Header logo is


2008


no image
BCPy2000

Hill, N., Schreiner, T., Puzicha, C., Farquhar, J.

Workshop "Machine Learning Open-Source Software" at NIPS, December 2008 (talk)

ei

Web [BibTex]

2008


Web [BibTex]


no image
Stereo Matching for Calibrated Cameras without Correspondence

Helmke, U., Hüper, K., Vences, L.

In CDC 2008, pages: 2408-2413, IEEE Service Center, Piscataway, NJ, USA, 47th IEEE Conference on Decision and Control, December 2008 (inproceedings)

Abstract
We study the stereo matching problem for reconstruction of the location of 3D-points on an unknown surface patch from two calibrated identical cameras without using any a priori information about the pointwise correspondences. We assume that camera parameters and the pose between the cameras are known. Our approach follows earlier work for coplanar cameras where a gradient flow algorithm was proposed to match associated Gramians. Here we extend this method by allowing arbitrary poses for the cameras. We introduce an intrinsic Riemannian Newton algorithm that achieves local quadratic convergence rates. A closed form solution is presented, too. The efficiency of both algorithms is demonstrated by numerical experiments.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Joint Kernel Support Estimation for Structured Prediction

Lampert, C., Blaschko, M.

In Proceedings of the NIPS 2008 Workshop on "Structured Input - Structured Output" (NIPS SISO 2008), pages: 1-4, NIPS Workshop on "Structured Input - Structured Output" (NIPS SISO), December 2008 (inproceedings)

Abstract
We present a new technique for structured prediction that works in a hybrid generative/ discriminative way, using a one-class support vector machine to model the joint probability of (input, output)-pairs in a joint reproducing kernel Hilbert space. Compared to discriminative techniques, like conditional random elds or structured out- put SVMs, the proposed method has the advantage that its training time depends only on the number of training examples, not on the size of the label space. Due to its generative aspect, it is also very tolerant against ambiguous, incomplete or incorrect labels. Experiments on realistic data show that our method works eciently and robustly in situations for which discriminative techniques have computational or statistical problems.

ei

PDF Web [BibTex]

PDF Web [BibTex]


no image
A Predictive Model for Imitation Learning in Partially Observable Environments

Boularias, A.

In ICMLA 2008, pages: 83-90, (Editors: Wani, M. A., X.-W. Chen, D. Casasent, L. A. Kurgan, T. Hu, K. Hafeez), IEEE, Piscataway, NJ, USA, Seventh International Conference on Machine Learning and Applications, December 2008 (inproceedings)

Abstract
Learning by imitation has shown to be a powerful paradigm for automated learning in autonomous robots. This paper presents a general framework of learning by imitation for stochastic and partially observable systems. The model is a Predictive Policy Representation (PPR) whose goal is to represent the teacher‘s policies without any reference to states. The model is fully described in terms of actions and observations only. We show how this model can efficiently learn the personal behavior and preferences of an assistive robot user.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Frequent Subgraph Retrieval in Geometric Graph Databases

Nowozin, S., Tsuda, K.

In ICDM 2008, pages: 953-958, (Editors: Giannotti, F. , D. Gunopulos, F. Turini, C. Zaniolo, N. Ramakrishnan, X. Wu), IEEE Computer Society, Los Alamitos, CA, USA, 8th IEEE International Conference on Data Mining, December 2008 (inproceedings)

Abstract
Discovery of knowledge from geometric graph databases is of particular importance in chemistry and biology, because chemical compounds and proteins are represented as graphs with 3D geometric coordinates. In such applications, scientists are not interested in the statistics of the whole database. Instead they need information about a novel drug candidate or protein at hand, represented as a query graph. We propose a polynomial-delay algorithm for geometric frequent subgraph retrieval. It enumerates all subgraphs of a single given query graph which are frequent geometric $epsilon$-subgraphs under the entire class of rigid geometric transformations in a database. By using geometric$epsilon$-subgraphs, we achieve tolerance against variations in geometry. We compare the proposed algorithm to gSpan on chemical compound data, and we show that for a given minimum support the total number of frequent patterns is substantially limited by requiring geometric matching. Although the computation time per pattern is lar ger than for non-geometric graph mining,the total time is within a reasonable level even for small minimum support.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Block Iterative Algorithms for Non-negative Matrix Approximation

Sra, S.

In ICDM 2008, pages: 1037-1042, (Editors: Giannotti, F. , D. Gunopulos, F. Turini, C. Zaniolo, N. Ramakrishnan, X. Wu), IEEE Service Center, Piscataway, NJ, USA, Eighth IEEE International Conference on Data Mining, December 2008 (inproceedings)

Abstract
In this paper we present new algorithms for non-negative matrix approximation (NMA), commonly known as the NMF problem. Our methods improve upon the well-known methods of Lee & Seung~cite{lee00} for both the Frobenius norm as well the Kullback-Leibler divergence versions of the problem. For the latter problem, our results are especially interesting because it seems to have witnessed much lesser algorithmic progress as compared to the Frobenius norm NMA problem. Our algorithms are based on a particular textbf {block-iterative} acceleration technique for EM, which preserves the multiplicative nature of the updates and also ensures monotonicity. Furthermore, our algorithms also naturally apply to the Bregman-divergence NMA algorithms of~cite{suv.nips}. Experimentally, we show that our algorithms outperform the traditional Lee/Seung approach most of the time.

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
Metropolis Algorithms for Representative Subgraph Sampling

Hübler, C., Kriegel, H., Borgwardt, K., Ghahramani, Z.

In pages: 283-292, (Editors: Giannotti, F.), IEEE, Piscataway, NJ, USA, Eighth IEEE International Conference on Data Mining (ICDM '08) , December 2008 (inproceedings)

Abstract
While data mining in chemoinformatics studied graph data with dozens of nodes, systems biology and the Internet are now generating graph data with thousands and millions of nodes. Hence data mining faces the algorithmic challenge of coping with this significant increase in graph size: Classic algorithms for data analysis are often too expensive and too slow on large graphs. While one strategy to overcome this problem is to design novel efficient algorithms, the other is to 'reduce' the size of the large graph by sampling. This is the scope of this paper: We will present novel Metropolis algorithms for sampling a 'representative' small subgraph from the original large graph, with 'representative' describing the requirement that the sample shall preserve crucial graph properties of the original graph. In our experiments, we improve over the pioneering work of Leskovec and Faloutsos (KDD 2006), by producing representative subgraph samples that are both smaller and of higher quality than those produced by other methods from the literature.

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
A Bayesian Approach to Switching Linear Gaussian State-Space Models for Unsupervised Time-Series Segmentation

Chiappa, S.

In ICMLA 2008, pages: 3-9, (Editors: Wani, M. A., X.-W. Chen, D. Casasent, L. Kurgan, T. Hu, K. Hafeez), IEEE Computer Society, Los Alamitos, CA, USA, 7th International Conference on Machine Learning and Applications, December 2008 (inproceedings)

Abstract
Time-series segmentation in the fully unsupervised scenario in which the number of segment-types is a priori unknown is a fundamental problem in many applications. We propose a Bayesian approach to a segmentation model based on the switching linear Gaussian state-space model that enforces a sparse parametrization, such as to use only a small number of a priori available different dynamics to explain the data. This enables us to estimate the number of segment-types within the model, in contrast to previous non-Bayesian approaches where training and comparing several separate models was required. As the resulting model is computationally intractable, we introduce a variational approximation where a reformulation of the problem enables the use of efficient inference algorithms.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Infinite Kernel Learning

Gehler, P., Nowozin, S.

In Proceedings of the NIPS 2008 Workshop on "Kernel Learning: Automatic Selection of Optimal Kernels", pages: 1-4, NIPS Workshop on "Kernel Learning: Automatic Selection of Optimal Kernels" (LK ASOK´08), December 2008 (inproceedings)

Abstract
In this paper we build upon the Multiple Kernel Learning (MKL) framework and in particular on [1] which generalized it to infinitely many kernels. We rewrite the problem in the standard MKL formulation which leads to a Semi-Infinite Program. We devise a new algorithm to solve it (Infinite Kernel Learning, IKL). The IKL algorithm is applicable to both the finite and infinite case and we find it to be faster and more stable than SimpleMKL [2]. Furthermore we present the first large scale comparison of SVMs to MKL on a variety of benchmark datasets, also comparing IKL. The results show two things: a) for many datasets there is no benefit in using MKL/IKL instead of the SVM classifier, thus the flexibility of using more than one kernel seems to be of no use, b) on some datasets IKL yields massive increases in accuracy over SVM/MKL due to the possibility of using a largely increased kernel set. For those cases parameter selection through Cross-Validation or MKL is not applicable.

ei

PDF Web [BibTex]

PDF Web [BibTex]


no image
Logistic Regression for Graph Classification

Shervashidze, N., Tsuda, K.

NIPS Workshop on "Structured Input - Structured Output" (NIPS SISO), December 2008 (talk)

Abstract
In this paper we deal with graph classification. We propose a new algorithm for performing sparse logistic regression for graphs, which is comparable in accuracy with other methods of graph classification and produces probabilistic output in addition. Sparsity is required for the reason of interpretability, which is often necessary in domains such as bioinformatics or chemoinformatics.

ei

Web [BibTex]

Web [BibTex]


no image
New Projected Quasi-Newton Methods with Applications

Sra, S.

Microsoft Research Tech-talk, December 2008 (talk)

Abstract
Box-constrained convex optimization problems are central to several applications in a variety of fields such as statistics, psychometrics, signal processing, medical imaging, and machine learning. Two fundamental examples are the non-negative least squares (NNLS) problem and the non-negative Kullback-Leibler (NNKL) divergence minimization problem. The non-negativity constraints are usually based on an underlying physical restriction, for e.g., when dealing with applications in astronomy, tomography, statistical estimation, or image restoration, the underlying parameters represent physical quantities such as concentration, weight, intensity, or frequency counts and are therefore only interpretable with non-negative values. Several modern optimization methods can be inefficient for simple problems such as NNLS and NNKL as they are really designed to handle far more general and complex problems. In this work we develop two simple quasi-Newton methods for solving box-constrained (differentiable) convex optimization problems that utilize the well-known BFGS and limited memory BFGS updates. We position our method between projected gradient (Rosen, 1960) and projected Newton (Bertsekas, 1982) methods, and prove its convergence under a simple Armijo step-size rule. We illustrate our method by showing applications to: Image deblurring, Positron Emission Tomography (PET) image reconstruction, and Non-negative Matrix Approximation (NMA). On medium sized data we observe performance competitive to established procedures, while for larger data the results are even better.

ei

PDF [BibTex]

PDF [BibTex]


no image
Prediction-Directed Compression of POMDPs

Boularias, A., Izadi, M., Chaib-Draa, B.

In ICMLA 2008, pages: 99-105, (Editors: Wani, M. A., X.-W. Chen, D. Casasent, L. A. Kurgan, T. Hu, K. Hafeez), IEEE, Piscataway, NJ, USA, Seventh International Conference on Machine Learning and Applications, December 2008 (inproceedings)

Abstract
High dimensionality of belief space in partially observable Markov decision processes (POMDPs) is one of the major causes that severely restricts the applicability of this model. Previous studies have demonstrated that the dimensionality of a POMDP can eventually be reduced by transforming it into an equivalent predictive state representation (PSR). In this paper, we address the problem of finding an approximate and compact PSR model corresponding to a given POMDP model. We formulate this problem in an optimization framework. Our algorithm tries to minimize the potential error that missing some core tests may cause. We also present an empirical evaluation on benchmark problems, illustrating the performance of this approach.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Iterative Subgraph Mining for Principal Component Analysis

Saigo, H., Tsuda, K.

In ICDM 2008, pages: 1007-1012, (Editors: Giannotti, F. , D. Gunopulos, F. Turini, C. Zaniolo, N. Ramakrishnan, X. Wu), IEEE Computer Society, Los Alamitos, CA, USA, IEEE International Conference on Data Mining, December 2008 (inproceedings)

Abstract
Graph mining methods enumerate frequent subgraphs efficiently, but they are not necessarily good features for machine learning due to high correlation among features. Thus it makes sense to perform principal component analysis to reduce the dimensionality and create decorrelated features. We present a novel iterative mining algorithm that captures informative patterns corresponding to major entries of top principal components. It repeatedly calls weighted substructure mining where example weights are updated in each iteration. The Lanczos algorithm, a standard algorithm of eigendecomposition, is employed to update the weights. In experiments, our patterns are shown to approximate the principal components obtained by frequent mining.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
A GPU-Based Approach for Real-Time Haptic Rendering of 3D Fluids

Yang, M., Lu, J., Zhou, Z., Safonova, A., Kuchenbecker, K. J.

In Proc. SIGGRAPH Asia Conference, Singapore, December 2008, Oral presentation given by Yang (inproceedings)

hi

[BibTex]

[BibTex]


no image
Modelling contrast discrimination data suggest both the pedestal effect and stochastic resonance to be caused by the same mechanism

Goris, R., Wagemans, J., Wichmann, F.

Journal of Vision, 8(15):1-21, November 2008 (article)

Abstract
Computational models of spatial vision typically make use of a (rectified) linear filter, a nonlinearity and dominant late noise to account for human contrast discrimination data. Linear–nonlinear cascade models predict an improvement in observers' contrast detection performance when low, subthreshold levels of external noise are added (i.e., stochastic resonance). Here, we address the issue whether a single contrast gain-control model of early spatial vision can account for both the pedestal effect, i.e., the improved detectability of a grating in the presence of a low-contrast masking grating, and stochastic resonance. We measured contrast discrimination performance without noise and in both weak and moderate levels of noise. Making use of a full quantitative description of our data with few parameters combined with comprehensive model selection assessments, we show the pedestal effect to be more reduced in the presence of weak noise than in moderate noise. This reduction rules out independent, additive sources of performance improvement and, together with a simulation study, supports the parsimonious explanation that a single mechanism underlies the pedestal effect and stochastic resonance in contrast perception.

ei

Web DOI [BibTex]


no image
Frequent Subgraph Retrieval in Geometric Graph Databases

Nowozin, S., Tsuda, K.

(180), Max-Planck Institute for Biological Cybernetics, Tübingen, Germany, November 2008 (techreport)

Abstract
Discovery of knowledge from geometric graph databases is of particular importance in chemistry and biology, because chemical compounds and proteins are represented as graphs with 3D geometric coordinates. In such applications, scientists are not interested in the statistics of the whole database. Instead they need information about a novel drug candidate or protein at hand, represented as a query graph. We propose a polynomial-delay algorithm for geometric frequent subgraph retrieval. It enumerates all subgraphs of a single given query graph which are frequent geometric epsilon-subgraphs under the entire class of rigid geometric transformations in a database. By using geometric epsilon-subgraphs, we achieve tolerance against variations in geometry. We compare the proposed algorithm to gSpan on chemical compound data, and we show that for a given minimum support the total number of frequent patterns is substantially limited by requiring geometric matching. Although the computation time per pattern is larger than for non-geometric graph mining, the total time is within a reasonable level even for small minimum support.

ei

PDF [BibTex]

PDF [BibTex]


no image
gBoost: A Mathematical Programming Approach to Graph Classification and Regression

Saigo, H., Nowozin, S., Kadowaki, T., Kudo, T., Tsuda, K.

Machine Learning, 75(1):69-89, November 2008 (article)

Abstract
Graph mining methods enumerate frequently appearing subgraph patterns, which can be used as features for subsequent classification or regression. However, frequent patterns are not necessarily informative for the given learning problem. We propose a mathematical programming boosting method (gBoost) that progressively collects informative patterns. Compared to AdaBoost, gBoost can build the prediction rule with fewer iterations. To apply the boosting method to graph data, a branch-and-bound pattern search algorithm is developed based on the DFS code tree. The constructed search space is reused in later iterations to minimize the computation time. Our method can learn more efficiently than the simpler method based on frequent substructure mining, because the output labels are used as an extra information source for pruning the search space. Furthermore, by engineering the mathematical program, a wide range of machine learning problems can be solved without modifying the pattern search algorithm.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


no image
Variational Bayesian Model Selection in Linear Gaussian State-Space based Models

Chiappa, S.

International Workshop on Flexible Modelling: Smoothing and Robustness (FMSR 2008), 2008, pages: 1, November 2008 (poster)

ei

Web [BibTex]

Web [BibTex]


no image
The Effect of Mutual Information on Independent Component Analysis in EEG/MEG Analysis: A Simulation Study

Neumann, A., Grosse-Wentrup, M., Buss, M., Gramann, K.

International Journal of Neuroscience, 118(11):1534-1546, November 2008 (article)

Abstract
Objective: This study investigated the influence of mutual information (MI) on temporal and dipole reconstruction based on independent components (ICs) derived from independent component analysis (ICA). Method: Artificial electroencephalogram (EEG) datasets were created by means of a neural mass model simulating cortical activity of two neural sources within a four-shell spherical head model. Mutual information between neural sources was systematicallyvaried. Results: Increasing spatial error for reconstructed locations of ICs with increasing MI was observed. By contrast, the reconstruction error for the time course of source activity was largely independent of MI but varied systematically with Gaussianity of the sources. Conclusion: Independent component analysis is a viable tool for analyzing the temporal activity of EEG/MEG (magnetoencephalography) sources even if the underlying neural sources are mutually dependent. However, if ICA is used as a preprocessing algorithm for source localization, mutual information between sources introduces a bias in the reconstructed locations of the sources. Significance: Studies using ICA-algorithms based on MI have to be aware of possible errors in the spatial reconstruction of sources if these are coupled with other neural sources.

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
Machine Learning for Motor Skills in Robotics

Peters, J.

K{\"u}nstliche Intelligenz, 2008(4):41-43, November 2008 (article)

Abstract
Autonomous robots that can adapt to novel situations has been a long standing vision of robotics, artificial intelligence, and the cognitive sciences. Early approaches to this goal during the heydays of artificial intelligence research in the late 1980s, however, made it clear that an approach purely based on reasoning or human insights would not be able to model all the perceptuomotor tasks of future robots. Instead, new hope was put in the growing wake of machine learning that promised fully adaptive control algorithms which learn both by observation and trial-and-error. However, to date, learning techniques have yet to fulfill this promise as only few methods manage to scale into the high-dimensional domains of manipulator and humanoid robotics and usually scaling was only achieved in precisely pre-structured domains. We have investigated the ingredients for a general approach to motor skill learning in order to get one step closer towards human-like performance. For doing so, we study two major components for such an approach, i.e., firstly, a theoretically well-founded general approach to representing the required control structures for task representation and execution and, secondly, appropriate learning algorithms which can be applied in this setting.

ei

PDF Web [BibTex]

PDF Web [BibTex]


no image
Kernels, Regularization and Differential Equations

Steinke, F., Schölkopf, B.

Pattern Recognition, 41(11):3271-3286, November 2008 (article)

Abstract
Many common machine learning methods such as Support Vector Machines or Gaussian process inference make use of positive definite kernels, reproducing kernel Hilbert spaces, Gaussian processes, and regularization operators. In this work these objects are presented in a general, unifying framework, and interrelations are highlighted. With this in mind we then show how linear stochastic differential equation models can be incorporated naturally into the kernel framework. And vice versa, many kernel machines can be interpreted in terms of differential equations. We focus especially on ordinary differential equations, also known as dynamical systems, and it is shown that standard kernel inference algorithms are equivalent to Kalman filter methods based on such models. In order not to cloud qualitative insights with heavy mathematical machinery, we restrict ourselves to finite domains, implying that differential equations are treated via their corresponding finite difference equations.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


no image
Probabilistic Inference for Fast Learning in Control

Rasmussen, CE., Deisenroth, MP.

In EWRL 2008, pages: 229-242, (Editors: Girgin, S. , M. Loth, R. Munos, P. Preux, D. Ryabko), Springer, Berlin, Germany, 8th European Workshop on Reinforcement Learning, November 2008 (inproceedings)

Abstract
We provide a novel framework for very fast model-based reinforcement learning in continuous state and action spaces. The framework requires probabilistic models that explicitly characterize their levels of confidence. Within this framework, we use flexible, non-parametric models to describe the world based on previously collected experience. We demonstrate learning on the cart-pole problem in a setting where we provide very limited prior knowledge about the task. Learning progresses rapidly, and a good policy is found after only a hand-full of iterations.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Simultaneous Implicit Surface Reconstruction and Meshing

Giesen, J., Maier, M., Schölkopf, B.

(179), Max-Planck Institute for Biological Cybernetics, Tübingen, Germany, November 2008 (techreport)

Abstract
We investigate an implicit method to compute a piecewise linear representation of a surface from a set of sample points. As implicit surface functions we use the weighted sum of piecewise linear kernel functions. For such a function we can partition Rd in such a way that these functions are linear on the subsets of the partition. For each subset in the partition we can then compute the zero level set of the function exactly as the intersection of a hyperplane with the subset.

ei

PDF [BibTex]

PDF [BibTex]


no image
Policy Learning: A Unified Perspective with Applications in Robotics

Peters, J., Kober, J., Nguyen-Tuong, D.

In EWRL 2008, pages: 220-228, (Editors: Girgin, S. , M. Loth, R. Munos, P. Preux, D. Ryabko), Springer, Berlin, Germany, 8th European Workshop on Reinforcement Learning, November 2008 (inproceedings)

Abstract
Policy Learning approaches are among the best suited methods for high-dimensional, continuous control systems such as anthropomorphic robot arms and humanoid robots. In this paper, we show two contributions: firstly, we show a unified perspective which allows us to derive several policy learning algorithms from a common point of view, i.e, policy gradient algorithms, natural-gradient algorithms and EM-like policy learning. Secondly, we present several applications to both robot motor primitive learning as well as to robot control in task space. Results both from simulation and several different real robots are shown.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Taxonomy Inference Using Kernel Dependence Measures

Blaschko, M., Gretton, A.

(181), Max-Planck Institute for Biological Cybernetics, Tübingen, Germany, November 2008 (techreport)

Abstract
We introduce a family of unsupervised algorithms, numerical taxonomy clustering, to simultaneously cluster data, and to learn a taxonomy that encodes the relationship between the clusters. The algorithms work by maximizing the dependence between the taxonomy and the original data. The resulting taxonomy is a more informative visualization of complex data than simple clustering; in addition, taking into account the relations between different clusters is shown to substantially improve the quality of the clustering, when compared with state-of-the-art algorithms in the literature (both spectral clustering and a previous dependence maximization approach). We demonstrate our algorithm on image and text data.

ei

PDF [BibTex]

PDF [BibTex]


no image
The genome of the simian and human malaria parasite Plasmodium knowlesi

Pain, A., Böhme, U., Berry, A., Mungall, K., Finn, R., Jackson, A., Mourier, T., Mistry, J., Pasini, E., Aslett, M., Balasubrammaniam, S., Borgwardt, K., Brooks, K., Carret, C., Carver, T., Cherevach, I., Chillingworth, T., Clarke, T., Galinski, M., Hall, N., Harper, D., Harris, D., Hauser, H., Ivens, A., Janssen, C., Keane, T., Larke, N., Lapp, S., Marti, M., Moule, S., Meyer, I., Ormond, D., Peters, N., Sanders, M., Sanders, T., Sergeant, T., Simmonds, M., Smith, F., Squares, R., Thurston, S., Tivey, A., Walker, D., White, B., Zuiderwijk, E., Churcher, C., Quail, M., Cowman, A., Turner, C., Rajandream, M., Kocken, C., Thomas, A., Newbold, C., Barrell, B., Berriman, M.

Nature, 455(7214):799-803, October 2008 (article)

Abstract
Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the 'kra' monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia1, 2. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated3, and it has a close phylogenetic relationship to Plasmodium vivax 4, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone5) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome4 and other sequenced Plasmodium genomes6, 7, 8. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs9, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


no image
Learning to Localize Objects with Structured Output Regression

Blaschko, MB., Lampert, CH.

In ECCV 2008, pages: 2-15, (Editors: Forsyth, D. A., P. H.S. Torr, A. Zisserman), Springer, Berlin, Germany, 10th European Conference on Computer Vision, October 2008, Best Student Paper Award (inproceedings)

Abstract
Sliding window classifiers are among the most successful and widely applied techniques for object localization. However, training is typically done in a way that is not specific to the localization task. First a binary classifier is trained using a sample of positive and negative examples, and this classifier is subsequently applied to multiple regions within test images. We propose instead to treat object localization in a principled way by posing it as a problem of predicting structured data: we model the problem not as binary classification, but as the prediction of the bounding box of objects located in images. The use of a joint-kernel framework allows us to formulate the training procedure as a generalization of an SVM, which can be solved efficiently. We further improve computational efficiency by using a branch-and-bound strategy for localization during both training and testing. Experimental evaluation on the PASCAL VOC and TU Darmstadt datasets show that the structured training procedure improves pe rformance over binary training as well as the best previously published scores.

ei

PDF Web DOI Project Page [BibTex]

PDF Web DOI Project Page [BibTex]


no image
Two-Channel Control for Scaled Teleoperation

Son, HI., Lee, DY.

In International Conference on Control, Automation and Systems, pages: 1284-1289, IEEE, Piscataway, NJ, USA, International Conference on Control, Automation and Systems (ICCAS), October 2008 (inproceedings)

Abstract
There is a trade-off between stability and performance in haptic control systems. In this paper, a stability and performance analysis is presented for a scaled teleoperation system in an effort to increase the performance of the system while maintaining the stability. The stability is quantitatively defined as a metric using Llewellynpsilas absolute stability criterion. Position tracking and kinesthetic perception are used as the performance indices. The analysis is carried out using various scaling factors and impedances of human and environment. A two-channel position-position (PP) controller and a two-channel force-position (FP) controller are applied for the analysis and simulation.

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
Mixture Models for Protein Structure Ensembles

Hirsch, M., Habeck, M.

Bioinformatics, 24(19):2184-2192, October 2008 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
Automatic Image Colorization Via Multimodal Predictions

Charpiat, G., Hofmann, M., Schölkopf, B.

In Computer Vision - ECCV 2008, Lecture Notes in Computer Science, Vol. 5304, pages: 126-139, (Editors: DA Forsyth and PHS Torr and A Zisserman), Springer, Berlin, Germany, 10th European Conference on Computer Vision, October 2008 (inproceedings)

Abstract
We aim to color automatically greyscale images, without any manual intervention. The color proposition could then be interactively corrected by user-provided color landmarks if necessary. Automatic colorization is nontrivial since there is usually no one-to-one correspondence between color and local texture. The contribution of our framework is that we deal directly with multimodality and estimate, for each pixel of the image to be colored, the probability distribution of all possible colors, instead of choosing the most probable color at the local level. We also predict the expected variation of color at each pixel, thus defining a nonuniform spatial coherency criterion. We then use graph cuts to maximize the probability of the whole colored image at the global level. We work in the L-a-b color space in order to approximate the human perception of distances between colors, and we use machine learning tools to extract as much information as possible from a dataset of colored examples. The resulting algorithm is fast, designed to be more robust to texture noise, and is above all able to deal with ambiguity, in contrary to previous approaches.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
A BOLD window into brain waves

Balduzzi, D., Riedner, B., Tononi, G.

Proceedings of the National Academy of Sciences of the United States of America, 105(41):15641-15642 , October 2008 (article)

Abstract
The brain is never inactive. Neurons fire at leisurely rates most of the time, even in sleep (1), although occasionally they fire more intensely, for example, when presented with certain stimuli. Coordinated changes in the activity and excitability of many neurons underlie spontaneous fluctuations in the electroencephalogram (EEG), first observed almost a century ago. These fluctuations can be very slow (infraslow oscillations, <0.1 Hz; slow oscillations, <1 Hz; and slow waves or delta waves, 1–4 Hz), intermediate (theta, 4–8 Hz; alpha, 8–12 Hz; and beta, 13–20 Hz), and fast (gamma, >30 Hz). Moreover, slower fluctuations appear to group and modulate faster ones (1, 2). The BOLD signal underlying functional magnetic resonance imaging (fMRI) also exhibits spontaneous fluctuations at the timescale of tens of seconds (infraslow, <0.1 Hz), which occurs at all times, during task-performance as well as during quiet wakefulness, rapid eye movement (REM) sleep, and non-REM sleep (NREM). Although the precise mechanism underlying the BOLD signal is still being investigated (3–5), it is becoming clear that spontaneous BOLD fluctuations are not just noise, but are tied to fluctuations in neural activity. In this issue of PNAS, He et al. (6) have been able to directly investigate the relationship between BOLD fluctuations and fluctuations in the brain's electrical activity in human subjects. He et al. (6) took advantage of the seminal observation by Biswal et al. (7) that spontaneous BOLD fluctuations in regions belonging to the same functional system are strongly correlated. As expected, He et al. saw that fMRI BOLD fluctuations were strongly correlated among regions within the sensorimotor system, but much less between sensorimotor regions and control regions (nonsensorimotor). The twist was that they did the fMRI recordings in subjects who had been implanted with intracranial electrocorticographic (ECoG) electrodes to record regional EEG signals (to localize epileptic foci). In a separate session, He et al. examined correlations in EEG signals between different regions. They found that, just like the BOLD fluctuations, infraslow and slow fluctuations in the EEG signal from sensorimotor-sensorimotor pairs of electrodes were positively correlated, whereas signals from sensorimotor-control pairs were not. Moreover, the correlation persisted across arousal states: in waking, NREM, and REM sleep. Finally, using several statistical approaches, they found a remarkable correspondence between regional correlations in the infraslow BOLD signal and regional correlations in the infraslow-slow EEG signal (<0.5 Hz or 1–4 Hz). Notably, another report has just appeared showing that mirror sites of auditory cortex across the two hemispheres, which show correlated BOLD activity, also show correlated infraslow EEG fluctuations recorded with ECoG electrodes (8). In this case, the correlated fluctuations reflected infraslow changes in EEG power in the gamma range [however, no significant correlations were found for slow ECoG frequencies (1–4 Hz)].

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
Structure of the human voltage-dependent anion channel

Bayrhuber, M., Meins, T., Habeck, M., Becker, S., Giller, K., Villinger, S., Vonrhein, C., Griesinger, C., Zweckstetter, M., Zeth, K.

Proceedings of the National Academy of Sciences of the United States of America, 105(40):15370-15375, October 2008 (article)

Abstract
The voltage-dependent anion channel (VDAC), also known as mitochondrial porin, is the most abundant protein in the mitochondrial outer membrane (MOM). VDAC is the channel known to guide the metabolic flux across the MOM and plays a key role in mitochondrially induced apoptosis. Here, we present the 3D structure of human VDAC1, which was solved conjointly by NMR spectroscopy and x-ray crystallography. Human VDAC1 (hVDAC1) adopts a &amp;#946;-barrel architecture composed of 19 &amp;#946;-strands with an &amp;#945;-helix located horizontally midway within the pore. Bioinformatic analysis indicates that this channel architecture is common to all VDAC proteins and is adopted by the general import pore TOM40 of mammals, which is also located in the MOM.

ei

Web DOI Project Page [BibTex]

Web DOI Project Page [BibTex]


no image
MRI-Based Attenuation Correction for PET/MRI: A Novel Approach Combining Pattern Recognition and Atlas Registration

Hofmann, M., Steinke, F., Scheel, V., Charpiat, G., Farquhar, J., Aschoff, P., Brady, M., Schölkopf, B., Pichler, B.

Journal of Nuclear Medicine, 49(11):1875-1883, October 2008 (article)

Abstract
For quantitative PET information, correction of tissue photon attenuation is mandatory. Generally in conventional PET, the attenuation map is obtained from a transmission scan, which uses a rotating radionuclide source, or from the CT scan in a combined PET/CT scanner. In the case of PET/MRI scanners currently under development, insufficient space for the rotating source exists; the attenuation map can be calculated from the MR image instead. This task is challenging because MR intensities correlate with proton densities and tissue-relaxation properties, rather than with attenuation-related mass density. METHODS: We used a combination of local pattern recognition and atlas registration, which captures global variation of anatomy, to predict pseudo-CT images from a given MR image. These pseudo-CT images were then used for attenuation correction, as the process would be performed in a PET/CT scanner. RESULTS: For human brain scans, we show on a database of 17 MR/CT image pairs that our method reliably enables e stimation of a pseudo-CT image from the MR image alone. On additional datasets of MRI/PET/CT triplets of human brain scans, we compare MRI-based attenuation correction with CT-based correction. Our approach enables PET quantification with a mean error of 3.2% for predefined regions of interest, which we found to be clinically not significant. However, our method is not specific to brain imaging, and we show promising initial results on 1 whole-body animal dataset. CONCLUSION: This method allows reliable MRI-based attenuation correction for human brain scans. Further work is necessary to validate the method for whole-body imaging.

ei

Web DOI Project Page [BibTex]


no image
Infinite Kernel Learning

Gehler, P., Nowozin, S.

(178), Max-Planck Institute for Biological Cybernetics, Tübingen, Germany, October 2008 (techreport)

Abstract
In this paper we consider the problem of automatically learning the kernel from general kernel classes. Specifically we build upon the Multiple Kernel Learning (MKL) framework and in particular on the work of (Argyriou, Hauser, Micchelli, & Pontil, 2006). We will formulate a Semi-Infinite Program (SIP) to solve the problem and devise a new algorithm to solve it (Infinite Kernel Learning, IKL). The IKL algorithm is applicable to both the finite and infinite case and we find it to be faster and more stable than SimpleMKL (Rakotomamonjy, Bach, Canu, & Grandvalet, 2007) for cases of many kernels. In the second part we present the first large scale comparison of SVMs to MKL on a variety of benchmark datasets, also comparing IKL. The results show two things: a) for many datasets there is no benefit in linearly combining kernels with MKL/IKL instead of the SVM classifier, thus the flexibility of using more than one kernel seems to be of no use, b) on some datasets IKL yields impressive increases in accuracy over SVM/MKL due to the possibility of using a largely increased kernel set. In those cases, IKL remains practical, whereas both cross-validation or standard MKL is infeasible.

ei

PDF Web [BibTex]

PDF Web [BibTex]


no image
MR-Based PET Attenuation Correction: Initial Results for Whole Body

Hofmann, M., Steinke, F., Aschoff, P., Lichy, M., Brady, M., Schölkopf, B., Pichler, B.

Medical Imaging Conference, October 2008 (talk)

ei

[BibTex]

[BibTex]


no image
Support Vector Machines and Kernels for Computational Biology

Ben-Hur, A., Ong, C., Sonnenburg, S., Schölkopf, B., Rätsch, G.

PLoS Computational Biology, 4(10: e1000173):1-10, October 2008 (article)

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Nonparametric Independence Tests: Space Partitioning and Kernel Approaches

Gretton, A., Györfi, L.

In ALT08, pages: 183-198, (Editors: Freund, Y. , L. Györfi, G. Turán, T. Zeugmann), Springer, Berlin, Germany, 19th International Conference on Algorithmic Learning Theory (ALT08), October 2008 (inproceedings)

Abstract
Three simple and explicit procedures for testing the independence of two multi-dimensional random variables are described. Two of the associated test statistics (L1, log-likelihood) are defined when the empirical distribution of the variables is restricted to finite partitions. A third test statistic is defined as a kernel-based independence measure. All tests reject the null hypothesis of independence if the test statistics become large. The large deviation and limit distribution properties of all three test statistics are given. Following from these results, distributionfree strong consistent tests of independence are derived, as are asymptotically alpha-level tests. The performance of the tests is evaluated experimentally on benchmark data.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Approximations for Binary Gaussian Process Classification

Nickisch, H., Rasmussen, C.

Journal of Machine Learning Research, 9, pages: 2035-2078, October 2008 (article)

Abstract
We provide a comprehensive overview of many recent algorithms for approximate inference in Gaussian process models for probabilistic binary classification. The relationships between several approaches are elucidated theoretically, and the properties of the different algorithms are corroborated by experimental results. We examine both 1) the quality of the predictive distributions and 2) the suitability of the different marginal likelihood approximations for model selection (selecting hyperparameters) and compare to a gold standard based on MCMC. Interestingly, some methods produce good predictive distributions although their marginal likelihood approximations are poor. Strong conclusions are drawn about the methods: The Expectation Propagation algorithm is almost always the method of choice unless the computational budget is very tight. We also extend existing methods in various ways, and provide unifying code implementing all approaches.

ei

PDF PDF Project Page [BibTex]

PDF PDF Project Page [BibTex]


no image
Nonparametric Indepedence Tests: Space Partitioning and Kernel Approaches

Gretton, A., Györfi, L.

19th International Conference on Algorithmic Learning Theory (ALT08), October 2008 (talk)

ei

PDF Web Project Page [BibTex]

PDF Web Project Page [BibTex]


no image
Interactive images

Schölkopf, B., Toyama, K., Uyttendaele, M.

United States Patent, No 7444015, October 2008 (patent)

ei

[BibTex]

[BibTex]


Thumb xl learningflow
Learning Optical Flow

Sun, D., Roth, S., Lewis, J., Black, M. J.

In European Conf. on Computer Vision, ECCV, 5304, pages: 83-97, LNCS, (Editors: Forsyth, D. and Torr, P. and Zisserman, A.), Springer-Verlag, October 2008 (inproceedings)

Abstract
Assumptions of brightness constancy and spatial smoothness underlie most optical flow estimation methods. In contrast to standard heuristic formulations, we learn a statistical model of both brightness constancy error and the spatial properties of optical flow using image sequences with associated ground truth flow fields. The result is a complete probabilistic model of optical flow. Specifically, the ground truth enables us to model how the assumption of brightness constancy is violated in naturalistic sequences, resulting in a probabilistic model of "brightness inconstancy". We also generalize previous high-order constancy assumptions, such as gradient constancy, by modeling the constancy of responses to various linear filters in a high-order random field framework. These filters are free variables that can be learned from training data. Additionally we study the spatial structure of the optical flow and how motion boundaries are related to image intensity boundaries. Spatial smoothness is modeled using a Steerable Random Field, where spatial derivatives of the optical flow are steered by the image brightness structure. These models provide a statistical motivation for previous methods and enable the learning of all parameters from training data. All proposed models are quantitatively compared on the Middlebury flow dataset.

ps

pdf Springerlink version [BibTex]

pdf Springerlink version [BibTex]


no image
Interactive images

Schölkopf, B., Toyama, K., Uyttendaele, M.

United States Patent, No 7444016, October 2008 (patent)

ei

[BibTex]

[BibTex]


Thumb xl octave
GNU Octave Manual Version 3

John W. Eaton, David Bateman, Soren Hauberg

Network Theory Ltd., October 2008 (book)

ps

Publishers site GNU Octave [BibTex]

Publishers site GNU Octave [BibTex]


no image
Probabilistic Roadmap Method and Real Time Gait Changing Technique Implementation for Travel Time Optimization on a Designed Six-legged Robot

Ahmad, A., Dhang, N.

In pages: 1-5, 39th International Symposium on Robotics (ISR), October 2008 (inproceedings)

Abstract
This paper presents design and development of a six legged robot with a total of 12 degrees of freedom, two in each limb and then an implementation of 'obstacle and undulated terrain-based' probabilistic roadmap method for motion planning of this hexaped which is able to negotiate large undulations as obstacles. The novelty in this implementation is that, it doesnt require the complete view of the robot's configuration space at any given time during the traversal. It generates a map of the area that is in visibility range and finds the best suitable point in that field of view to make it as the next node of the algorithm. A particular category of undulations which are small enough are automatically 'run-over' as a part of the terrain and not considered as obstacles. The traversal between the nodes is optimized by taking the shortest path and the most optimum gait at that instance which the hexaped can assume. This is again a novel approach to have a real time gait changing technique to optimize the travel time. The hexaped limb can swing in the robot's X-Y plane and the lower link of the limb can move in robot's Z plane by an implementation of a four-bar mechanism. A GUI based server 'Yellow Ladybird' eventually which is the name of the hexaped, is made for real time monitoring and communicating to it the final destination co-ordinates.

ps

link (url) [BibTex]


Thumb xl eccv08
The naked truth: Estimating body shape under clothing,

Balan, A., Black, M. J.

In European Conf. on Computer Vision, ECCV, 5304, pages: 15-29, LNCS, (Editors: D. Forsyth and P. Torr and A. Zisserman), Springer-Verlag, Marseilles, France, October 2008 (inproceedings)

Abstract
We propose a method to estimate the detailed 3D shape of a person from images of that person wearing clothing. The approach exploits a model of human body shapes that is learned from a database of over 2000 range scans. We show that the parameters of this shape model can be recovered independently of body pose. We further propose a generalization of the visual hull to account for the fact that observed silhouettes of clothed people do not provide a tight bound on the true 3D shape. With clothed subjects, different poses provide different constraints on the possible underlying 3D body shape. We consequently combine constraints across pose to more accurately estimate 3D body shape in the presence of occluding clothing. Finally we use the recovered 3D shape to estimate the gender of subjects and then employ gender-specific body models to refine our shape estimates. Results on a novel database of thousands of images of clothed and "naked" subjects, as well as sequences from the HumanEva dataset, suggest the method may be accurate enough for biometric shape analysis in video.

ps

pdf pdf with higher quality images Springerlink version YouTube video on applications data slides [BibTex]

pdf pdf with higher quality images Springerlink version YouTube video on applications data slides [BibTex]


Thumb xl screen shot 2012 06 06 at 11.28.04 am
Infinite Kernel Learning

Gehler, P., Nowozin, S.

(178), Max Planck Institute, octomber 2008 (techreport)

ps

project page pdf [BibTex]

project page pdf [BibTex]


no image
Accurate NMR Structures Through Minimization of an Extended Hybrid Energy

Nilges, M., Bernard, A., Bardiaux, B., Malliavin, T., Habeck, M., Rieping, W.

Structure, 16(9):1305-1312, September 2008 (article)

Abstract
The use of generous distance bounds has been the hallmark of NMR structure determination. However, bounds necessitate the estimation of data quality before the calculation, reduce the information content, introduce human bias, and allow for major errors in the structures. Here, we propose a new rapid structure calculation scheme based on Bayesian analysis. The minimization of an extended energy function, including a new type of distance restraint and a term depending on the data quality, results in an estimation of the data quality in addition to coordinates. This allows for the determination of the optimal weight on the experimental information. The resulting structures are of better quality and closer to the X–ray crystal structure of the same molecule. With the new calculation approach, the analysis of discrepancies from the target distances becomes meaningful. The strategy may be useful in other applications—for example, in homology modeling.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


no image
Automatic 3D Face Reconstruction from Single Images or Video

Breuer, P., Kim, K., Kienzle, W., Schölkopf, B., Blanz, V.

In FG 2008, pages: 1-8, IEEE Computer Society, Los Alamitos, CA, USA, 8th IEEE International Conference on Automatic Face and Gesture Recognition, September 2008 (inproceedings)

Abstract
This paper presents a fully automated algorithm for reconstructing a textured 3D model of a face from a single photograph or a raw video stream. The algorithm is based on a combination of Support Vector Machines (SVMs) and a Morphable Model of 3D faces. After SVM face detection, individual facial features are detected using a novel regression- and classification-based approach, and probabilistically plausible configurations of features are selected to produce a list of candidates for several facial feature positions. In the next step, the configurations of feature points are evaluated using a novel criterion that is based on a Morphable Model and a combination of linear projections. To make the algorithm robust with respect to head orientation, this process is iterated while the estimate of pose is refined. Finally, the feature points initialize a model-fitting procedure of the Morphable Model. The result is a highresolution 3D surface model.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


no image
Kernel Measures of Conditional Dependence

Fukumizu, K., Gretton, A., Sun, X., Schölkopf, B.

In Advances in neural information processing systems 20, pages: 489-496, (Editors: JC Platt and D Koller and Y Singer and S Roweis), Curran, Red Hook, NY, USA, 21st Annual Conference on Neural Information Processing Systems (NIPS), September 2008 (inproceedings)

Abstract
We propose a new measure of conditional dependence of random variables, based on normalized cross-covariance operators on reproducing kernel Hilbert spaces. Unlike previous kernel dependence measures, the proposed criterion does not depend on the choice of kernel in the limit of infinite data, for a wide class of kernels. At the same time, it has a straightforward empirical estimate with good convergence behaviour. We discuss the theoretical properties of the measure, and demonstrate its application in experiments.

ei

PDF Web [BibTex]

PDF Web [BibTex]


no image
An Analysis of Inference with the Universum

Sinz, F., Chapelle, O., Agarwal, A., Schölkopf, B.

In Advances in neural information processing systems 20, pages: 1369-1376, (Editors: JC Platt and D Koller and Y Singer and S Roweis), Curran, Red Hook, NY, USA, 21st Annual Conference on Neural Information Processing Systems (NIPS), September 2008 (inproceedings)

Abstract
We study a pattern classification algorithm which has recently been proposed by Vapnik and coworkers. It builds on a new inductive principle which assumes that in addition to positive and negative data, a third class of data is available, termed the Universum. We assay the behavior of the algorithm by establishing links with Fisher discriminant analysis and oriented PCA, as well as with an SVM in a projected subspace (or, equivalently, with a data-dependent reduced kernel). We also provide experimental results.

ei

PDF Web [BibTex]

PDF Web [BibTex]