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2017


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Improving performance of linear field generation with multi-coil setup by optimizing coils position

Aghaeifar, A., Loktyushin, A., Eschelbach, M., Scheffler, K.

Magnetic Resonance Materials in Physics, Biology and Medicine, 30(Supplement 1):S259, 34th Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB), October 2017 (poster)

ei

link (url) DOI [BibTex]

2017


link (url) DOI [BibTex]


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Estimating B0 inhomogeneities with projection FID navigator readouts

Loktyushin, A., Ehses, P., Schölkopf, B., Scheffler, K.

25th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2017 (poster)

ei

link (url) [BibTex]

link (url) [BibTex]


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Image Quality Improvement by Applying Retrospective Motion Correction on Quantitative Susceptibility Mapping and R2*

Feng, X., Loktyushin, A., Deistung, A., Reichenbach, J.

25th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2017 (poster)

ei

link (url) [BibTex]

link (url) [BibTex]


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Elements of Causal Inference - Foundations and Learning Algorithms

Peters, J., Janzing, D., Schölkopf, B.

Adaptive Computation and Machine Learning Series, The MIT Press, Cambridge, MA, USA, 2017 (book)

ei

PDF [BibTex]

PDF [BibTex]


Thumb xl 9780262036436
Mobile Microrobotics

Sitti, M.

Mobile Microrobotics, The MIT Press, Cambridge, MA, 2017 (book)

Abstract
Progress in micro- and nano-scale science and technology has created a demand for new microsystems for high-impact applications in healthcare, biotechnology, manufacturing, and mobile sensor networks. The new robotics field of microrobotics has emerged to extend our interactions and explorations to sub-millimeter scales. This is the first textbook on micron-scale mobile robotics, introducing the fundamentals of design, analysis, fabrication, and control, and drawing on case studies of existing approaches. The book covers the scaling laws that can be used to determine the dominant forces and effects at the micron scale; models forces acting on microrobots, including surface forces, friction, and viscous drag; and describes such possible microfabrication techniques as photo-lithography, bulk micromachining, and deep reactive ion etching. It presents on-board and remote sensing methods, noting that remote sensors are currently more feasible; studies possible on-board microactuators; discusses self-propulsion methods that use self-generated local gradients and fields or biological cells in liquid environments; and describes remote microrobot actuation methods for use in limited spaces such as inside the human body. It covers possible on-board powering methods, indispensable in future medical and other applications; locomotion methods for robots on surfaces, in liquids, in air, and on fluid-air interfaces; and the challenges of microrobot localization and control, in particular multi-robot control methods for magnetic microrobots. Finally, the book addresses current and future applications, including noninvasive medical diagnosis and treatment, environmental remediation, and scientific tools.

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Mobile Microrobotics By Metin Sitti - Chapter 1 (PDF) link (url) [BibTex]

Mobile Microrobotics By Metin Sitti - Chapter 1 (PDF) link (url) [BibTex]


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New Directions for Learning with Kernels and Gaussian Processes (Dagstuhl Seminar 16481)

Gretton, A., Hennig, P., Rasmussen, C., Schölkopf, B.

Dagstuhl Reports, 6(11):142-167, 2017 (book)

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DOI [BibTex]

DOI [BibTex]


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Generalized phase locking analysis of electrophysiology data

Safavi, S., Panagiotaropoulos, T., Kapoor, V., Logothetis, N. K., Besserve, M.

ESI Systems Neuroscience Conference (ESI-SyNC 2017): Principles of Structural and Functional Connectivity, 2017 (poster)

ei

[BibTex]

[BibTex]

2009


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Machine Learning for Brain-Computer Interfaces

Hill, NJ.

Mini-Symposia on Assistive Machine Learning for People with Disabilities at NIPS (AMD), December 2009 (talk)

Abstract
Brain-computer interfaces (BCI) aim to be the ultimate in assistive technology: decoding a user‘s intentions directly from brain signals without involving any muscles or peripheral nerves. Thus, some classes of BCI potentially offer hope for users with even the most extreme cases of paralysis, such as in late-stage Amyotrophic Lateral Sclerosis, where nothing else currently allows communication of any kind. Other lines in BCI research aim to restore lost motor function in as natural a way as possible, reconnecting and in some cases re-training motor-cortical areas to control prosthetic, or previously paretic, limbs. Research and development are progressing on both invasive and non-invasive fronts, although BCI has yet to make a breakthrough to widespread clinical application. The high-noise high-dimensional nature of brain-signals, particularly in non-invasive approaches and in patient populations, 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‘t matter what classifier you use once you‘ve done your preprocessing right and extracted the right features." I shall show a few examples of how this runs counter to both the empirical reality and the spirit of what needs to be done to bring BCI into clinical application. Along the way I‘ll highlight some of the interesting problems that remain open for machine-learners.

ei

PDF Web Web [BibTex]

2009


PDF Web Web [BibTex]


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PAC-Bayesian Approach to Formulation of Clustering Objectives

Seldin, Y.

NIPS Workshop on "Clustering: Science or Art? Towards Principled Approaches", December 2009 (talk)

Abstract
Clustering is a widely used tool for exploratory data analysis. However, the theoretical understanding of clustering is very limited. We still do not have a well-founded answer to the seemingly simple question of "how many clusters are present in the data?", and furthermore a formal comparison of clusterings based on different optimization objectives is far beyond our abilities. The lack of good theoretical support gives rise to multiple heuristics that confuse the practitioners and stall development of the field. We suggest that the ill-posed nature of clustering problems is caused by the fact that clustering is often taken out of its subsequent application context. We argue that one does not cluster the data just for the sake of clustering it, but rather to facilitate the solution of some higher level task. By evaluation of the clustering‘s contribution to the solution of the higher level task it is possible to compare different clusterings, even those obtained by different optimization objectives. In the preceding work it was shown that such an approach can be applied to evaluation and design of co-clustering solutions. Here we suggest that this approach can be extended to other settings, where clustering is applied.

ei

PDF Web Web [BibTex]

PDF Web Web [BibTex]


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Semi-supervised Kernel Canonical Correlation Analysis of Human Functional Magnetic Resonance Imaging Data

Shelton, JA.

Women in Machine Learning Workshop (WiML), December 2009 (talk)

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

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Event-Related Potentials in Brain-Computer Interfacing

Hill, NJ.

Invited lecture on the bachelor & masters course "Introduction to Brain-Computer Interfacing", October 2009 (talk)

Abstract
An introduction to event-related potentials with specific reference to their use in brain-computer interfacing applications and research.

ei

PDF [BibTex]

PDF [BibTex]


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BCI2000 and Python

Hill, NJ.

Invited lecture at the 5th International BCI2000 Workshop, October 2009 (talk)

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

ei

PDF [BibTex]

PDF [BibTex]


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Implementing a Signal Processing Filter in BCI2000 Using C++

Hill, NJ., Mellinger, J.

Invited lecture at the 5th International BCI2000 Workshop, October 2009 (talk)

Abstract
This tutorial shows how the functionality of the BCI2000 software package can be extended with one‘s own code, using BCI2000‘s C++ API.

ei

PDF [BibTex]

PDF [BibTex]


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

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

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

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

ei

Web [BibTex]

Web [BibTex]


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

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

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

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

ei

PDF Web [BibTex]

PDF Web [BibTex]


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

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

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

ei

Web [BibTex]

Web [BibTex]


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

Lampert, C., Peters, J.

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

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

ei

PDF Web [BibTex]

PDF Web [BibTex]


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

Macke, J., Wichmann, F.

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

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

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Semi-supervised Analysis of Human fMRI Data

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

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

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

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Learning Motor Primitives for Robotics

Kober, J., Peters, J., Oztop, E.

Advanced Telecommunications Research Center ATR, June 2009 (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.

ei

[BibTex]

[BibTex]


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Learning To Detect Unseen Object Classes by Between-Class Attribute Transfer

Lampert, C.

IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), June 2009 (talk)

ei

Web [BibTex]

Web [BibTex]


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Optimization of k-Space Trajectories by Bayesian Experimental Design

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

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

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

ei

PDF Web [BibTex]

PDF Web [BibTex]


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MR-Based Attenuation Correction for PET/MR

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

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

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

ei

PDF Web [BibTex]

PDF Web [BibTex]


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test jon
(book)

[BibTex]