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2016


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Analysis of multiparametric MRI using a semi-supervised random forest framework allows the detection of therapy response in ischemic stroke

Castaneda, S., Katiyar, P., Russo, F., Calaminus, C., Disselhorst, J. A., Ziemann, U., Kohlhofer, U., Quintanilla-Martinez, L., Poli, S., Pichler, B. J.

World Molecular Imaging Conference, 2016 (talk)

link (url) [BibTex]

2016

link (url) [BibTex]


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Multi-view learning on multiparametric PET/MRI quantifies intratumoral heterogeneity and determines therapy efficacy

Katiyar, P., Divine, M. R., Kohlhofer, U., Quintanilla-Martinez, L., Siegemund, M., Pfizenmaier, K., Kontermann, R., Pichler, B. J., Disselhorst, J. A.

World Molecular Imaging Conference, 2016 (talk)

link (url) [BibTex]

link (url) [BibTex]

2015


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Causal Inference for Empirical Time Series Based on the Postulate of Independence of Cause and Mechanism

Besserve, M.

53rd Annual Allerton Conference on Communication, Control, and Computing, September 2015 (talk)

[BibTex]

2015

[BibTex]


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Independence of cause and mechanism in brain networks

Besserve, M.

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

[BibTex]

[BibTex]


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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]

Web link (url) [BibTex]


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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)

[BibTex]

[BibTex]


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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)

[BibTex]

[BibTex]


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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]

link (url) [BibTex]

2008


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BCPy2000

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

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

Web [BibTex]

2008

Web [BibTex]


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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.

Web [BibTex]

Web [BibTex]


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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.

PDF [BibTex]

PDF [BibTex]


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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)

[BibTex]

[BibTex]


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Nonparametric Indepedence Tests: Space Partitioning and Kernel Approaches

Gretton, A., Györfi, L.

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

PDF Web [BibTex]

PDF Web [BibTex]


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Data-driven goodness-of-fit tests

Langovoy, M.

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

Web [BibTex]

Web [BibTex]


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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)

[BibTex]

[BibTex]


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Discovering Common Sequence Variation in Arabidopsis thaliana

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.

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

Web [BibTex]

Web [BibTex]


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Coding Theory in Brain-Computer Interfaces

Martens, SMM.

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

Web [BibTex]

Web [BibTex]


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Motor Skill Learning for Cognitive Robotics

Peters, J.

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.

Web [BibTex]

Web [BibTex]


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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.

PDF Web [BibTex]

PDF Web [BibTex]


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Reinforcement Learning for Robotics

Peters, J.

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

Web [BibTex]

Web [BibTex]


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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.

PDF Web [BibTex]

PDF Web [BibTex]


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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.

Web [BibTex]

Web [BibTex]


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Learning resolved velocity control

Peters, J.

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

Web [BibTex]

Web [BibTex]


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Bayesian methods for protein structure determination

Habeck, M.

Machine Learning in Structural Bioinformatics, April 2008 (talk)

Web [BibTex]

Web [BibTex]

2006


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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.

PDF [BibTex]

2006

PDF [BibTex]


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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)

Web [BibTex]

Web [BibTex]


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Reinforcement Learning by Reward-Weighted Regression

Peters, J.

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

Web [BibTex]

Web [BibTex]


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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.

Web [BibTex]

Web [BibTex]


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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.

Web [BibTex]


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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)

PDF Web [BibTex]

PDF Web [BibTex]


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Semi-Supervised Learning

Zien, A.

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

Web [BibTex]

Web [BibTex]


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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.

[BibTex]

[BibTex]


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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.

PDF Web [BibTex]


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Inferential Structure Determination: Probabilistic determination and validation of NMR structures

Habeck, M.

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

Web [BibTex]

Web [BibTex]


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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.

Web [BibTex]

Web [BibTex]


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Inferential structure determination: Overview and new developments

Habeck, M.

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

Web [BibTex]

Web [BibTex]


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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.

Web [BibTex]

Web [BibTex]


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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.

PDF [BibTex]

PDF [BibTex]


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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.

[BibTex]

[BibTex]


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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.

PDF [BibTex]

PDF [BibTex]