Publications | Max Planck Institute for Intelligent Systems

72 results (View BibTeX file of all listed publications)

2017

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)

link (url) DOI [BibTex]

2017

ei Aghaeifar, A., Loktyushin, A., Eschelbach, M., Scheffler, K. Improving performance of linear field generation with multi-coil setup by optimizing coils position 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)

link (url) DOI [BibTex]

Editorial for the Special Issue on Microdevices and Microsystems for Cell Manipulation

Hu, W., Ohta, A. T.

8, Multidisciplinary Digital Publishing Institute, September 2017 (misc)

DOI [BibTex]

pi Hu, W., Ohta, A. T. Editorial for the Special Issue on Microdevices and Microsystems for Cell Manipulation 8, Multidisciplinary Digital Publishing Institute, September 2017 (misc)

DOI [BibTex]

Physical and Behavioral Factors Improve Robot Hug Quality

Block, A. E., Kuchenbecker, K. J.

Workshop Paper (2 pages) presented at the RO-MAN Workshop on Social Interaction and Multimodal Expression for Socially Intelligent Robots, Lisbon, Portugal, August 2017 (misc)

Abstract

A hug is one of the most basic ways humans can express affection. As hugs are so common, a natural progression of robot development is to have robots one day hug humans as seamlessly as these intimate human-human interactions occur. This project’s purpose is to evaluate human responses to different robot physical characteristics and hugging behaviors. Specifically, we aim to test the hypothesis that a warm, soft, touch-sensitive PR2 humanoid robot can provide humans with satisfying hugs by matching both their hugging pressure and their hugging duration. Thirty participants experienced and evaluated twelve hugs with the robot, divided into three randomly ordered trials that focused on physical robot char- acteristics and nine randomly ordered trials with varied hug pressure and duration. We found that people prefer soft, warm hugs over hard, cold hugs. Furthermore, users prefer hugs that physically squeeze them and release immediately when they are ready for the hug to end.

Project Page [BibTex]

hi Block, A. E., Kuchenbecker, K. J. Physical and Behavioral Factors Improve Robot Hug Quality Workshop Paper (2 pages) presented at the RO-MAN Workshop on Social Interaction and Multimodal Expression for Socially Intelligent Robots, Lisbon, Portugal, August 2017 (misc)

Project Page [BibTex]

Crowdshaping Realistic 3D Avatars with Words

Streuber, S., Ramirez, M. Q., Black, M., Zuffi, S., O’Toole, A., Hill, M. Q., Hahn, C. A.

August 2017, Application PCT/EP2017/051954 (misc)

Abstract

A method for generating a body shape, comprising the steps: - receiving one or more linguistic descriptors related to the body shape; - retrieving an association between the one or more linguistic descriptors and a body shape; and - generating the body shape, based on the association.

Google Patents [BibTex]

ps Streuber, S., Ramirez, M. Q., Black, M., Zuffi, S., O’Toole, A., Hill, M. Q., Hahn, C. A. Crowdshaping Realistic 3D Avatars with Words August 2017, Application PCT/EP2017/051954 (misc)

Google Patents [BibTex]

Physically Interactive Exercise Games with a Baxter Robot

Fitter, N. T., Kuchenbecker, K. J.

Hands-on demonstration presented at the IEEE World Haptics Conference (WHC), Munich, Germany, June 2017 (misc)

Project Page [BibTex]

hi Fitter, N. T., Kuchenbecker, K. J. Physically Interactive Exercise Games with a Baxter Robot Hands-on demonstration presented at the IEEE World Haptics Conference (WHC), Munich, Germany, June 2017 (misc)

Project Page [BibTex]

Proton Pack: Visuo-Haptic Surface Data Recording

Burka, A., Kuchenbecker, K. J.

Hands-on demonstration presented at the IEEE World Haptics Conference (WHC), Munich, Germany, June 2017 (misc)

Project Page [BibTex]

hi Burka, A., Kuchenbecker, K. J. Proton Pack: Visuo-Haptic Surface Data Recording Hands-on demonstration presented at the IEEE World Haptics Conference (WHC), Munich, Germany, June 2017 (misc)

Project Page [BibTex]

Teaching a Robot to Collaborate with a Human Via Haptic Teleoperation

Hu, S., Kuchenbecker, K. J.

Work-in-progress paper (2 pages) presented at the IEEE World Haptics Conference (WHC), Munich, Germany, June 2017 (misc)

Project Page [BibTex]

hi Hu, S., Kuchenbecker, K. J. Teaching a Robot to Collaborate with a Human Via Haptic Teleoperation Work-in-progress paper (2 pages) presented at the IEEE World Haptics Conference (WHC), Munich, Germany, June 2017 (misc)

Project Page [BibTex]

How Should Robots Hug?

Block, A. E., Kuchenbecker, K. J.

Work-in-progress paper (2 pages) presented at the IEEE World Haptics Conference (WHC), Munich, Germany, June 2017 (misc)

Project Page [BibTex]

hi Block, A. E., Kuchenbecker, K. J. How Should Robots Hug? Work-in-progress paper (2 pages) presented at the IEEE World Haptics Conference (WHC), Munich, Germany, June 2017 (misc)

Project Page [BibTex]

An Interactive Augmented-Reality Video Training Platform for the da Vinci Surgical System

Carlson, J., Kuchenbecker, K. J.

Workshop paper (3 pages) presented at the ICRA Workshop on C4 Surgical Robots, Singapore, May 2017 (misc)

Abstract

Teleoperated surgical robots such as the Intuitive da Vinci Surgical System facilitate minimally invasive surgeries, which decrease risk to patients. However, these systems can be difficult to learn, and existing training curricula on surgical simulators do not offer students the realistic experience of a full operation. This paper presents an augmented-reality video training platform for the da Vinci that will allow trainees to rehearse any surgery recorded by an expert. While the trainee operates a da Vinci in free space, they see their own instruments overlaid on the expert video. Tools are identified in the source videos via color segmentation and kernelized correlation filter tracking, and their depth is calculated from the da Vinci’s stereoscopic video feed. The user tries to follow the expert’s movements, and if any of their tools venture too far away, the system provides instantaneous visual feedback and pauses to allow the user to correct their motion. The trainee can also rewind the expert video by bringing either da Vinci tool very close to the camera. This combined and augmented video provides the user with an immersive and interactive training experience.

[BibTex]

hi Carlson, J., Kuchenbecker, K. J. An Interactive Augmented-Reality Video Training Platform for the da Vinci Surgical System Workshop paper (3 pages) presented at the ICRA Workshop on C4 Surgical Robots, Singapore, May 2017 (misc)

[BibTex]

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)

link (url) [BibTex]

ei Loktyushin, A., Ehses, P., Schölkopf, B., Scheffler, K. Estimating B0 inhomogeneities with projection FID navigator readouts 25th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2017 (poster)

link (url) [BibTex]

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)

link (url) [BibTex]

ei Feng, X., Loktyushin, A., Deistung, A., Reichenbach, J. Image Quality Improvement by Applying Retrospective Motion Correction on Quantitative Susceptibility Mapping and R2* 25th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2017 (poster)

link (url) [BibTex]

Hand-Clapping Games with a Baxter Robot

Fitter, N. T., Kuchenbecker, K. J.

Hands-on demonstration presented at ACM/IEEE International Conference on Human-Robot Interaction (HRI), Vienna, Austria, March 2017 (misc)

Abstract

Robots that work alongside humans might be more effective if they could forge a strong social bond with their human partners. Hand-clapping games and other forms of rhythmic social-physical interaction may foster human-robot teamwork, but the design of such interactions has scarcely been explored. At the HRI 2017 conference, we will showcase several such interactions taken from our recent work with the Rethink Robotics Baxter Research Robot, including tempo-matching, Simon says, and Pat-a-cake-like games. We believe conference attendees will be both entertained and intrigued by this novel demonstration of social-physical HRI.

Project Page [BibTex]

hi Fitter, N. T., Kuchenbecker, K. J. Hand-Clapping Games with a Baxter Robot Hands-on demonstration presented at ACM/IEEE International Conference on Human-Robot Interaction (HRI), Vienna, Austria, March 2017 (misc)

Project Page [BibTex]

Automatic OSATS Rating of Trainee Skill at a Pediatric Laparoscopic Suturing Task

Oquendo, Y. A., Riddle, E. W., Hiller, D., Blinman, T. A., Kuchenbecker, K. J.

Surgical Endoscopy, 31(Supplement 1):S28, Extended abstract presented as a podium presentation at the Annual Meeting of the Society of American Gastrointestinal and Endoscopic Surgeons (SAGES), Springer, Houston, USA, March 2017 (misc)

Abstract

Introduction: Minimally invasive surgery has revolutionized surgical practice, but challenges remain. Trainees must acquire complex technical skills while minimizing patient risk, and surgeons must maintain their skills for rare procedures. These challenges are magnified in pediatric surgery due to the smaller spaces, finer tissue, and relative dearth of both inanimate and virtual simulators. To build technical expertise, trainees need opportunities for deliberate practice with specific performance feedback, which is typically provided via tedious human grading. This study aimed to validate a novel motion-tracking system and machine learning algorithm for automatically evaluating trainee performance on a pediatric laparoscopic suturing task using a 1–5 OSATS Overall Skill rating. Methods: Subjects (n=14) ranging from medical students to fellows per- formed one or two trials of an intracorporeal suturing task in a custom pediatric laparoscopy training box (Fig. 1) after watching a video of ideal performance by an expert. The position and orientation of the tools and endoscope were recorded over time using Ascension trakSTAR magnetic motion-tracking sensors, and both instrument grasp angles were recorded over time using flex sensors on the handles. The 27 trials were video-recorded and scored on the OSATS scale by a senior fellow; ratings ranged from 1 to 4. The raw motion data from each trial was processed to calculate over 200 preliminary motion parameters. Regularized least-squares regression (LASSO) was used to identify the most predictive parameters for inclusion in a regression tree. Model performance was evaluated by leave-one-subject-out cross validation, wherein the automatic scores given to each subject’s trials (by a model trained on all other data) are compared to the corresponding human rater scores. Results: The best-performing LASSO algorithm identified 14 predictive parameters for inclusion in the regression tree, including completion time, linear path length, angular path length, angular acceleration, grasp velocity, and grasp acceleration. The final model’s raw output showed a strong positive correlation of 0.87 with the reviewer-generated scores, and rounding the output to the nearest integer yielded a leave-one-subject-out cross-validation accuracy of 77.8%. Results are summarized in the confusion matrix (Table 1). Conclusions: Our novel motion-tracking system and regression model automatically gave previously unseen trials overall skill scores that closely match scores from an expert human rater. With additional data and further development, this system may enable creation of a motion-based training platform for pediatric laparoscopic surgery and could yield insights into the fundamental components of surgical skill.

[BibTex]

hi Oquendo, Y. A., Riddle, E. W., Hiller, D., Blinman, T. A., Kuchenbecker, K. J. Automatic OSATS Rating of Trainee Skill at a Pediatric Laparoscopic Suturing Task Surgical Endoscopy, 31(Supplement 1):S28, Extended abstract presented as a podium presentation at the Annual Meeting of the Society of American Gastrointestinal and Endoscopic Surgeons (SAGES), Springer, Houston, USA, March 2017 (misc)

[BibTex]

How Much Haptic Surface Data is Enough?

Burka, A., Kuchenbecker, K. J.

Workshop paper (5 pages) presented at the AAAI Spring Symposium on Interactive Multi-Sensory Object Perception for Embodied Agents, Stanford, USA, March 2017 (misc)

Abstract

The Proton Pack is a portable visuo-haptic surface interaction recording device that will be used to collect a vast multimodal dataset, intended for robots to use as part of an approach to understanding the world around them. In order to collect a useful dataset, we want to pick a suitable interaction duration for each surface, noting the tradeoff between data collection resources and completeness of data. One interesting approach frames the data collection process as an online learning problem, building an incremental surface model and using that model to decide when there is enough data. Here we examine how to do such online surface modeling and when to stop collecting data, using kinetic friction as a first domain in which to apply online modeling.

link (url) Project Page [BibTex]

hi Burka, A., Kuchenbecker, K. J. How Much Haptic Surface Data is Enough? Workshop paper (5 pages) presented at the AAAI Spring Symposium on Interactive Multi-Sensory Object Perception for Embodied Agents, Stanford, USA, March 2017 (misc)

link (url) Project Page [BibTex]

The right tool for the right question — beyond the encoding versus decoding dichotomy

Weichwald, S., Grosse-Wentrup, M.

2017 (misc)

ArXiv PDF [BibTex]

ei Weichwald, S., Grosse-Wentrup, M. The right tool for the right question — beyond the encoding versus decoding dichotomy 2017 (misc)

ArXiv PDF [BibTex]

Probabilistic Active Learning of Functions in Structural Causal Models

Rubenstein, P. K., Tolstikhin, I., Hennig, P., Schölkopf, B.

2017 (misc)

ei pn

Arxiv [BibTex]

ei pn Rubenstein, P. K., Tolstikhin, I., Hennig, P., Schölkopf, B. Probabilistic Active Learning of Functions in Structural Causal Models 2017 (misc)

Arxiv [BibTex]

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)

[BibTex]

ei Safavi, S., Panagiotaropoulos, T., Kapoor, V., Logothetis, N. K., Besserve, M. Generalized phase locking analysis of electrophysiology data ESI Systems Neuroscience Conference (ESI-SyNC 2017): Principles of Structural and Functional Connectivity, 2017 (poster)

[BibTex]

X-ray microscopy of spin wave focusing using a Fresnel zone plate

Gräfe, J., Decker, M., Keskinbora, K., Noske, M., Gawronski, P., Stoll, H., Back, C. H., Goering, E. J., Schütz, G.

2017 (misc)

mms

link (url) [BibTex]

mms Gräfe, J., Decker, M., Keskinbora, K., Noske, M., Gawronski, P., Stoll, H., Back, C. H., Goering, E. J., Schütz, G. X-ray microscopy of spin wave focusing using a Fresnel zone plate 2017 (misc)

link (url) [BibTex]

2016

Skinned multi-person linear model

Black, M.J., Loper, M., Mahmood, N., Pons-Moll, G., Romero, J.

December 2016, Application PCT/EP2016/064610 (misc)

Abstract

The invention comprises a learned model of human body shape and pose dependent shape variation that is more accurate than previous models and is compatible with existing graphics pipelines. Our Skinned Multi-Person Linear model (SMPL) is a skinned vertex based model that accurately represents a wide variety of body shapes in natural human poses. The parameters of the model are learned from data including the rest pose template, blend weights, pose-dependent blend shapes, identity- dependent blend shapes, and a regressor from vertices to joint locations. Unlike previous models, the pose-dependent blend shapes are a linear function of the elements of the pose rotation matrices. This simple formulation enables training the entire model from a relatively large number of aligned 3D meshes of different people in different poses. The invention quantitatively evaluates variants of SMPL using linear or dual- quaternion blend skinning and show that both are more accurate than a Blend SCAPE model trained on the same data. In a further embodiment, the invention realistically models dynamic soft-tissue deformations. Because it is based on blend skinning, SMPL is compatible with existing rendering engines and we make it available for research purposes.

Google Patents [BibTex]

2016

ps Black, M.J., Loper, M., Mahmood, N., Pons-Moll, G., Romero, J. Skinned multi-person linear model December 2016, Application PCT/EP2016/064610 (misc)

Google Patents [BibTex]

Autofocusing-based correction of B0 fluctuation-induced ghosting

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

24th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), May 2016 (poster)

link (url) [BibTex]

ei Loktyushin, A., Ehses, P., Schölkopf, B., Scheffler, K. Autofocusing-based correction of B0 fluctuation-induced ghosting 24th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), May 2016 (poster)

link (url) [BibTex]

Distinct adaptation to abrupt and gradual torque perturbations with a multi-joint exoskeleton robot

Oh, Y., Sutanto, G., Mistry, M., Schweighofer, N., Schaal, S.

Abstracts of Neural Control of Movement Conference (NCM 2016), Montego Bay, Jamaica, April 2016 (poster)

[BibTex]

am Oh, Y., Sutanto, G., Mistry, M., Schweighofer, N., Schaal, S. Distinct adaptation to abrupt and gradual torque perturbations with a multi-joint exoskeleton robot Abstracts of Neural Control of Movement Conference (NCM 2016), Montego Bay, Jamaica, April 2016 (poster)

[BibTex]

Special Issue on Causal Discovery and Inference

Zhang, K., Li, J., Bareinboim, E., Schölkopf, B., Pearl, J.

ACM Transactions on Intelligent Systems and Technology (TIST), 7(2), January 2016, (Guest Editors) (misc)

[BibTex]

ei Zhang, K., Li, J., Bareinboim, E., Schölkopf, B., Pearl, J. Special Issue on Causal Discovery and Inference ACM Transactions on Intelligent Systems and Technology (TIST), 7(2), January 2016, (Guest Editors) (misc)

[BibTex]

Empirical Inference (2010-2015)

Scientific Advisory Board Report, 2016 (misc)

pdf [BibTex]

ei Empirical Inference (2010-2015) Scientific Advisory Board Report, 2016 (misc)

pdf [BibTex]

A note on the expected minimum error probability in equientropic channels

Weichwald, S., Fomina, T., Schölkopf, B., Grosse-Wentrup, M.

2016 (misc)

PDF Arxiv [BibTex]

ei Weichwald, S., Fomina, T., Schölkopf, B., Grosse-Wentrup, M. A note on the expected minimum error probability in equientropic channels 2016 (misc)

PDF Arxiv [BibTex]

PGO wave-triggered functional MRI: mapping the networks underlying synaptic consolidation

Logothetis, N. K., Murayama, Y., Ramirez-Villegas, J. F., Besserve, M., Evrard, H.

47th Annual Meeting of the Society for Neuroscience (Neuroscience), 2016 (poster)

[BibTex]

ei Logothetis, N. K., Murayama, Y., Ramirez-Villegas, J. F., Besserve, M., Evrard, H. PGO wave-triggered functional MRI: mapping the networks underlying synaptic consolidation 47th Annual Meeting of the Society for Neuroscience (Neuroscience), 2016 (poster)

[BibTex]

Unsupervised Domain Adaptation in the Wild : Dealing with Asymmetric Label Set

Mittal, A., Raj, A., Namboodiri, V. P., Tuytelaars, T.

2016 (misc)

Arxiv [BibTex]

ei Mittal, A., Raj, A., Namboodiri, V. P., Tuytelaars, T. Unsupervised Domain Adaptation in the Wild : Dealing with Asymmetric Label Set 2016 (misc)

Arxiv [BibTex]

Perceiving Systems (2011-2015)

Scientific Advisory Board Report, 2016 (misc)

pdf [BibTex]

ps Perceiving Systems (2011-2015) Scientific Advisory Board Report, 2016 (misc)

pdf [BibTex]

Can Modular Finger Control for In-Hand Object Stabilization be accomplished by Independent Tactile Feedback Control Laws?

Veiga, F., Peters, J.

2016 (misc)

arXiv [BibTex]

ei Veiga, F., Peters, J. Can Modular Finger Control for In-Hand Object Stabilization be accomplished by Independent Tactile Feedback Control Laws? 2016 (misc)

arXiv [BibTex]

Statistical source separation of rhythmic LFP patterns during sharp wave ripples in the macaque hippocampus

Ramirez-Villegas, J. F., Logothetis, N. K., Besserve, M.

47th Annual Meeting of the Society for Neuroscience (Neuroscience), 2016 (poster)

[BibTex]

ei Ramirez-Villegas, J. F., Logothetis, N. K., Besserve, M. Statistical source separation of rhythmic LFP patterns during sharp wave ripples in the macaque hippocampus 47th Annual Meeting of the Society for Neuroscience (Neuroscience), 2016 (poster)

[BibTex]

Hippocampal neural events predict ongoing brain-wide BOLD activity

Besserve, M., Logothetis, N. K.

47th Annual Meeting of the Society for Neuroscience (Neuroscience), 2016 (poster)

[BibTex]

ei Besserve, M., Logothetis, N. K. Hippocampal neural events predict ongoing brain-wide BOLD activity 47th Annual Meeting of the Society for Neuroscience (Neuroscience), 2016 (poster)

[BibTex]

Extrapolation and learning equations

Martius, G., Lampert, C. H.

2016, arXiv preprint \url{https://arxiv.org/abs/1610.02995} (misc)

Project Page [BibTex]

al Martius, G., Lampert, C. H. Extrapolation and learning equations 2016, arXiv preprint \url{https://arxiv.org/abs/1610.02995} (misc)

Project Page [BibTex]

2007

Reaction graph kernels for discovering missing enzymes in the plant secondary metabolism

Saigo, H., Hattori, M., Tsuda, K.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Abstract

Secondary metabolic pathway in plant is important for finding druggable candidate enzymes. However, there are many enzymes whose functions are still undiscovered especially in organism-specific metabolic pathways. We propose reaction graph kernels for automatically assigning the EC numbers to unknown enzymatic reactions in a metabolic network. Experiments are carried out on KEGG/REACTION database and our method successfully predicted the first three digits of the EC number with 83% accuracy.We also exhaustively predicted missing enzymatic functions in the plant secondary metabolism pathways, and evaluated our results in biochemical validity.

Web [BibTex]

2007

ei Saigo, H., Hattori, M., Tsuda, K. Reaction graph kernels for discovering missing enzymes in the plant secondary metabolism NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Web [BibTex]

Positional Oligomer Importance Matrices

Sonnenburg, S., Zien, A., Philips, P., Rätsch, G.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Abstract

At the heart of many important bioinformatics problems, such as gene finding and function prediction, is the classification of biological sequences, above all of DNA and proteins. In many cases, the most accurate classifiers are obtained by training SVMs with complex sequence kernels, for instance for transcription starts or splice sites. However, an often criticized downside of SVMs with complex kernels is that it is very hard for humans to understand the learned decision rules and to derive biological insights from them. To close this gap, we introduce the concept of positional oligomer importance matrices (POIMs) and develop an efficient algorithm for their computation. We demonstrate how they overcome the limitations of sequence logos, and how they can be used to find relevant motifs for different biological phenomena in a straight-forward way. Note that the concept of POIMs is not limited to interpreting SVMs, but is applicable to general k−mer based scoring systems.

Web [BibTex]

ei Sonnenburg, S., Zien, A., Philips, P., Rätsch, G. Positional Oligomer Importance Matrices NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Web [BibTex]

Machine Learning Algorithms for Polymorphism Detection

Schweikert, G., Zeller, G., Weigel, D., Schölkopf, B., Rätsch, G.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Web [BibTex]

ei Schweikert, G., Zeller, G., Weigel, D., Schölkopf, B., Rätsch, G. Machine Learning Algorithms for Polymorphism Detection NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Web [BibTex]

An Automated Combination of Kernels for Predicting Protein Subcellular Localization

Zien, A., Ong, C.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Abstract

Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions.We propose a new class of protein sequence kernels which considers all motifs including motifs with gaps. This class of kernels allows the inclusion of pairwise amino acid distances into their computation. We utilize an extension of the multiclass support vector machine (SVM)method which directly solves protein subcellular localization without resorting to the common approach of splitting the problem into several binary classification problems. To automatically search over families of possible amino acid motifs, we optimize over multiple kernels at the same time. We compare our automated approach to four other predictors on three different datasets, and show that we perform better than the current state of the art. Furthermore, our method provides some insights as to which features are most useful for determining subcellular localization, which are in agreement with biological reasoning.

Web [BibTex]

ei Zien, A., Ong, C. An Automated Combination of Kernels for Predicting Protein Subcellular Localization NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Web [BibTex]

Challenges in Brain-Computer Interface Development: Induction, Measurement, Decoding, Integration

Hill, NJ.

Invited keynote talk at the launch of BrainGain, the Dutch BCI research consortium, November 2007 (talk)

Abstract

I‘ll present a perspective on Brain-Computer Interface development from T{\"u}bingen. Some of the benefits promised by BCI technology lie in the near foreseeable future, and some further away. Our motivation is to make BCI technology feasible for the people who could benefit from what it has to offer soon: namely, people in the "completely locked-in" state. I‘ll mention some of the challenges of working with this user group, and explain the specific directions they have motivated us to take in developing experimental methods, algorithms, and software.

[BibTex]

ei Hill, NJ. Challenges in Brain-Computer Interface Development: Induction, Measurement, Decoding, Integration Invited keynote talk at the launch of BrainGain, the Dutch BCI research consortium, November 2007 (talk)

[BibTex]

MR-Based PET Attenuation Correction: Method and Validation

Hofmann, M., Steinke, F., Scheel, V., Charpiat, G., Brady, M., Schölkopf, B., Pichler, B.

2007 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC 2007), 2007(M16-6):1-2, November 2007 (poster)

Abstract

PET/MR combines the high soft tissue contrast of Magnetic Resonance Imaging (MRI) and the functional information of Positron Emission Tomography (PET). For quantitative PET information, correction of tissue photon attenuation is mandatory. Usually in conventional PET, the attenuation map is obtained from a transmission scan, which uses a rotating source, or from the CT scan in case of combined PET/CT. In the case of a PET/MR scanner, there is insufficient space for the rotating source and ideally one would want to calculate the attenuation map from the MR image instead. Since MR images provide information about proton density of the different tissue types, it is not trivial to use this data for PET attenuation correction. We present a method for predicting the PET attenuation map from a given the MR image, using a combination of atlas-registration and recognition of local patterns. Using "leave one out cross validation" we show on a database of 16 MR-CT image pairs that our method reliably allows estimating the CT image from the MR image. Subsequently, as in PET/CT, the PET attenuation map can be predicted from the CT image. On an additional dataset of MR/CT/PET triplets we quantitatively validate that our approach allows PET quantification with an error that is smaller than what would be clinically significant. We demonstrate our approach on T1-weighted human brain scans. However, the presented methods are more general and current research focuses on applying the established methods to human whole body PET/MRI applications.

PDF PDF [BibTex]

ei Hofmann, M., Steinke, F., Scheel, V., Charpiat, G., Brady, M., Schölkopf, B., Pichler, B. MR-Based PET Attenuation Correction: Method and Validation 2007 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC 2007), 2007(M16-6):1-2, November 2007 (poster)

PDF PDF [BibTex]

Estimating receptive fields without spike-triggering

Macke, J., Zeck, G., Bethge, M.

37th annual Meeting of the Society for Neuroscience (Neuroscience 2007), 37(768.1):1, November 2007 (poster)

Web [BibTex]

ei Macke, J., Zeck, G., Bethge, M. Estimating receptive fields without spike-triggering 37th annual Meeting of the Society for Neuroscience (Neuroscience 2007), 37(768.1):1, November 2007 (poster)

Web [BibTex]

Evaluation of Deformable Registration Methods for MR-CT Atlas Alignment

Scheel, V., Hofmann, M., Rehfeld, N., Judenhofer, M., Claussen, C., Pichler, B.

2007 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC 2007), 2007(M13-121):1, November 2007 (poster)

Abstract

Deformable registration methods are essential for multimodality imaging. Many different methods exist but due to the complexity of the deformed images a direct comparison of the methods is difficult. One particular application that requires high accuracy registration of MR-CT images is atlas-based attenuation correction for PET/MR. We compare four deformable registration algorithms for 3D image data included in the Open Source "National Library of Medicine Insight Segmentation and Registration Toolkit" (ITK). An interactive landmark based registration using MiraView (Siemens) has been used as gold standard. The automatic algorithms provided by ITK are based on the metrics Mattes mutual information as well as on normalized mutual information. The transformations are calculated by interpolating over a uniform B-Spline grid laying over the image to be warped. The algorithms were tested on head images from 10 subjects. We implemented a measure which segments head interior bone and air based on the CT images and l ow intensity classes of corresponding MRI images. The segmentation of bone is performed by individually calculating the lowest Hounsfield unit threshold for each CT image. The compromise is made by quantifying the number of overlapping voxels of the remaining structures. We show that the algorithms provided by ITK achieve similar or better accuracy than the time-consuming interactive landmark based registration. Thus, ITK provides an ideal platform to generate accurately fused datasets from different modalities, required for example for building training datasets for Atlas-based attenuation correction.

PDF [BibTex]

ei Scheel, V., Hofmann, M., Rehfeld, N., Judenhofer, M., Claussen, C., Pichler, B. Evaluation of Deformable Registration Methods for MR-CT Atlas Alignment 2007 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC 2007), 2007(M13-121):1, November 2007 (poster)

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A time/frequency decomposition of information transmission by LFPs and spikes in the primary visual cortex

Belitski, A., Gretton, A., Magri, C., Murayama, Y., Montemurro, M., Logothetis, N., Panzeri, S.

37th Annual Meeting of the Society for Neuroscience (Neuroscience 2007), 37, pages: 1, November 2007 (poster)

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ei Belitski, A., Gretton, A., Magri, C., Murayama, Y., Montemurro, M., Logothetis, N., Panzeri, S. A time/frequency decomposition of information transmission by LFPs and spikes in the primary visual cortex 37th Annual Meeting of the Society for Neuroscience (Neuroscience 2007), 37, pages: 1, November 2007 (poster)

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Mining expression-dependent modules in the human interaction network

Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K.

BMC Bioinformatics, 8(Suppl. 8):S4, November 2007 (poster)

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ei Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K. Mining expression-dependent modules in the human interaction network BMC Bioinformatics, 8(Suppl. 8):S4, November 2007 (poster)

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Policy Learning for Robotics

Peters, J.

14th International Conference on Neural Information Processing (ICONIP), November 2007 (talk)

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ei Peters, J. Policy Learning for Robotics 14th International Conference on Neural Information Processing (ICONIP), November 2007 (talk)

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Hilbert Space Representations of Probability Distributions

Gretton, A.

2nd Workshop on Machine Learning and Optimization at the ISM, October 2007 (talk)

Abstract

Many problems in unsupervised learning require the analysis of features of probability distributions. At the most fundamental level, we might wish to determine whether two distributions are the same, based on samples from each - this is known as the two-sample or homogeneity problem. We use kernel methods to address this problem, by mapping probability distributions to elements in a reproducing kernel Hilbert space (RKHS). Given a sufficiently rich RKHS, these representations are unique: thus comparing feature space representations allows us to compare distributions without ambiguity. Applications include testing whether cancer subtypes are distinguishable on the basis of DNA microarray data, and whether low frequency oscillations measured at an electrode in the cortex have a different distribution during a neural spike. A more difficult problem is to discover whether two random variables drawn from a joint distribution are independent. It turns out that any dependence between pairs of random variables can be encoded in a cross-covariance operator between appropriate RKHS representations of the variables, and we may test independence by looking at a norm of the operator. We demonstrate this independence test by establishing dependence between an English text and its French translation, as opposed to French text on the same topic but otherwise unrelated. Finally, we show that this operator norm is itself a difference in feature means.

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ei Gretton, A. Hilbert Space Representations of Probability Distributions 2nd Workshop on Machine Learning and Optimization at the ISM, October 2007 (talk)

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Regression with Intervals

Kashima, H., Yamazaki, K., Saigo, H., Inokuchi, A.

International Workshop on Data-Mining and Statistical Science (DMSS2007), October 2007, JSAI Incentive Award. Talk was given by Hisashi Kashima. (talk)

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ei Kashima, H., Yamazaki, K., Saigo, H., Inokuchi, A. Regression with Intervals International Workshop on Data-Mining and Statistical Science (DMSS2007), October 2007, JSAI Incentive Award. Talk was given by Hisashi Kashima. (talk)

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A Hilbert Space Embedding for Distributions

Smola, A., Gretton, A., Song, L., Schölkopf, B.

Proceedings of the 10th International Conference on Discovery Science (DS 2007), 10, pages: 40-41, October 2007 (poster)

Abstract

While kernel methods are the basis of many popular techniques in supervised learning, they are less commonly used in testing, estimation, and analysis of probability distributions, where information theoretic approaches rule the roost. However it becomes difficult to estimate mutual information or entropy if the data are high dimensional.

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ei Smola, A., Gretton, A., Song, L., Schölkopf, B. A Hilbert Space Embedding for Distributions Proceedings of the 10th International Conference on Discovery Science (DS 2007), 10, pages: 40-41, October 2007 (poster)

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MR-Based PET Attenuation Correction: Method and Validation

Hofmann, M., Steinke, F., Scheel, V., Brady, M., Schölkopf, B., Pichler, B.

Joint Molecular Imaging Conference, September 2007 (talk)

Abstract

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ei Hofmann, M., Steinke, F., Scheel, V., Brady, M., Schölkopf, B., Pichler, B. MR-Based PET Attenuation Correction: Method and Validation Joint Molecular Imaging Conference, September 2007 (talk)

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Studying the effects of noise correlations on population coding using a sampling method

Ecker, A., Berens, P., Bethge, M., Logothetis, N., Tolias, A.

Neural Coding, Computation and Dynamics (NCCD 07), 1, pages: 21, September 2007 (poster)

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ei Ecker, A., Berens, P., Bethge, M., Logothetis, N., Tolias, A. Studying the effects of noise correlations on population coding using a sampling method Neural Coding, Computation and Dynamics (NCCD 07), 1, pages: 21, September 2007 (poster)

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Bayesian methods for NMR structure determination

Habeck, M.

29th Annual Discussion Meeting: Magnetic Resonance in Biophysical Chemistry, September 2007 (talk)

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ei Habeck, M. Bayesian methods for NMR structure determination 29th Annual Discussion Meeting: Magnetic Resonance in Biophysical Chemistry, September 2007 (talk)

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Near-Maximum Entropy Models for Binary Neural Representations of Natural Images

Berens, P., Bethge, M.

Neural Coding, Computation and Dynamics (NCCD 07), 1, pages: 19, September 2007 (poster)

Abstract

Maximum entropy analysis of binary variables provides an elegant way for studying the role of pairwise correlations in neural populations. Unfortunately, these approaches suffer from their poor scalability to high dimensions. In sensory coding, however, high-dimensional data is ubiquitous. Here, we introduce a new approach using a near-maximum entropy model, that makes this type of analysis feasible for very high-dimensional data---the model parameters can be derived in closed form and sampling is easy. We demonstrate its usefulness by studying a simple neural representation model of natural images. For the first time, we are able to directly compare predictions from a pairwise maximum entropy model not only in small groups of neurons, but also in larger populations of more than thousand units. Our results indicate that in such larger networks interactions exist that are not predicted by pairwise correlations, despite the fact that pairwise correlations explain the lower-dimensional marginal statistics extrem ely well up to the limit of dimensionality where estimation of the full joint distribution is feasible.

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