Publications | Empirical Inference - Max Planck Institute for Intelligent Systems

Independence of cause and mechanism in brain networks

Besserve, M.

DALI workshop on Networks: Processes and Causality, April 2015 (talk)

Besserve, M. Independence of cause and mechanism in brain networks DALI workshop on Networks: Processes and Causality, April 2015 (talk)

Information-Theoretic Implications of Classical and Quantum Causal Structures

Chaves, R., Majenz, C., Luft, L., Maciel, T., Janzing, D., Schölkopf, B., Gross, D.

18th Conference on Quantum Information Processing (QIP), 2015 (talk)

Web link (url) [BibTex]

Chaves, R., Majenz, C., Luft, L., Maciel, T., Janzing, D., Schölkopf, B., Gross, D. Information-Theoretic Implications of Classical and Quantum Causal Structures 18th Conference on Quantum Information Processing (QIP), 2015 (talk)

Web link (url) [BibTex]

Assessment of brain tissue damage in the Sub-Acute Stroke Region by Multiparametric Imaging using [89-Zr]-Desferal-EPO-PET/MRI

Castaneda, S. G., Katiyar, P., Russo, F., Disselhorst, J. A., Calaminus, C., Poli, S., Maurer, A., Ziemann, U., Pichler, B. J.

World Molecular Imaging Conference, 2015 (talk)

Castaneda, S. G., Katiyar, P., Russo, F., Disselhorst, J. A., Calaminus, C., Poli, S., Maurer, A., Ziemann, U., Pichler, B. J. Assessment of brain tissue damage in the Sub-Acute Stroke Region by Multiparametric Imaging using [89-Zr]-Desferal-EPO-PET/MRI World Molecular Imaging Conference, 2015 (talk)

Early time point in vivo PET/MR is a promising biomarker for determining efficacy of a novel Db(\alphaEGFR)-scTRAIL fusion protein therapy in a colon cancer model

Divine, M. R., Harant, M., Katiyar, P., Disselhorst, J. A., Bukala, D., Aidone, S., Siegemund, M., Pfizenmaier, K., Kontermann, R., Pichler, B. J.

World Molecular Imaging Conference, 2015 (talk)

Divine, M. R., Harant, M., Katiyar, P., Disselhorst, J. A., Bukala, D., Aidone, S., Siegemund, M., Pfizenmaier, K., Kontermann, R., Pichler, B. J. Early time point in vivo PET/MR is a promising biomarker for determining efficacy of a novel Db(\alphaEGFR)-scTRAIL fusion protein therapy in a colon cancer model World Molecular Imaging Conference, 2015 (talk)

The search for single exoplanet transits in the Kepler light curves

Foreman-Mackey, D., Hogg, D. W., Schölkopf, B.

IAU General Assembly, 22, pages: 2258352, 2015 (talk)

link (url) [BibTex]

Foreman-Mackey, D., Hogg, D. W., Schölkopf, B. The search for single exoplanet transits in the Kepler light curves IAU General Assembly, 22, pages: 2258352, 2015 (talk)

link (url) [BibTex]

2010

Comparative Quantitative Evaluation of MR-Based Attenuation Correction Methods in Combined Brain PET/MR

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

2010(M08-4), 2010 Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC), November 2010 (talk)

Abstract

Combined PET/MR provides at the same time molecular and functional imaging as well as excellent soft tissue contrast. It does not allow one to directly measure the attenuation properties of scanned tissues, despite the fact that accurate attenuation maps are necessary for quantitative PET imaging. Several methods have therefore been proposed for MR-based attenuation correction (MR-AC). So far, they have only been evaluated on data acquired from separate MR and PET scanners. We evaluated several MR-AC methods on data from 10 patients acquired on a combined BrainPET/MR scanner. This allowed the consideration of specific PET/MR issues, such as the RF coil that attenuates and scatters 511 keV gammas. We evaluated simple MR thresholding methods as well as atlas and machine learning-based MR-AC. CT-based AC served as gold standard reference. To comprehensively evaluate the MR-AC accuracy, we used RoIs from 2 anatomic brain atlases with different levels of detail. Visual inspection of the PET images indicated that even the basic FLASH threshold MR-AC may be sufficient for several applications. Using a UTE sequence for bone prediction in MR-based thresholding occasionally led to false prediction of bone tissue inside the brain, causing a significant overestimation of PET activity. Although it yielded a lower mean underestimation of activity, it exhibited the highest variance of all methods. The atlas averaging approach had a smaller mean error, but showed high maximum overestimation on the RoIs of the more detailed atlas. The Nave Bayes and Atlas-Patch MR-AC yielded the smallest variance, and the Atlas-Patch also showed the smallest mean error. In conclusion, Atlas-based AC using only MR information on the BrainPET/MR yields a high level of accuracy that is sufficient for clinical quantitative imaging requirements. The Atlas-Patch approach was superior to alternative atlas-based methods, yielding a quantification error below 10% for all RoIs except very small ones.

2010

Mantlik, F., Hofmann, M., Bezrukov, I., Kolb, A., Beyer, T., Reimold, M., Pichler, B., Schölkopf, B. Comparative Quantitative Evaluation of MR-Based Attenuation Correction Methods in Combined Brain PET/MR 2010(M08-4), 2010 Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC), November 2010 (talk)

Statistical image analysis and percolation theory

Davies, P., Langovoy, M., Wittich, O.

73rd Annual Meeting of the Institute of Mathematical Statistics (IMS), August 2010 (talk)

Abstract

We develop a novel method for detection of signals and reconstruction of images in the presence of random noise. The method uses results from percolation theory. We specifically address the problem of detection of objects of unknown shapes in the case of nonparametric noise. The noise density is unknown and can be heavy-tailed. We view the object detection problem as hypothesis testing for discrete statistical inverse problems. We present an algorithm that allows to detect objects of various shapes in noisy images. We prove results on consistency and algorithmic complexity of our procedures.

Davies, P., Langovoy, M., Wittich, O. Statistical image analysis and percolation theory 73rd Annual Meeting of the Institute of Mathematical Statistics (IMS), August 2010 (talk)

Statistical image analysis and percolation theory

Langovoy, M., Wittich, O.

28th European Meeting of Statisticians (EMS), August 2010 (talk)

Langovoy, M., Wittich, O. Statistical image analysis and percolation theory 28th European Meeting of Statisticians (EMS), August 2010 (talk)

Cooperative Cuts: Graph Cuts with Submodular Edge Weights

Jegelka, S., Bilmes, J.

24th European Conference on Operational Research (EURO XXIV), July 2010 (talk)

Abstract

We introduce cooperative cut, a minimum cut problem whose cost is a submodular function on sets of edges: the cost of an edge that is added to a cut set depends on the edges in the set. Applications are e.g. in probabilistic graphical models and image processing. We prove NP hardness and a polynomial lower bound on the approximation factor, and upper bounds via four approximation algorithms based on different techniques. Our additional heuristics have attractive practical properties, e.g., to rely only on standard min-cut. Both our algorithms and heuristics appear to do well in practice.

Jegelka, S., Bilmes, J. Cooperative Cuts: Graph Cuts with Submodular Edge Weights 24th European Conference on Operational Research (EURO XXIV), July 2010 (talk)

BCI and robotics framework for stroke rehabilitation

Gomez Rodriguez, M., Grosse-Wentrup, M., Hill, J., Peters, J., Schölkopf, B., Gharabaghi, A.

4th International BCI Meeting, June 2010 (talk)

Gomez Rodriguez, M., Grosse-Wentrup, M., Hill, J., Peters, J., Schölkopf, B., Gharabaghi, A. BCI and robotics framework for stroke rehabilitation 4th International BCI Meeting, June 2010 (talk)

Solving Large-Scale Nonnegative Least Squares

Sra, S.

16th Conference of the International Linear Algebra Society (ILAS), June 2010 (talk)

Abstract

We study the fundamental problem of nonnegative least squares. This problem was apparently introduced by Lawson and Hanson [1] under the name NNLS. As is evident from its name, NNLS seeks least-squares solutions that are also nonnegative. Owing to its wide-applicability numerous algorithms have been derived for NNLS, beginning from the active-set approach of Lawson and Han- son [1] leading up to the sophisticated interior-point method of Bellavia et al. [2]. We present a new algorithm for NNLS that combines projected subgradients with the non-monotonic gradient descent idea of Barzilai and Borwein [3]. Our resulting algorithm is called BBSG, and we guarantee its convergence by ex- ploiting properties of NNLS in conjunction with projected subgradients. BBSG is surprisingly simple and scales well to large problems. We substantiate our claims by empirically evaluating BBSG and comparing it with established con- vex solvers and specialized NNLS algorithms. The numerical results suggest that BBSG is a practical method for solving large-scale NNLS problems.

PDF PDF [BibTex]

Sra, S. Solving Large-Scale Nonnegative Least Squares 16th Conference of the International Linear Algebra Society (ILAS), June 2010 (talk)

PDF PDF [BibTex]

Matrix Approximation Problems

Sra, S.

EU Regional School: Rheinisch-Westf{\"a}lische Technische Hochschule Aachen, May 2010 (talk)

PDF AVI [BibTex]

Sra, S. Matrix Approximation Problems EU Regional School: Rheinisch-Westf{\"a}lische Technische Hochschule Aachen, May 2010 (talk)

PDF AVI [BibTex]

BCI2000 and Python

Hill, NJ.

Invited lecture at the 7th International BCI2000 Workshop, Pacific Grove, CA, USA, May 2010 (talk)

Abstract

A tutorial, with exercises, on how to integrate your own Python code with the BCI2000 realtime software package.

Hill, NJ. BCI2000 and Python Invited lecture at the 7th International BCI2000 Workshop, Pacific Grove, CA, USA, May 2010 (talk)

Extending BCI2000 Functionality with Your Own C++ Code

Hill, NJ.

Invited lecture at the 7th International BCI2000 Workshop, Pacific Grove, CA, USA, May 2010 (talk)

Abstract

A tutorial, with exercises, on how to use BCI2000 C++ framework to write your own real-time signal-processing modules.

Hill, NJ. Extending BCI2000 Functionality with Your Own C++ Code Invited lecture at the 7th International BCI2000 Workshop, Pacific Grove, CA, USA, May 2010 (talk)

Machine-Learning Methods for Decoding Intentional Brain States

Hill, NJ.

Symposium "Non-Invasive Brain Computer Interfaces: Current Developments and Applications" (BIOMAG), March 2010 (talk)

Abstract

Brain-computer interfaces (BCI) work by making the user perform a specific mental task, such as imagining moving body parts or performing some other covert mental activity, or attending to a particular stimulus out of an array of options, in order to encode their intention into a measurable brain signal. Signal-processing and machine-learning techniques are then used to decode the measured signal to identify the encoded mental state and hence extract the user&amp;lsquo;s initial intention. The high-noise high-dimensional nature of brain-signals make robust decoding techniques a necessity. Generally, the approach has been to use relatively simple feature extraction techniques, such as template matching and band-power estimation, coupled to simple linear classifiers. This has led to a prevailing view among applied BCI researchers that (sophisticated) machine-learning is irrelevant since it doesn&amp;lsquo;t matter what classifier you use once your features are extracted. Using examples from our own MEG and EEG experiments, I&amp;lsquo;ll demonstrate how machine-learning principles can be applied in order to improve BCI performance, if they are formulated in a domain-specific way. The result is a type of data-driven analysis that is more than just classification, and can be used to find better feature extractors.

Hill, NJ. Machine-Learning Methods for Decoding Intentional Brain States Symposium "Non-Invasive Brain Computer Interfaces: Current Developments and Applications" (BIOMAG), March 2010 (talk)

PAC-Bayesian Analysis in Unsupervised Learning

Seldin, Y.

Foundations and New Trends of PAC Bayesian Learning Workshop, March 2010 (talk)

Seldin, Y. PAC-Bayesian Analysis in Unsupervised Learning Foundations and New Trends of PAC Bayesian Learning Workshop, March 2010 (talk)

Learning Motor Primitives for Robotics

Kober, J., Peters, J.

EVENT Lab: Reinforcement Learning in Robotics and Virtual Reality, January 2010 (talk)

Abstract

The acquisition and self-improvement of novel motor skills is among the most important problems in robotics. Motor primitives offer one of the most promising frameworks for the application of machine learning techniques in this context. Employing the Dynamic Systems Motor primitives originally introduced by Ijspeert et al. (2003), appropriate learning algorithms for a concerted approach of both imitation and reinforcement learning are presented. Using these algorithms new motor skills, i.e., Ball-in-a-Cup, Ball-Paddling and Dart-Throwing, are learned.

Kober, J., Peters, J. Learning Motor Primitives for Robotics EVENT Lab: Reinforcement Learning in Robotics and Virtual Reality, January 2010 (talk)

2008

BCPy2000

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

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

2008

Hill, N., Schreiner, T., Puzicha, C., Farquhar, J. BCPy2000 Workshop "Machine Learning Open-Source Software" at NIPS, December 2008 (talk)

Shervashidze, N., Tsuda, K.

Logistic Regression for Graph Classification

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.

Shervashidze, N., Tsuda, K. Logistic Regression for Graph Classification NIPS Workshop on "Structured Input - Structured Output" (NIPS SISO), December 2008 (talk)

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.

Sra, S. New Projected Quasi-Newton Methods with Applications Microsoft Research Tech-talk, December 2008 (talk)

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)

Hofmann, M., Steinke, F., Aschoff, P., Lichy, M., Brady, M., Schölkopf, B., Pichler, B. MR-Based PET Attenuation Correction: Initial Results for Whole Body Medical Imaging Conference, October 2008 (talk)

Nonparametric Indepedence Tests: Space Partitioning and Kernel Approaches

Gretton, A., Györfi, L.

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

Gretton, A., Györfi, L. Nonparametric Indepedence Tests: Space Partitioning and Kernel Approaches 19th International Conference on Algorithmic Learning Theory (ALT08), October 2008 (talk)

Data-driven goodness-of-fit tests

Langovoy, M.

2008 Barcelona Conference on Asymptotic Statistics (BAS), September 2008 (talk)

Langovoy, M. Data-driven goodness-of-fit tests 2008 Barcelona Conference on Asymptotic Statistics (BAS), September 2008 (talk)

mGene: A Novel Discriminative Gene Finder

Schweikert, G., Zeller, G., Zien, A., Behr, J., Sonnenburg, S., Philips, P., Ong, C., Rätsch, G.

Worm Genomics and Systems Biology meeting, July 2008 (talk)

Schweikert, G., Zeller, G., Zien, A., Behr, J., Sonnenburg, S., Philips, P., Ong, C., Rätsch, G. mGene: A Novel Discriminative Gene Finder Worm Genomics and Systems Biology meeting, July 2008 (talk)

Discovering Common Sequence Variation in Arabidopsis thaliana

16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB), July 2008 (talk)

Rätsch, G., Clark, R., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthman, N., Hu, T., Fu, G., Hinds, D., Cheng, H., Frazer, K., Huson, D., Schölkopf, B., Nordborg, M., Ecker, J., Weigel, D., Schneeberger, K., Bohlen, A. Discovering Common Sequence Variation in Arabidopsis thaliana 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB), July 2008 (talk)

Coding Theory in Brain-Computer Interfaces

Martens, SMM.

Soria Summerschool on Computational Mathematics "Algebraic Coding Theory" (S3CM), July 2008 (talk)

Martens, SMM. Coding Theory in Brain-Computer Interfaces Soria Summerschool on Computational Mathematics "Algebraic Coding Theory" (S3CM), July 2008 (talk)

Motor Skill Learning for Cognitive Robotics

6th International Cognitive Robotics Workshop (CogRob), July 2008 (talk)

Abstract

Autonomous robots that can assist humans in situations of daily life have been a long standing vision of robotics, artificial intelligence, and cognitive sciences. A first step towards this goal is to create robots that can learn tasks triggered by environmental context or higher level instruction. However, learning techniques have yet to live up to this promise as only few methods manage to scale to high-dimensional manipulator or humanoid robots. In this tutorial, we give a general overview on motor skill learning for cognitive robotics using research at ATR, USC, CMU and Max-Planck in order to illustrate the problems in motor skill learning. For doing so, we discuss task-appropriate representations and algorithms for learning robot motor skills. Among the topics are the learning basic movements or motor primitives by imitation and reinforcement learning, learning rhytmic and discrete movements, fast regression methods for learning inverse dynamics and setups for learning task-space policies. Examples on various robots, e.g., SARCOS DB, the SARCOS Master Arm, BDI Little Dog and a Barrett WAM, are shown and include Ball-in-a-Cup, T-Ball, Juggling, Devil-Sticking, Operational Space Control and many others.

Peters, J. Motor Skill Learning for Cognitive Robotics 6th International Cognitive Robotics Workshop (CogRob), July 2008 (talk)

Painless Embeddings of Distributions: the Function Space View (Part 1)

Fukumizu, K., Gretton, A., Smola, A.

25th International Conference on Machine Learning (ICML), July 2008 (talk)

Abstract

This tutorial will give an introduction to the recent understanding and methodology of the kernel method: dealing with higher order statistics by embedding painlessly random variables/probability distributions. In the early days of kernel machines research, the "kernel trick" was considered a useful way of constructing nonlinear algorithms from linear ones. More recently, however, it has become clear that a potentially more far reaching use of kernels is as a linear way of dealing with higher order statistics by embedding distributions in a suitable reproducing kernel Hilbert space (RKHS). Notably, unlike the straightforward expansion of higher order moments or conventional characteristic function approach, the use of kernels or RKHS provides a painless, tractable way of embedding distributions. This line of reasoning leads naturally to the questions: what does it mean to embed a distribution in an RKHS? when is this embedding injective (and thus, when do different distributions have unique mappings)? what implications are there for learning algorithms that make use of these embeddings? This tutorial aims at answering these questions. There are a great variety of applications in machine learning and computer science, which require distribution estimation and/or comparison.

Fukumizu, K., Gretton, A., Smola, A. Painless Embeddings of Distributions: the Function Space View (Part 1) 25th International Conference on Machine Learning (ICML), July 2008 (talk)

Reinforcement Learning for Robotics

8th European Workshop on Reinforcement Learning for Robotics (EWRL), July 2008 (talk)

Peters, J. Reinforcement Learning for Robotics 8th European Workshop on Reinforcement Learning for Robotics (EWRL), July 2008 (talk)

Multi-Classification by Categorical Features via Clustering

Seldin, Y.

25th International Conference on Machine Learning (ICML), June 2008 (talk)

Abstract

We derive a generalization bound for multi-classification schemes based on grid clustering in categorical parameter product spaces. Grid clustering partitions the parameter space in the form of a Cartesian product of partitions for each of the parameters. The derived bound provides a means to evaluate clustering solutions in terms of the generalization power of a built-on classifier. For classification based on a single feature the bound serves to find a globally optimal classification rule. Comparison of the generalization power of individual features can then be used for feature ranking. Our experiments show that in this role the bound is much more precise than mutual information or normalized correlation indices.

Seldin, Y. Multi-Classification by Categorical Features via Clustering 25th International Conference on Machine Learning (ICML), June 2008 (talk)

Thin-Plate Splines Between Riemannian Manifolds

Steinke, F., Hein, M., Schölkopf, B.

Workshop on Geometry and Statistics of Shapes, June 2008 (talk)

Abstract

With the help of differential geometry we describe a framework to define a thin-plate spline like energy for maps between arbitrary Riemannian manifolds. The so-called Eells energy only depends on the intrinsic geometry of the input and output manifold, but not on their respective representation. The energy can then be used for regression between manifolds, we present results for cases where the outputs are rotations, sets of angles, or points on 3D surfaces. In the future we plan to also target regression where the output is an element of "shape space", understood as a Riemannian manifold. One could also further explore the meaning of the Eells energy when applied to diffeomorphisms between shapes, especially with regard to its potential use as a distance measure between shapes that does not depend on the embedding or the parametrisation of the shapes.

Steinke, F., Hein, M., Schölkopf, B. Thin-Plate Splines Between Riemannian Manifolds Workshop on Geometry and Statistics of Shapes, June 2008 (talk)

Learning resolved velocity control

2008 IEEE International Conference on Robotics and Automation (ICRA), May 2008 (talk)

Peters, J. Learning resolved velocity control 2008 IEEE International Conference on Robotics and Automation (ICRA), May 2008 (talk)

Bayesian methods for protein structure determination

Habeck, M.

Machine Learning in Structural Bioinformatics, April 2008 (talk)

Habeck, M. Bayesian methods for protein structure determination Machine Learning in Structural Bioinformatics, April 2008 (talk)

2006

A Kernel Method for the Two-Sample-Problem

Gretton, A., Borgwardt, K., Rasch, M., Schölkopf, B., Smola, A.

20th Annual Conference on Neural Information Processing Systems (NIPS), December 2006 (talk)

Abstract

We propose two statistical tests to determine if two samples are from different distributions. Our test statistic is in both cases the distance between the means of the two samples mapped into a reproducing kernel Hilbert space (RKHS). The first test is based on a large deviation bound for the test statistic, while the second is based on the asymptotic distribution of this statistic. We show that the test statistic can be computed in $O(m^2)$ time. We apply our approach to a variety of problems, including attribute matching for databases using the Hungarian marriage method, where our test performs strongly. We also demonstrate excellent performance when comparing distributions over graphs, for which no alternative tests currently exist.

2006

Gretton, A., Borgwardt, K., Rasch, M., Schölkopf, B., Smola, A. A Kernel Method for the Two-Sample-Problem 20th Annual Conference on Neural Information Processing Systems (NIPS), December 2006 (talk)

Ab-initio gene finding using machine learning

Schweikert, G., Zeller, G., Zien, A., Ong, C., de Bona, F., Sonnenburg, S., Phillips, P., Rätsch, G.

NIPS Workshop on New Problems and Methods in Computational Biology, December 2006 (talk)

Schweikert, G., Zeller, G., Zien, A., Ong, C., de Bona, F., Sonnenburg, S., Phillips, P., Rätsch, G. Ab-initio gene finding using machine learning NIPS Workshop on New Problems and Methods in Computational Biology, December 2006 (talk)

Reinforcement Learning by Reward-Weighted Regression

NIPS Workshop: Towards a New Reinforcement Learning? , December 2006 (talk)

Peters, J. Reinforcement Learning by Reward-Weighted Regression NIPS Workshop: Towards a New Reinforcement Learning? , December 2006 (talk)

Graph boosting for molecular QSAR analysis

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

NIPS Workshop on New Problems and Methods in Computational Biology, December 2006 (talk)

Abstract

We propose a new boosting method that systematically combines graph mining and mathematical programming-based machine learning. Informative and interpretable subgraph features are greedily found by a series of graph mining calls. Due to our mathematical programming formulation, subgraph features and pre-calculated real-valued features are seemlessly integrated. We tested our algorithm on a quantitative structure-activity relationship (QSAR) problem, which is basically a regression problem when given a set of chemical compounds. In benchmark experiments, the prediction accuracy of our method favorably compared with the best results reported on each dataset.

Saigo, H., Kadowaki, T., Kudo, T., Tsuda, K. Graph boosting for molecular QSAR analysis NIPS Workshop on New Problems and Methods in Computational Biology, December 2006 (talk)

Inferring Causal Directions by Evaluating the Complexity of Conditional Distributions

Sun, X., Janzing, D., Schölkopf, B.

NIPS Workshop on Causality and Feature Selection, December 2006 (talk)

Abstract

We propose a new approach to infer the causal structure that has generated the observed statistical dependences among n random variables. The idea is that the factorization of the joint measure of cause and effect into P(cause)P(effect|cause) leads typically to simpler conditionals than non-causal factorizations. To evaluate the complexity of the conditionals we have tried two methods. First, we have compared them to those which maximize the conditional entropy subject to the observed first and second moments since we consider the latter as the simplest conditionals. Second, we have fitted the data with conditional probability measures being exponents of functions in an RKHS space and defined the complexity by a Hilbert-space semi-norm. Such a complexity measure has several properties that are useful for our purpose. We describe some encouraging results with both methods applied to real-world data. Moreover, we have combined constraint-based approaches to causal discovery (i.e., methods using only information on conditional statistical dependences) with our method in order to distinguish between causal hypotheses which are equivalent with respect to the imposed independences. Furthermore, we compare the performance to Bayesian approaches to causal inference.

Sun, X., Janzing, D., Schölkopf, B. Inferring Causal Directions by Evaluating the Complexity of Conditional Distributions NIPS Workshop on Causality and Feature Selection, December 2006 (talk)

Learning Optimal EEG Features Across Time, Frequency and Space

Farquhar, J., Hill, J., Schölkopf, B.

NIPS Workshop on Current Trends in Brain-Computer Interfacing, December 2006 (talk)

Farquhar, J., Hill, J., Schölkopf, B. Learning Optimal EEG Features Across Time, Frequency and Space NIPS Workshop on Current Trends in Brain-Computer Interfacing, December 2006 (talk)

Semi-Supervised Learning

Zien, A.

Advanced Methods in Sequence Analysis Lectures, November 2006 (talk)

Zien, A. Semi-Supervised Learning Advanced Methods in Sequence Analysis Lectures, November 2006 (talk)

A Machine Learning Approach for Determining the PET Attenuation Map from Magnetic Resonance Images

Hofmann, M., Steinke, F., Judenhofer, M., Claussen, C., Schölkopf, B., Pichler, B.

IEEE Medical Imaging Conference, November 2006 (talk)

Abstract

A promising new combination in multimodality imaging is MR-PET, where the high soft tissue contrast of Magnetic Resonance Imaging (MRI) and the functional information of Positron Emission Tomography (PET) are combined. Although many technical problems have recently been solved, it is still an open problem to determine the attenuation map from the available MR scan, as the MR intensities are not directly related to the attenuation values. One standard approach is an atlas registration where the atlas MR image is aligned with the patient MR thus also yielding an attenuation image for the patient. We also propose another approach, which to our knowledge has not been tried before: Using Support Vector Machines we predict the attenuation value directly from the local image information. We train this well-established machine learning algorithm using small image patches. Although both approaches sometimes yielded acceptable results, they also showed their specific shortcomings: The registration often fails with large deformations whereas the prediction approach is problematic when the local image structure is not characteristic enough. However, the failures often do not coincide and integration of both information sources is promising. We therefore developed a combination method extending Support Vector Machines to use not only local image structure but also atlas registered coordinates. We demonstrate the strength of this combination approach on a number of examples.

Hofmann, M., Steinke, F., Judenhofer, M., Claussen, C., Schölkopf, B., Pichler, B. A Machine Learning Approach for Determining the PET Attenuation Map from Magnetic Resonance Images IEEE Medical Imaging Conference, November 2006 (talk)

Semi-Supervised Support Vector Machines and Application to Spam Filtering

Zien, A.

ECML Discovery Challenge Workshop, September 2006 (talk)

Abstract

After introducing the semi-supervised support vector machine (aka TSVM for "transductive SVM"), a few popular training strategies are briefly presented. Then the assumptions underlying semi-supervised learning are reviewed. Finally, two modern TSVM optimization techniques are applied to the spam filtering data sets of the workshop; it is shown that they can achieve excellent results, if the problem of the data being non-iid can be handled properly.

Zien, A. Semi-Supervised Support Vector Machines and Application to Spam Filtering ECML Discovery Challenge Workshop, September 2006 (talk)

Inferential Structure Determination: Probabilistic determination and validation of NMR structures

Habeck, M.

Gordon Research Conference on Computational Aspects of Biomolecular NMR, September 2006 (talk)

Habeck, M. Inferential Structure Determination: Probabilistic determination and validation of NMR structures Gordon Research Conference on Computational Aspects of Biomolecular NMR, September 2006 (talk)

Machine Learning Algorithms for Polymorphism Detection

Schweikert, G., Zeller, G., Clark, R., Ossowski, S., Warthmann, N., Shinn, P., Frazer, K., Ecker, J., Huson, D., Weigel, D., Schölkopf, B., Rätsch, G.

2nd ISCB Student Council Symposium, August 2006 (talk)

Abstract

Analyzing resequencing array data using machine learning, we obtain a genome-wide inventory of polymorphisms in 20 wild strains of Arabidopsis thaliana, including 750,000 single nucleotide poly- morphisms (SNPs) and thousands of highly polymorphic regions and deletions. We thus provide an unprecedented resource for the study of natural variation in plants.

Schweikert, G., Zeller, G., Clark, R., Ossowski, S., Warthmann, N., Shinn, P., Frazer, K., Ecker, J., Huson, D., Weigel, D., Schölkopf, B., Rätsch, G. Machine Learning Algorithms for Polymorphism Detection 2nd ISCB Student Council Symposium, August 2006 (talk)

Inferential structure determination: Overview and new developments

Habeck, M.

Sixth CCPN Annual Conference: Efficient and Rapid Structure Determination by NMR, July 2006 (talk)

Habeck, M. Inferential structure determination: Overview and new developments Sixth CCPN Annual Conference: Efficient and Rapid Structure Determination by NMR, July 2006 (talk)

MCMC inference in (Conditionally) Conjugate Dirichlet Process Gaussian Mixture Models

Rasmussen, C., Görür, D.

ICML Workshop on Learning with Nonparametric Bayesian Methods, June 2006 (talk)

Abstract

We compare the predictive accuracy of the Dirichlet Process Gaussian mixture models using conjugate and conditionally conjugate priors and show that better density models result from using the wider class of priors. We explore several MCMC schemes exploiting conditional conjugacy and show their computational merits on several multidimensional density estimation problems.

Rasmussen, C., Görür, D. MCMC inference in (Conditionally) Conjugate Dirichlet Process Gaussian Mixture Models ICML Workshop on Learning with Nonparametric Bayesian Methods, June 2006 (talk)

Sampling for non-conjugate infinite latent feature models

Görür, D., Rasmussen, C.

(Editors: Bernardo, J. M.), 8th Valencia International Meeting on Bayesian Statistics (ISBA), June 2006 (talk)

Abstract

Latent variable models are powerful tools to model the underlying structure in data. Infinite latent variable models can be defined using Bayesian nonparametrics. Dirichlet process (DP) models constitute an example of infinite latent class models in which each object is assumed to belong to one of the, mutually exclusive, infinitely many classes. Recently, the Indian buffet process (IBP) has been defined as an extension of the DP. IBP is a distribution over sparse binary matrices with infinitely many columns which can be used as a distribution for non-exclusive features. Inference using Markov chain Monte Carlo (MCMC) in conjugate IBP models has been previously described, however requiring conjugacy restricts the use of IBP. We describe an MCMC algorithm for non-conjugate IBP models. Modelling the choice behaviour is an important topic in psychology, economics and related fields. Elimination by Aspects (EBA) is a choice model that assumes each alternative has latent features with associated weights that lead to the observed choice outcomes. We formulate a non-parametric version of EBA by using IBP as the prior over the latent binary features. We infer the features of objects that lead to the choice data by using our sampling scheme for inference.

Görür, D., Rasmussen, C. Sampling for non-conjugate infinite latent feature models (Editors: Bernardo, J. M.), 8th Valencia International Meeting on Bayesian Statistics (ISBA), June 2006 (talk)

An Inventory of Sequence Polymorphisms For Arabidopsis

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

17th International Conference on Arabidopsis Research, April 2006 (talk)

Abstract

We have used high-density oligonucleotide arrays to characterize common sequence variation in 20 wild strains of Arabidopsis thaliana that were chosen for maximal genetic diversity. Both strands of each possible SNP of the 119 Mb reference genome were represented on the arrays, which were hybridized with whole genome, isothermally amplified DNA to minimize ascertainment biases. Using two complementary approaches, a model based algorithm, and a newly developed machine learning method, we identified over 550,000 SNPs with a false discovery rate of ~ 0.03 (average of 1 SNP for every 216 bp of the genome). A heuristic algorithm predicted in addition ~700 highly polymorphic or deleted regions per accession. Over 700 predicted polymorphisms with major functional effects (e.g., premature stop codons, or deletions of coding sequence) were validated by dideoxy sequencing. Using this data set, we provide the first systematic description of the types of genes that harbor major effect polymorphisms in natural populations at moderate allele frequencies. The data also provide an unprecedented resource for the study of genetic variation in an experimentally tractable, multicellular model organism.

Clark, R., Ossowski, S., Schweikert, G., Rätsch, G., Shinn, P., Zeller, G., Warthmann, N., Fu, G., Hinds, D., Chen, H., Frazer, K., Huson, D., Schölkopf, B., Nordborg, M., Ecker, J., Weigel, D. An Inventory of Sequence Polymorphisms For Arabidopsis 17th International Conference on Arabidopsis Research, April 2006 (talk)

Machine Learning and Applications in Biology

Shin, H.

6th Course in Bioinformatics for Molecular Biologist, March 2006 (talk)

Abstract

The emergence of the fields of computational biology and bioinformatics has alleviated the burden of solving many biological problems, saving the time and cost required for experiments and also providing predictions that guide new experiments. Within computational biology, machine learning algorithms have played a central role in dealing with the flood of biological data. The goal of this tutorial is to raise awareness and comprehension of machine learning so that biologists can properly match the task at hand to the corresponding analytical approach. We start by categorizing biological problem settings and introduce the general machine learning schemes that fit best to each or these categories. We then explore representative models in further detail, from traditional statistical models to recent kernel models, presenting several up-to-date research projects in bioinfomatics to exemplify how biological questions can benefit from a machine learning approach. Finally, we discuss how cooperation between biologists and machine learners might be made smoother.

Shin, H. Machine Learning and Applications in Biology 6th Course in Bioinformatics for Molecular Biologist, March 2006 (talk)