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2007


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Gene selection via the BAHSIC family of algorithms

Song, L., Bedo, J., Borgwardt, K., Gretton, A., Smola, A.

Bioinformatics, 23(13: ISMB/ECCB 2007 Conference Proceedings):i490-i498, July 2007 (article)

Abstract
Motivation: Identifying significant genes among thousands of sequences on a microarray is a central challenge for cancer research in bioinformatics. The ultimate goal is to detect the genes that are involved in disease outbreak and progression. A multitude of methods have been proposed for this task of feature selection, yet the selected gene lists differ greatly between different methods. To accomplish biologically meaningful gene selection from microarray data, we have to understand the theoretical connections and the differences between these methods. In this article, we define a kernel-based framework for feature selection based on the Hilbert–Schmidt independence criterion and backward elimination, called BAHSIC. We show that several well-known feature selectors are instances of BAHSIC, thereby clarifying their relationship. Furthermore, by choosing a different kernel, BAHSIC allows us to easily define novel feature selection algorithms. As a further advantage, feature selection via BAHSIC works directly on multiclass problems. Results: In a broad experimental evaluation, the members of the BAHSIC family reach high levels of accuracy and robustness when compared to other feature selection techniques. Experiments show that features selected with a linear kernel provide the best classification performance in general, but if strong non-linearities are present in the data then non-linear kernels can be more suitable.

ei

Web DOI [BibTex]

2007


Web DOI [BibTex]


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Phenotyping of Chondrocytes In Vivo and In Vitro Using cDNA Array Technology

Zien, A., Gebhard, P., Fundel, K., Aigner, T.

Clinical Orthopaedics and Related Research, 460, pages: 226-233, July 2007 (article)

Abstract
The cDNA array technology is a powerful tool to analyze a high number of genes in parallel. We investigated whether large-scale gene expression analysis allows clustering and identification of cellular phenotypes of chondrocytes in different in vivo and in vitro conditions. In 100% of cases, clustering analysis distinguished between in vivo and in vitro samples, suggesting fundamental differences in chondrocytes in situ and in vitro regardless of the culture conditions or disease status. It also allowed us to differentiate between healthy and osteoarthritic cartilage. The clustering also revealed the relative importance of the investigated culturing conditions (stimulation agent, stimulation time, bead/monolayer). We augmented the cluster analysis with a statistical search for genes showing differential expression. The identified genes provided hints to the molecular basis of the differences between the sample classes. Our approach shows the power of modern bioinformatic algorithms for understanding and class ifying chondrocytic phenotypes in vivo and in vitro. Although it does not generate new experimental data per se, it provides valuable information regarding the biology of chondrocytes and may provide tools for diagnosing and staging the osteoarthritic disease process.

ei

DOI [BibTex]

DOI [BibTex]


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Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

Clark, R., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T., Fu, G., Hinds, D., Chen, H., Frazer, K., Huson, D., Schölkopf, B., Nordborg, M., Rätsch, G., Ecker, J., Weigel, D.

Science, 317(5836):338-342, July 2007 (article)

Abstract
The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and ~4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Graph Laplacians and their Convergence on Random Neighborhood Graphs

Hein, M., Audibert, J., von Luxburg, U.

Journal of Machine Learning Research, 8, pages: 1325-1370, June 2007 (article)

Abstract
Given a sample from a probability measure with support on a submanifold in Euclidean space one can construct a neighborhood graph which can be seen as an approximation of the submanifold. The graph Laplacian of such a graph is used in several machine learning methods like semi-supervised learning, dimensionality reduction and clustering. In this paper we determine the pointwise limit of three different graph Laplacians used in the literature as the sample size increases and the neighborhood size approaches zero. We show that for a uniform measure on the submanifold all graph Laplacians have the same limit up to constants. However in the case of a non-uniform measure on the submanifold only the so called random walk graph Laplacian converges to the weighted Laplace-Beltrami operator.

ei

PDF PDF [BibTex]

PDF PDF [BibTex]


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Asymptotic stability of the solution of the M/MB/1 queueing model

Haji, A., Radl, A.

Computers and Mathematics with Applications, 53(9):1411-1420, May 2007 (article)

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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MR Angiography of Dural Arteriovenous Fistulas: Diagnosis and Follow-Up after Treatment Using a Time-Resolved 3D Contrast-Enhanced Technique

Meckel, S., Maier, M., San Millan Ruiz, D., Yilmaz, H., Scheffler, K., Radü, E., Wetzel, S.

American Journal of Neuroradiology, 28(5):877-884, May 2007 (article)

Abstract
BACKGROUND AND PURPOSE: Digital subtraction angiography (DSA) is the method of reference for imaging of dural arteriovenous fistula (DAVF). The goal of this study was to analyze the value of different MR images including 3D contrast-enhanced MR angiography (MRA) with a high temporal resolution in diagnostic and follow-up imaging of DAVFs. MATERIALS AND METHODS: A total of 18 MR/MRA examinations from 14 patients with untreated (n = 9) and/or treated (n = 9) DAVFs were evaluated. Two observers assessed all MR and MRA investigations for signs indicating the presence of a DAVF, for fistula characteristics such as fistula grading, location of fistulous point, and fistula obliteration after treatment. All results were compared with DSA findings. RESULTS: On time-resolved 3D contrast-enhanced (TR 3D) MRA, the side and presence of all patent fistulas (n = 13) were correctly indicated, and no false-positive findings were observed in occluded DAVFs (n = 5). Grading of fistulas with this imaging technique was correct in 77% and 85% of patent fistulas for both readers, respectively. On T2-weighted images, signs indicative of a DAVF were encountered only in fistulas with cortical venous reflux (56%), whereas on 3D time-of-flight (TOF) MRA, most fistulas (88%) were correctly detected. In complete fistula occlusion, false-positive findings were encountered on both T2-weighted images and on TOF MRA images. CONCLUSION: In this study, TR 3D MRA proved reliable in detecting DAVFs and suitable for follow-up imaging. The technique allowed—within limitations—to grade DAVFs. Although 3D TOF MRA can depict signs of DAVFs, its value for follow-up imaging is limited.

ei

Web [BibTex]

Web [BibTex]


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Bayesian Reconstruction of the Density of States

Habeck, M.

Physical Review Letters, 98(20, 200601):1-4, May 2007 (article)

Abstract
A Bayesian framework is developed to reconstruct the density of states from multiple canonical simulations. The framework encompasses the histogram reweighting method of Ferrenberg and Swendsen. The new approach applies to nonparametric as well as parametric models and does not require simulation data to be discretized. It offers a means to assess the precision of the reconstructed density of states and of derived thermodynamic quantities.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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PALMA: mRNA to Genome Alignments using Large Margin Algorithms

Schulze, U., Hepp, B., Ong, C., Rätsch, G.

Bioinformatics, 23(15):1892-1900, May 2007 (article)

Abstract
Motivation: Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to genomic DNA is still a challenging task. Results: We present a novel approach based on large margin learning that combines accurate plice site predictions with common sequence alignment techniques. By solving a convex optimization problem, our algorithm – called PALMA – tunes the parameters of the model such that true alignments score higher than other alignments. We study the accuracy of alignments of mRNAs containing artificially generated micro-exons to genomic DNA. In a carefully designed experiment, we show that our algorithm accurately identifies the intron boundaries as well as boundaries of the optimal local alignment. It outperforms all other methods: for 5702 artificially shortened EST sequences from C. elegans and human it correctly identifies the intron boundaries in all except two cases. The best other method is a recently proposed method called exalin which misaligns 37 of the sequences. Our method also demonstrates robustness to mutations, insertions and deletions, retaining accuracy even at high noise levels. Availability: Datasets for training, evaluation and testing, additional results and a stand-alone alignment tool implemented in C++ and python are available at http://www.fml.mpg.de/raetsch/projects/palma.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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The role of the striatum in adaptation learning: a computational model

Grosse-Wentrup, M., Contreras-Vidal, J.

Biological Cybernetics, 96(4):377-388, April 2007 (article)

Abstract
To investigate the functional role of the striatum in visuo-motor adaptation, we extend the DIRECT-model for visuo-motor reaching movements formulated by Bullock et al.(J Cogn Neurosci 5:408–435,1993) through two parallel loops, each modeling a distinct contribution of the cortico–cerebellar–thalamo–cortical and the cortico–striato–thalamo–cortical networks to visuo-motor adaptation. Based on evidence of Robertson and Miall(Neuroreport 10(5): 1029–1034, 1999), we implement the function of the cortico–cerebellar–thalamo–cortical loop as a module that gradually adapts to small changes in sensorimotor relationships. The cortico–striato–thalamo–cortical loop on the other hand is hypothesized to act as an adaptive search element, guessing new sensorimotor-transformations and reinforcing successful guesses while punishing unsuccessful ones. In a first step, we show that the model reproduces trajectories and error curves of healthy subjects in a two dimensional center-out reaching task with rotated screen cursor visual feedback. In a second step, we disable learning processes in the cortico–striato– thalamo–cortical loop to simulate subjects with Parkinson’s disease (PD), and show that this leads to error curves typical of subjects with PD. We conclude that the results support our hypothesis, i.e., that the role of the cortico–striato–thalamo–cortical loop in visuo-motor adaptation is that of an adaptive search element.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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A robust fetal ECG detection method for abdominal recordings

Martens, SMM., Rabotti, C., Mischi, M., Sluijter, RJ.

Physiological Measurement, 28(4):373-388, April 2007, Martin Black Prize for best paper Physiological Measurement 2007 (article)

Abstract
In this paper, we propose a new method for FECG detection in abdominal recordings. The method consists of a sequential analysis approach, in which the a priori information about the interference signals is used for the detection of the FECG. Our method is evaluated on a set of 20 abdominal recordings from pregnant women with different gestational ages. Its performance in terms of fetal heart rate (FHR) detection success is compared with that of independent component analysis (ICA). The results show that our sequential estimation method outperforms ICA with a FHR detection rate of 85% versus 60% of ICA. The superior performance of our method is especially evident in recordings with a low signal-to-noise ratio (SNR). This indicates that our method is more robust than ICA for FECG detection.

ei

DOI [BibTex]

DOI [BibTex]


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Neighborhood Property based Pattern Selection for Support Vector Machines

Shin, H., Cho, S.

Neural Computation, 19(3):816-855, March 2007 (article)

Abstract
The support vector machine (SVM) has been spotlighted in the machine learning community because of its theoretical soundness and practical performance. When applied to a large data set, however, it requires a large memory and a long time for training. To cope with the practical difficulty, we propose a pattern selection algorithm based on neighborhood properties. The idea is to select only the patterns that are likely to be located near the decision boundary. Those patterns are expected to be more informative than the randomly selected patterns. The experimental results provide promising evidence that it is possible to successfully employ the proposed algorithm ahead of SVM training.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Training a Support Vector Machine in the Primal

Chapelle, O.

Neural Computation, 19(5):1155-1178, March 2007 (article)

Abstract
Most literature on Support Vector Machines (SVMs) concentrate on the dual optimization problem. In this paper, we would like to point out that the primal problem can also be solved efficiently, both for linear and non-linear SVMs, and that there is no reason for ignoring this possibilty. On the contrary, from the primal point of view new families of algorithms for large scale SVM training can be investigated.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning

Rätsch, G., Sonnenburg, S., Srinivasan, J., Witte, H., Müller, K., Sommer, R., Schölkopf, B.

PLoS Computational Biology, 3(2, e20):0313-0322, February 2007 (article)

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Statistical Consistency of Kernel Canonical Correlation Analysis

Fukumizu, K., Bach, F., Gretton, A.

Journal of Machine Learning Research, 8, pages: 361-383, February 2007 (article)

Abstract
While kernel canonical correlation analysis (CCA) has been applied in many contexts, the convergence of finite sample estimates of the associated functions to their population counterparts has not yet been established. This paper gives a mathematical proof of the statistical convergence of kernel CCA, providing a theoretical justification for the method. The proof uses covariance operators defined on reproducing kernel Hilbert spaces, and analyzes the convergence of their empirical estimates of finite rank to their population counterparts, which can have infinite rank. The result also gives a sufficient condition for convergence on the regularization coefficient involved in kernel CCA: this should decrease as n^{-1/3}, where n is the number of data.

ei

PDF [BibTex]

PDF [BibTex]


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Some observations on the pedestal effect

Henning, G., Wichmann, F.

Journal of Vision, 7(1:3):1-15, January 2007 (article)

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

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Cue Combination and the Effect of Horizontal Disparity and Perspective on Stereoacuity

Zalevski, AM., Henning, GB., Hill, NJ.

Spatial Vision, 20(1):107-138, January 2007 (article)

Abstract
Relative depth judgments of vertical lines based on horizontal disparity deteriorate enormously when the lines form part of closed configurations (Westheimer, 1979). In studies showing this effect, perspective was not manipulated and thus produced inconsistency between horizontal disparity and perspective. We show that stereoacuity improves dramatically when perspective and horizontal disparity are made consistent. Observers appear to use unhelpful perspective cues in judging the relative depth of the vertical sides of rectangles in a way not incompatible with a form of cue weighting. However, 95% confidence intervals for the weights derived for cues usually exceed the a-priori [0-1] range.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Classificazione di immagini telerilevate satellitari per agricoltura di precisione

Arnoldi, E., Bruzzone, L., Carlin, L., Pedron, L., Persello, C.

MondoGis: Il Mondo dei Sistemi Informativi Geografici, 63, pages: 13-17, 2007 (article)

ei

[BibTex]

[BibTex]


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Separating convolutive mixtures by pairwise mutual information minimization", IEEE Signal Processing Letters

Zhang, K., Chan, L.

IEEE Signal Processing Letters, 14(12):992-995, 2007 (article)

Abstract
Blind separation of convolutive mixtures by minimizing the mutual information between output sequences can avoid the side effect of temporally whitening the outputs, but it involves the score function difference, whose estimation may be problematic when the data dimension is greater than two. This greatly limits the application of this method. Fortunately, for separating convolutive mixtures, pairwise independence of outputs leads to their mutual independence. As an implementation of this idea, we propose a way to separate convolutive mixtures by enforcing pairwise independence. This approach can be applied to separate convolutive mixtures of a moderate number of sources.

ei

Web [BibTex]