [1] for a recent review. They can be divided into (a) stimulus-driven paradigms, using e.g. event-related potentials or visual evoked potentials from an EEG signal, and (b) patient-driven paradigms such as those that use premotor potentials correlated with imagined action, or slow cortical potentials (e.g. [2]). Our aim is to develop a stimulus-driven paradigm that is applicable in practice to patients. Due to the unreliability of visual perception in “locked-in” patients in the later stages of disorders such as Amyotrophic Lateral Sclerosis, we concentrate on the auditory modality. Speci- cally, we look for the effects, in the EEG signal, of selective attention to one of two concurrent auditory stimulus streams, exploiting the increased activation to attended stimuli that is seen under some circumstances [3]. We present the results of our preliminary experiments on normal subjects. On each of 400 trials, two repetitive stimuli (sequences of drum-beats or other pulsed stimuli) could be heard simultaneously. The two stimuli were distinguishable from one another by their acoustic properties, by their source location (one from a speaker to the left of the subject, the other from the right), and by their differing periodicities. A visual cue preceded the stimulus by 500 msec, indicating which of the two stimuli to attend to, and the subject was instructed to count the beats in the attended stimulus stream. There were up to 6 beats of each stimulus: with equal probability on each trial, all 6 were played, or the fourth was omitted, or the fth was omitted. The 40-channel EEG signals were analyzed ofine to reconstruct which of the streams was attended on each trial. A linear Support Vector Machine [4] was trained on a random subset of the data and tested on the remainder. Results are compared from two types of pre-processing of the signal: for each stimulus stream, (a) EEG signals at the stream's beat periodicity are emphasized, or (b) EEG signals following beats are contrasted with those following missing beats. Both forms of pre-processing show promising results, i.e. that selective attention to one or the other auditory stream yields signals that are classiable signicantly above chance performance. In particular, the second pre-processing was found to be robust to reduction in the number of features used for classication (cf. [5]), helping us to eliminate noise.

PDF Web [BibTex]

PDF Web [BibTex]


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Texture and Haptic Cues in Slant Discrimination: Measuring the Effect of Texture Type

Rosas, P., Wichmann, F., Ernst, M., Wagemans, J.

7, pages: 165, (Editors: Bülthoff, H. H., H. A. Mallot, R. Ulrich, F. A. Wichmann), 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
In a number of models of depth cue combination the depth percept is constructed via a weighted average combination of independent depth estimations. The inuence of each cue in such average depends on the reliability of the source of information [1,5]. In particular, Ernst and Banks (2002) formulate such combination as that of the minimum variance unbiased estimator that can be constructed from the available cues. We have observed systematic differences in slant discrimination performance of human observers when different types of textures were used as cue to slant [4]. If the depth percept behaves as described above, our measurements of the slopes of the psychometric functions provide the predicted weights for the texture cue for the ranked texture types. However, the results for slant discrimination obtained when combining these texture types with object motion results are difcult to reconcile with the minimum variance unbiased estimator model [3]. This apparent failure of such model might be explained by the existence of a coupling of texture and motion, violating the assumption of independence of cues. Hillis, Ernst, Banks, and Landy (2002) [2] have shown that while for between-modality combination the human visual system has access to the single-cue information, for withinmodality combination (visual cues) the single-cue information is lost. This suggests a coupling between visual cues and independence between visual and haptic cues. Then, in the present study we combined the different texture types with haptic information in a slant discrimination task, to test whether in the between-modality condition these cues are combined as predicted by an unbiased, minimum variance estimator model. The measured weights for the cues were consistent with a combination rule sensitive to the reliability of the sources of information, but did not match the predictions of a statistically optimal combination.

PDF Web [BibTex]

PDF Web [BibTex]


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EEG Channel Selection for Brain Computer Interface Systems Based on Support Vector Methods

Schröder, M., Lal, T., Bogdan, M., Schölkopf, B.

7, pages: 50, (Editors: Bülthoff, H.H., H.A. Mallot, R. Ulrich and F.A. Wichmann), 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
A Brain Computer Interface (BCI) system allows the direct interpretation of brain activity patterns (e.g. EEG signals) by a computer. Typical BCI applications comprise spelling aids or environmental control systems supporting paralyzed patients that have lost motor control completely. The design of an EEG based BCI system requires good answers for the problem of selecting useful features during the performance of a mental task as well as for the problem of classifying these features. For the special case of choosing appropriate EEG channels from several available channels, we propose the application of variants of the Support Vector Machine (SVM) for both problems. Although these algorithms do not rely on prior knowledge they can provide more accurate solutions than standard lter methods [1] for feature selection which usually incorporate prior knowledge about neural activity patterns during the performed mental tasks. For judging the importance of features we introduce a new relevance measure and apply it to EEG channels. Although we base the relevance measure for this purpose on the previously introduced algorithms, it does in general not depend on specic algorithms but can be derived using arbitrary combinations of feature selectors and classifiers.

Web [BibTex]

Web [BibTex]


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Learning Depth

Sinz, F., Franz, MO.

pages: 69, (Editors: H.H.Bülthoff, H.A.Mallot, R.Ulrich,F.A.Wichmann), 7th T{\"u}bingen Perception Conference (TWK), February 2004 (poster)

Abstract
The depth of a point in space can be estimated by observing its image position from two different viewpoints. The classical approach to stereo vision calculates depth from the two projection equations which together form a stereocamera model. An unavoidable preparatory work for this solution is a calibration procedure, i.e., estimating the external (position and orientation) and internal (focal length, lens distortions etc.) parameters of each camera from a set of points with known spatial position and their corresponding image positions. This is normally done by iteratively linearizing the single camera models and reestimating their parameters according to the error on the known datapoints. The advantage of the classical method is the maximal usage of prior knowledge about the underlying physical processes and the explicit estimation of meaningful model parameters such as focal length or camera position in space. However, the approach neglects the nonlinear nature of the problem such that the results critically depend on the choice of the initial values for the parameters. In this study, we approach the depth estimation problem from a different point of view by applying generic machine learning algorithms to learn the mapping from image coordinates to spatial position. These algorithms do not require any domain knowledge and are able to learn nonlinear functions by mapping the inputs into a higher-dimensional space. Compared to classical calibration, machine learning methods give a direct solution to the depth estimation problem which means that the values of the stereocamera parameters cannot be extracted from the learned mapping. On the poster, we compare the performance of classical camera calibration to that of different machine learning algorithms such as kernel ridge regression, gaussian processes and support vector regression. Our results indicate that generic learning approaches can lead to higher depth accuracies than classical calibration although no domain knowledge is used.

PDF Web [BibTex]

PDF Web [BibTex]


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Gaussian Processes in Machine Learning

Rasmussen, CE.

In 3176, pages: 63-71, Lecture Notes in Computer Science, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, 2004, Copyright by Springer (inbook)

Abstract
We give a basic introduction to Gaussian Process regression models. We focus on understanding the role of the stochastic process and how it is used to define a distribution over functions. We present the simple equations for incorporating training data and examine how to learn the hyperparameters using the marginal likelihood. We explain the practical advantages of Gaussian Process and end with conclusions and a look at the current trends in GP work.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Neural mechanisms underlying control of a Brain-Computer-Interface (BCI): Simultaneous recording of bold-response and EEG

Hinterberger, T., Wilhelm, B., Veit, R., Weiskopf, N., Lal, TN., Birbaumer, N.

2004 (poster)

Abstract
Brain computer interfaces (BCI) enable humans or animals to communicate or activate external devices without muscle activity using electric brain signals. The BCI Thought Translation Device (TTD) uses learned regulation of slow cortical potentials (SCPs), a skill most people and paralyzed patients can acquire with training periods of several hours up to months. The neurophysiological mechanisms and anatomical sources of SCPs and other event-related brain macro-potentials are well understood, but the neural mechanisms underlying learning of the self-regulation skill for BCI-use are unknown. To uncover the relevant areas of brain activation during regulation of SCPs, the TTD was combined with functional MRI and EEG was recorded inside the MRI scanner in twelve healthy participants who have learned to regulate their SCP with feedback and reinforcement. The results demonstrate activation of specific brain areas during execution of the brain regulation skill: successf! ul control of cortical positivity allowing a person to activate an external device was closely related to an increase of BOLD (blood oxygen level dependent) response in the basal ganglia and frontal premotor deactivation indicating learned regulation of a cortical-striatal loop responsible for local excitation thresholds of cortical assemblies. The data suggest that human users of a BCI learn the regulation of cortical excitation thresholds of large neuronal assemblies as a prerequisite of direct brain communication: the learning of this skill depends critically on an intact and flexible interaction between these cortico-basal ganglia-circuits. Supported by the Deutsche Forschungsgemeinschaft (DFG) and the National Institute of Health (NIH).

[BibTex]

[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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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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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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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]