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2020


Learning to Predict Perceptual Distributions of Haptic Adjectives
Learning to Predict Perceptual Distributions of Haptic Adjectives

Richardson, B. A., Kuchenbecker, K. J.

Frontiers in Neurorobotics, 13(116):1-16, Febuary 2020 (article)

Abstract
When humans touch an object with their fingertips, they can immediately describe its tactile properties using haptic adjectives, such as hardness and roughness; however, human perception is subjective and noisy, with significant variation across individuals and interactions. Recent research has worked to provide robots with similar haptic intelligence but was focused on identifying binary haptic adjectives, ignoring both attribute intensity and perceptual variability. Combining ordinal haptic adjective labels gathered from human subjects for a set of 60 objects with features automatically extracted from raw multi-modal tactile data collected by a robot repeatedly touching the same objects, we designed a machine-learning method that incorporates partial knowledge of the distribution of object labels into training; then, from a single interaction, it predicts a probability distribution over the set of ordinal labels. In addition to analyzing the collected labels (10 basic haptic adjectives) and demonstrating the quality of our method's predictions, we hold out specific features to determine the influence of individual sensor modalities on the predictive performance for each adjective. Our results demonstrate the feasibility of modeling both the intensity and the variation of haptic perception, two crucial yet previously neglected components of human haptic perception.

hi

DOI [BibTex]

2020


DOI [BibTex]


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Exercising with Baxter: preliminary support for assistive social-physical human-robot interaction

Fitter, N. T., Mohan, M., Kuchenbecker, K. J., Johnson, M. J.

Journal of NeuroEngineering and Rehabilitation, 17(19), Febuary 2020 (article)

Abstract
Background: The worldwide population of older adults will soon exceed the capacity of assisted living facilities. Accordingly, we aim to understand whether appropriately designed robots could help older adults stay active at home. Methods: Building on related literature as well as guidance from experts in game design, rehabilitation, and physical and occupational therapy, we developed eight human-robot exercise games for the Baxter Research Robot, six of which involve physical human-robot contact. After extensive iteration, these games were tested in an exploratory user study including 20 younger adult and 20 older adult users. Results: Only socially and physically interactive games fell in the highest ranges for pleasantness, enjoyment, engagement, cognitive challenge, and energy level. Our games successfully spanned three different physical, cognitive, and temporal challenge levels. User trust and confidence in Baxter increased significantly between pre- and post-study assessments. Older adults experienced higher exercise, energy, and engagement levels than younger adults, and women rated the robot more highly than men on several survey questions. Conclusions: The results indicate that social-physical exercise with a robot is more pleasant, enjoyable, engaging, cognitively challenging, and energetic than similar interactions that lack physical touch. In addition to this main finding, researchers working in similar areas can build on our design practices, our open-source resources, and the age-group and gender differences that we found.

hi

DOI [BibTex]

DOI [BibTex]


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Sliding Mode Control with Gaussian Process Regression for Underwater Robots

Lima, G. S., Trimpe, S., Bessa, W. M.

Journal of Intelligent & Robotic Systems, January 2020 (article)

ics

DOI [BibTex]

DOI [BibTex]


Hierarchical Event-triggered Learning for Cyclically Excited Systems with Application to Wireless Sensor Networks
Hierarchical Event-triggered Learning for Cyclically Excited Systems with Application to Wireless Sensor Networks

Beuchert, J., Solowjow, F., Raisch, J., Trimpe, S., Seel, T.

IEEE Control Systems Letters, 4(1):103-108, January 2020 (article)

ics

arXiv PDF DOI Project Page [BibTex]

arXiv PDF DOI Project Page [BibTex]


Learning Multi-Human Optical Flow
Learning Multi-Human Optical Flow

Ranjan, A., Hoffmann, D. T., Tzionas, D., Tang, S., Romero, J., Black, M. J.

International Journal of Computer Vision (IJCV), January 2020 (article)

Abstract
The optical flow of humans is well known to be useful for the analysis of human action. Recent optical flow methods focus on training deep networks to approach the problem. However, the training data used by them does not cover the domain of human motion. Therefore, we develop a dataset of multi-human optical flow and train optical flow networks on this dataset. We use a 3D model of the human body and motion capture data to synthesize realistic flow fields in both single-and multi-person images. We then train optical flow networks to estimate human flow fields from pairs of images. We demonstrate that our trained networks are more accurate than a wide range of top methods on held-out test data and that they can generalize well to real image sequences. The code, trained models and the dataset are available for research.

ps

Paper Publisher Version poster link (url) DOI [BibTex]


Control-guided Communication: Efficient Resource Arbitration and Allocation in Multi-hop Wireless Control Systems
Control-guided Communication: Efficient Resource Arbitration and Allocation in Multi-hop Wireless Control Systems

Baumann, D., Mager, F., Zimmerling, M., Trimpe, S.

IEEE Control Systems Letters, 4(1):127-132, January 2020 (article)

ics

arXiv PDF DOI [BibTex]

arXiv PDF DOI [BibTex]


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Self-supervised motion deblurring

Liu, P., Janai, J., Pollefeys, M., Sattler, T., Geiger, A.

IEEE Robotics and Automation Letters, 2020 (article)

avg

[BibTex]

[BibTex]


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Effect of the soft layer thickness of magnetization reversal process of exchange-spring nanomagnet patterns

Son, K., Schütz, G., Goering, E.

{Current Applied Physics}, 20(4):477-483, Elsevier B.V., Amsterdam, 2020 (article)

mms

DOI [BibTex]


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Tuning the magnetic properties of permalloy-based magnetoplasmonic crystals for sensor applications

Murzin, D. V., Belyaev, V. K., Groß, F., Gräfe, J., Rivas, M., Rodionova, V. V.

{Japanese Journal of Applied Physics}, 59(SE), IOP Publishing Ltd, Bristol, England, 2020 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Element-resolved study of the evolution of magnetic response in FexN compounds

Chen, Y., Gölden, D., Dirba, I., Huang, M., Gutfleisch, O., Nagel, P., Merz, M., Schuppler, S., Schütz, G., Alff, L., Goering, E.

{Journal of Magnetism and Magnetic Materials}, 498, NH, Elsevier, Amsterdam, 2020 (article)

mms

DOI [BibTex]

DOI [BibTex]


Controlling two-dimensional collective formation and cooperative behavior of magnetic microrobot swarms
Controlling two-dimensional collective formation and cooperative behavior of magnetic microrobot swarms

Dong, X., Sitti, M.

The International Journal of Robotics Research, 2020 (article)

Abstract
Magnetically actuated mobile microrobots can access distant, enclosed, and small spaces, such as inside microfluidic channels and the human body, making them appealing for minimally invasive tasks. Despite their simplicity when scaling down, creating collective microrobots that can work closely and cooperatively, as well as reconfigure their formations for different tasks, would significantly enhance their capabilities such as manipulation of objects. However, a challenge of realizing such cooperative magnetic microrobots is to program and reconfigure their formations and collective motions with under-actuated control signals. This article presents a method of controlling 2D static and time-varying formations among collective self-repelling ferromagnetic microrobots (100 μm to 350 μm in diameter, up to 260 in number) by spatially and temporally programming an external magnetic potential energy distribution at the air–water interface or on solid surfaces. A general design method is introduced to program external magnetic potential energy using ferromagnets. A predictive model of the collective system is also presented to predict the formation and guide the design procedure. With the proposed method, versatile complex static formations are experimentally demonstrated and the programmability and scaling effects of formations are analyzed. We also demonstrate the collective mobility of these magnetic microrobots by controlling them to exhibit bio-inspired collective behaviors such as aggregation, directional motion with arbitrary swarm headings, and rotational swarming motion. Finally, the functions of the produced microrobotic swarm are demonstrated by controlling them to navigate through cluttered environments and complete reconfigurable cooperative manipulation tasks.

pi

DOI [BibTex]


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The role of temperature and drive current in skyrmion dynamics

Litzius, K., Leliaert, J., Bassirian, P., Rodrigues, D., Kromin, S., Lemesh, I., Zazvorka, J., Lee, K., Mulkers, J., Kerber, N., Heinze, D., Keil, N., Reeve, R. M., Weigand, M., Van Waeyenberge, B., Schütz, G., Everschor-Sitte, K., Beach, G. S. D., Kläui, M.

{Nature Electronics}, 3(1):30-36, Springer Nature, London, 2020 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Magnetic flux penetration into micron-sized superconductor/ferromagnet bilayers

Simmendinger, J., Weigand, M., Schütz, G., Albrecht, J.

{Superconductor Science and Technology}, 33(2), IOP Pub., Bristol, 2020 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Analytical classical density functionals from an equation learning network

Lin, S., Martius, G., Oettel, M.

The Journal of Chemical Physics, 152(2):021102, 2020, arXiv preprint \url{https://arxiv.org/abs/1910.12752} (article)

al

Preprint_PDF DOI [BibTex]

Preprint_PDF DOI [BibTex]


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Fabrication and temperature-dependent magnetic properties of large-area L10-FePt/Co exchange-spring magnet nanopatterns

Son, K., Schütz, G.

{Physica E: Low-Dimensional Systems And Nanostructures}, 115, North-Holland, Amsterdam, 2020 (article)

mms

DOI [BibTex]

DOI [BibTex]


General Movement Assessment from videos of computed {3D} infant body models is equally effective compared to conventional {RGB} Video rating
General Movement Assessment from videos of computed 3D infant body models is equally effective compared to conventional RGB Video rating

Schroeder, S., Hesse, N., Weinberger, R., Tacke, U., Gerstl, L., Hilgendorff, A., Heinen, F., Arens, M., Bodensteiner, C., Dijkstra, L. J., Pujades, S., Black, M., Hadders-Algra, M.

Early Human Development, 2020 (article)

Abstract
Background: General Movement Assessment (GMA) is a powerful tool to predict Cerebral Palsy (CP). Yet, GMA requires substantial training hampering its implementation in clinical routine. This inspired a world-wide quest for automated GMA. Aim: To test whether a low-cost, marker-less system for three-dimensional motion capture from RGB depth sequences using a whole body infant model may serve as the basis for automated GMA. Study design: Clinical case study at an academic neurodevelopmental outpatient clinic. Subjects: Twenty-nine high-risk infants were recruited and assessed at their clinical follow-up at 2-4 month corrected age (CA). Their neurodevelopmental outcome was assessed regularly up to 12-31 months CA. Outcome measures: GMA according to Hadders-Algra by a masked GMA-expert of conventional and computed 3D body model (“SMIL motion”) videos of the same GMs. Agreement between both GMAs was assessed, and sensitivity and specificity of both methods to predict CP at ≥12 months CA. Results: The agreement of the two GMA ratings was substantial, with κ=0.66 for the classification of definitely abnormal (DA) GMs and an ICC of 0.887 (95% CI 0.762;0.947) for a more detailed GM-scoring. Five children were diagnosed with CP (four bilateral, one unilateral CP). The GMs of the child with unilateral CP were twice rated as mildly abnormal. DA-ratings of both videos predicted bilateral CP well: sensitivity 75% and 100%, specificity 88% and 92% for conventional and SMIL motion videos, respectively. Conclusions: Our computed infant 3D full body model is an attractive starting point for automated GMA in infants at risk of CP.

ps

[BibTex]

[BibTex]


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Visual-Inertial Mapping with Non-Linear Factor Recovery

Usenko, V., Demmel, N., Schubert, D., Stückler, J., Cremers, D.

IEEE Robotics and Automation Letters (RA-L), 5, 2020, accepted for presentation at IEEE International Conference on Robotics and Automation (ICRA) 2020, to appear, arXiv:1904.06504 (article)

Abstract
Cameras and inertial measurement units are complementary sensors for ego-motion estimation and environment mapping. Their combination makes visual-inertial odometry (VIO) systems more accurate and robust. For globally consistent mapping, however, combining visual and inertial information is not straightforward. To estimate the motion and geometry with a set of images large baselines are required. Because of that, most systems operate on keyframes that have large time intervals between each other. Inertial data on the other hand quickly degrades with the duration of the intervals and after several seconds of integration, it typically contains only little useful information. In this paper, we propose to extract relevant information for visual-inertial mapping from visual-inertial odometry using non-linear factor recovery. We reconstruct a set of non-linear factors that make an optimal approximation of the information on the trajectory accumulated by VIO. To obtain a globally consistent map we combine these factors with loop-closing constraints using bundle adjustment. The VIO factors make the roll and pitch angles of the global map observable, and improve the robustness and the accuracy of the mapping. In experiments on a public benchmark, we demonstrate superior performance of our method over the state-of-the-art approaches.

ev

[BibTex]

[BibTex]


Trunk pitch oscillations for energy trade-offs in bipedal running birds and robots
Trunk pitch oscillations for energy trade-offs in bipedal running birds and robots

Oezge Drama, , Badri-Spröwitz, A.

Bioinspiration & Biomimetics, 2020 (article)

Abstract
Bipedal animals have diverse morphologies and advanced locomotion abilities. Terrestrial birds, in particular, display agile, efficient, and robust running motion, in which they exploit the interplay between the body segment masses and moment of inertias. On the other hand, most legged robots are not able to generate such versatile and energy-efficient motion and often disregard trunk movements as a means to enhance their locomotion capabilities. Recent research investigated how trunk motions affect the gait characteristics of humans, but there is a lack of analysis across different bipedal morphologies. To address this issue, we analyze avian running based on a spring-loaded inverted pendulum model with a pronograde (horizontal) trunk. We use a virtual point based control scheme and modify the alignment of the ground reaction forces to assess how our control strategy influences the trunk pitch oscillations and energetics of the locomotion. We derive three potential key strategies to leverage trunk pitch motions that minimize either the energy fluctuations of the center of mass or the work performed by the hip and leg. We suggest how these strategies could be used in legged robotics.

dlg

link (url) DOI [BibTex]


Spatial Scheduling of Informative Meetings for Multi-Agent Persistent Coverage
Spatial Scheduling of Informative Meetings for Multi-Agent Persistent Coverage

Haksar, R. N., Trimpe, S., Schwager, M.

IEEE Robotics and Automation Letters, 2020 (article) Accepted

ics

DOI [BibTex]

DOI [BibTex]


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Thermal nucleation and high-resolution imaging of submicrometer magnetic bubbles in thin thulium iron garnet films with perpendicular anisotropy

Büttner, F., Mawass, M. A., Bauer, J., Rosenberg, E., Caretta, L., Avci, C. O., Gräfe, J., Finizio, S., Vaz, C. A. F., Novakovic, N., Weigand, M., Litzius, K., Förster, J., Träger, N., Groß, F., Suzuki, D., Huang, M., Bartell, J., Kronast, F., Raabe, J., Schütz, G., Ross, C. A., Beach, G. S. D.

{Physical Review Materials}, 4(1), American Physical Society, College Park, MD, 2020 (article)

mms

DOI [BibTex]

DOI [BibTex]


Safe and Fast Tracking on a Robot Manipulator: Robust MPC and Neural Network Control
Safe and Fast Tracking on a Robot Manipulator: Robust MPC and Neural Network Control

Nubert, J., Koehler, J., Berenz, V., Allgower, F., Trimpe, S.

IEEE Robotics and Automation Letters, 2020 (article) Accepted

Abstract
Fast feedback control and safety guarantees are essential in modern robotics. We present an approach that achieves both by combining novel robust model predictive control (MPC) with function approximation via (deep) neural networks (NNs). The result is a new approach for complex tasks with nonlinear, uncertain, and constrained dynamics as are common in robotics. Specifically, we leverage recent results in MPC research to propose a new robust setpoint tracking MPC algorithm, which achieves reliable and safe tracking of a dynamic setpoint while guaranteeing stability and constraint satisfaction. The presented robust MPC scheme constitutes a one-layer approach that unifies the often separated planning and control layers, by directly computing the control command based on a reference and possibly obstacle positions. As a separate contribution, we show how the computation time of the MPC can be drastically reduced by approximating the MPC law with a NN controller. The NN is trained and validated from offline samples of the MPC, yielding statistical guarantees, and used in lieu thereof at run time. Our experiments on a state-of-the-art robot manipulator are the first to show that both the proposed robust and approximate MPC schemes scale to real-world robotic systems.

am ics

arXiv PDF DOI [BibTex]

arXiv PDF DOI [BibTex]

2007


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A Tutorial on Spectral Clustering

von Luxburg, U.

Statistics and Computing, 17(4):395-416, December 2007 (article)

Abstract
In recent years, spectral clustering has become one of the most popular modern clustering algorithms. It is simple to implement, can be solved efficiently by standard linear algebra software, and very often outperforms traditional clustering algorithms such as the k-means algorithm. On the first glance spectral clustering appears slightly mysterious, and it is not obvious to see why it works at all and what it really does. The goal of this tutorial is to give some intuition on those questions. We describe different graph Laplacians and their basic properties, present the most common spectral clustering algorithms, and derive those algorithms from scratch by several different approaches. Advantages and disadvantages of the different spectral clustering algorithms are discussed.

ei

PDF PDF DOI [BibTex]

2007


PDF PDF DOI [BibTex]


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A Tutorial on Kernel Methods for Categorization

Jäkel, F., Schölkopf, B., Wichmann, F.

Journal of Mathematical Psychology, 51(6):343-358, December 2007 (article)

Abstract
The abilities to learn and to categorize are fundamental for cognitive systems, be it animals or machines, and therefore have attracted attention from engineers and psychologists alike. Modern machine learning methods and psychological models of categorization are remarkably similar, partly because these two fields share a common history in artificial neural networks and reinforcement learning. However, machine learning is now an independent and mature field that has moved beyond psychologically or neurally inspired algorithms towards providing foundations for a theory of learning that is rooted in statistics and functional analysis. Much of this research is potentially interesting for psychological theories of learning and categorization but also hardly accessible for psychologists. Here, we provide a tutorial introduction to a popular class of machine learning tools, called kernel methods. These methods are closely related to perceptrons, radial-basis-function neural networks and exemplar theories of catego rization. Recent theoretical advances in machine learning are closely tied to the idea that the similarity of patterns can be encapsulated in a positive definite kernel. Such a positive definite kernel can define a reproducing kernel Hilbert space which allows one to use powerful tools from functional analysis for the analysis of learning algorithms. We give basic explanations of some key concepts—the so-called kernel trick, the representer theorem and regularization—which may open up the possibility that insights from machine learning can feed back into psychology.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Accurate Splice site Prediction Using Support Vector Machines

Sonnenburg, S., Schweikert, G., Philips, P., Behr, J., Rätsch, G.

BMC Bioinformatics, 8(Supplement 10):1-16, December 2007 (article)

Abstract
Background: For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to solve these tasks. Results: In this work we consider Support Vector Machines for splice site recognition. We employ the so-called weighted degree kernel which turns out well suited for this task, as we will illustrate in several experiments where we compare its prediction accuracy with that of recently proposed systems. We apply our method to the genome-wide recognition of splice sites in Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Danio rerio, and Homo sapiens. Our performance estimates indicate that splice sites can be recognized very accurately in these genomes and that our method outperforms many other methods including Markov Chains, GeneSplicer and SpliceMachine. We provide genome-wide predictions of splice sites and a stand-alone prediction tool ready to be used for incorporation in a gene finder. Availability: Data, splits, additional information on the model selection, the whole genome predictions, as well as the stand-alone prediction tool are available for download at http:// www.fml.mpg.de/raetsch/projects/splice.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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A unifying framework for robot control with redundant DOFs

Peters, J., Mistry, M., Udwadia, F., Nakanishi, J., Schaal, S.

Autonomous Robots, 24(1):1-12, October 2007 (article)

Abstract
Recently, Udwadia (Proc. R. Soc. Lond. A 2003:1783–1800, 2003) suggested to derive tracking controllers for mechanical systems with redundant degrees-of-freedom (DOFs) using a generalization of Gauss’ principle of least constraint. This method allows reformulating control problems as a special class of optimal controllers. In this paper, we take this line of reasoning one step further and demonstrate that several well-known and also novel nonlinear robot control laws can be derived from this generic methodology. We show experimental verifications on a Sarcos Master Arm robot for some of the derived controllers. The suggested approach offers a promising unification and simplification of nonlinear control law design for robots obeying rigid body dynamics equations, both with or without external constraints, with over-actuation or underactuation, as well as open-chain and closed-chain kinematics.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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The Need for Open Source Software in Machine Learning

Sonnenburg, S., Braun, M., Ong, C., Bengio, S., Bottou, L., Holmes, G., LeCun, Y., Müller, K., Pereira, F., Rasmussen, C., Rätsch, G., Schölkopf, B., Smola, A., Vincent, P., Weston, J., Williamson, R.

Journal of Machine Learning Research, 8, pages: 2443-2466, October 2007 (article)

Abstract
Open source tools have recently reached a level of maturity which makes them suitable for building large-scale real-world systems. At the same time, the field of machine learning has developed a large body of powerful learning algorithms for diverse applications. However, the true potential of these methods is not realized, since existing implementations are not openly shared, resulting in software with low usability, and weak interoperability. We argue that this situation can be significantly improved by increasing incentives for researchers to publish their software under an open source model. Additionally, we outline the problems authors are faced with when trying to publish algorithmic implementations of machine learning methods. We believe that a resource of peer reviewed software accompanied by short articles would be highly valuable to both the machine learning and the general scientific community.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Some observations on the masking effects of Mach bands

Curnow, T., Cowie, DA., Henning, GB., Hill, NJ.

Journal of the Optical Society of America A, 24(10):3233-3241, October 2007 (article)

Abstract
There are 8 cycle / deg ripples or oscillations in performance as a function of location near Mach bands in experiments measuring Mach bands’ masking effects on random polarity signal bars. The oscillations with increments are 180 degrees out of phase with those for decrements. The oscillations, much larger than the measurement error, appear to relate to the weighting function of the spatial-frequency-tuned channel detecting the broad- band signals. The ripples disappear with step maskers and become much smaller at durations below 25 ms, implying either that the site of masking has changed or that the weighting function and hence spatial-frequency tuning is slow to develop.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Mining complex genotypic features for predicting HIV-1 drug resistance

Saigo, H., Uno, T., Tsuda, K.

Bioinformatics, 23(18):2455-2462, September 2007 (article)

Abstract
Human immunodeficiency virus type 1 (HIV-1) evolves in human body, and its exposure to a drug often causes mutations that enhance the resistance against the drug. To design an effective pharmacotherapy for an individual patient, it is important to accurately predict the drug resistance based on genotype data. Notably, the resistance is not just the simple sum of the effects of all mutations. Structural biological studies suggest that the association of mutations is crucial: Even if mutations A or B alone do not affect the resistance, a significant change might happen when the two mutations occur together. Linear regression methods cannot take the associations into account, while decision tree methods can reveal only limited associations. Kernel methods and neural networks implicitly use all possible associations for prediction, but cannot select salient associations explicitly. Our method, itemset boosting, performs linear regression in the complete space of power sets of mutations. It implements a forward feature selection procedure where, in each iteration, one mutation combination is found by an efficient branch-and-bound search. This method uses all possible combinations, and salient associations are explicitly shown. In experiments, our method worked particularly well for predicting the resistance of nucleotide reverse transcriptase inhibitors (NRTIs). Furthermore, it successfully recovered many mutation associations known in biological literature.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Advances in Neural Information Processing Systems 19: Proceedings of the 2006 Conference

Schölkopf, B., Platt, J., Hofmann, T.

Proceedings of the Twentieth Annual Conference on Neural Information Processing Systems (NIPS 2006), pages: 1690, MIT Press, Cambridge, MA, USA, 20th Annual Conference on Neural Information Processing Systems (NIPS), September 2007 (proceedings)

Abstract
The annual Neural Information Processing Systems (NIPS) conference is the flagship meeting on neural computation and machine learning. It draws a diverse group of attendees--physicists, neuroscientists, mathematicians, statisticians, and computer scientists--interested in theoretical and applied aspects of modeling, simulating, and building neural-like or intelligent systems. The presentations are interdisciplinary, with contributions in algorithms, learning theory, cognitive science, neuroscience, brain imaging, vision, speech and signal processing, reinforcement learning, and applications. Only twenty-five percent of the papers submitted are accepted for presentation at NIPS, so the quality is exceptionally high. This volume contains the papers presented at the December 2006 meeting, held in Vancouver.

ei

Web [BibTex]

Web [BibTex]


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Real-Time Fetal Heart Monitoring in Biomagnetic Measurements Using Adaptive Real-Time ICA

Waldert, S., Bensch, M., Bogdan, M., Rosenstiel, W., Schölkopf, B., Lowery, C., Eswaran, H., Preissl, H.

IEEE Transactions on Biomedical Engineering, 54(10):1867-1874, September 2007 (article)

Abstract
Electrophysiological signals of the developing fetal brain and heart can be investigated by fetal magnetoencephalography (fMEG). During such investigations, the fetal heart activity and that of the mother should be monitored continuously to provide an important indication of current well-being. Due to physical constraints of an fMEG system, it is not possible to use clinically established heart monitors for this purpose. Considering this constraint, we developed a real-time heart monitoring system for biomagnetic measurements and showed its reliability and applicability in research and for clinical examinations. The developed system consists of real-time access to fMEG data, an algorithm based on Independent Component Analysis (ICA), and a graphical user interface (GUI). The algorithm extracts the current fetal and maternal heart signal from a noisy and artifact-contaminated data stream in real-time and is able to adapt automatically to continuously varying environmental parameters. This algorithm has been na med Adaptive Real-time ICA (ARICA) and is applicable to real-time artifact removal as well as to related blind signal separation problems.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Feature Selection for Trouble Shooting in Complex Assembly Lines

Pfingsten, T., Herrmann, D., Schnitzler, T., Feustel, A., Schölkopf, B.

IEEE Transactions on Automation Science and Engineering, 4(3):465-469, July 2007 (article)

Abstract
The final properties of sophisticated products can be affected by many unapparent dependencies within the manufacturing process, and the products’ integrity can often only be checked in a final measurement. Troubleshooting can therefore be very tedious if not impossible in large assembly lines. In this paper we show that Feature Selection is an efficient tool for serial-grouped lines to reveal causes for irregularities in product attributes. We compare the performance of several methods for Feature Selection on real-world problems in mass-production of semiconductor devices. Note to Practitioners— We present a data based procedure to localize flaws in large production lines: using the results of final quality inspections and information about which machines processed which batches, we are able to identify machines which cause low yield.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Gene selection via the BAHSIC family of algorithms

Song, L., Bedo, J., Borgwardt, K., Gretton, A., Smola, A.

Bioinformatics, 23(13: ISMB/ECCB 2007 Conference Proceedings):i490-i498, July 2007 (article)

Abstract
Motivation: Identifying significant genes among thousands of sequences on a microarray is a central challenge for cancer research in bioinformatics. The ultimate goal is to detect the genes that are involved in disease outbreak and progression. A multitude of methods have been proposed for this task of feature selection, yet the selected gene lists differ greatly between different methods. To accomplish biologically meaningful gene selection from microarray data, we have to understand the theoretical connections and the differences between these methods. In this article, we define a kernel-based framework for feature selection based on the Hilbert–Schmidt independence criterion and backward elimination, called BAHSIC. We show that several well-known feature selectors are instances of BAHSIC, thereby clarifying their relationship. Furthermore, by choosing a different kernel, BAHSIC allows us to easily define novel feature selection algorithms. As a further advantage, feature selection via BAHSIC works directly on multiclass problems. Results: In a broad experimental evaluation, the members of the BAHSIC family reach high levels of accuracy and robustness when compared to other feature selection techniques. Experiments show that features selected with a linear kernel provide the best classification performance in general, but if strong non-linearities are present in the data then non-linear kernels can be more suitable.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Phenotyping of Chondrocytes In Vivo and In Vitro Using cDNA Array Technology

Zien, A., Gebhard, P., Fundel, K., Aigner, T.

Clinical Orthopaedics and Related Research, 460, pages: 226-233, July 2007 (article)

Abstract
The cDNA array technology is a powerful tool to analyze a high number of genes in parallel. We investigated whether large-scale gene expression analysis allows clustering and identification of cellular phenotypes of chondrocytes in different in vivo and in vitro conditions. In 100% of cases, clustering analysis distinguished between in vivo and in vitro samples, suggesting fundamental differences in chondrocytes in situ and in vitro regardless of the culture conditions or disease status. It also allowed us to differentiate between healthy and osteoarthritic cartilage. The clustering also revealed the relative importance of the investigated culturing conditions (stimulation agent, stimulation time, bead/monolayer). We augmented the cluster analysis with a statistical search for genes showing differential expression. The identified genes provided hints to the molecular basis of the differences between the sample classes. Our approach shows the power of modern bioinformatic algorithms for understanding and class ifying chondrocytic phenotypes in vivo and in vitro. Although it does not generate new experimental data per se, it provides valuable information regarding the biology of chondrocytes and may provide tools for diagnosing and staging the osteoarthritic disease process.

ei

DOI [BibTex]

DOI [BibTex]


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Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

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

Science, 317(5836):338-342, July 2007 (article)

Abstract
The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and ~4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Graph Laplacians and their Convergence on Random Neighborhood Graphs

Hein, M., Audibert, J., von Luxburg, U.

Journal of Machine Learning Research, 8, pages: 1325-1370, June 2007 (article)

Abstract
Given a sample from a probability measure with support on a submanifold in Euclidean space one can construct a neighborhood graph which can be seen as an approximation of the submanifold. The graph Laplacian of such a graph is used in several machine learning methods like semi-supervised learning, dimensionality reduction and clustering. In this paper we determine the pointwise limit of three different graph Laplacians used in the literature as the sample size increases and the neighborhood size approaches zero. We show that for a uniform measure on the submanifold all graph Laplacians have the same limit up to constants. However in the case of a non-uniform measure on the submanifold only the so called random walk graph Laplacian converges to the weighted Laplace-Beltrami operator.

ei

PDF PDF [BibTex]

PDF PDF [BibTex]


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Bayesian Reconstruction of the Density of States

Habeck, M.

Physical Review Letters, 98(20, 200601):1-4, May 2007 (article)

Abstract
A Bayesian framework is developed to reconstruct the density of states from multiple canonical simulations. The framework encompasses the histogram reweighting method of Ferrenberg and Swendsen. The new approach applies to nonparametric as well as parametric models and does not require simulation data to be discretized. It offers a means to assess the precision of the reconstructed density of states and of derived thermodynamic quantities.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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PALMA: mRNA to Genome Alignments using Large Margin Algorithms

Schulze, U., Hepp, B., Ong, C., Rätsch, G.

Bioinformatics, 23(15):1892-1900, May 2007 (article)

Abstract
Motivation: Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to genomic DNA is still a challenging task. Results: We present a novel approach based on large margin learning that combines accurate plice site predictions with common sequence alignment techniques. By solving a convex optimization problem, our algorithm – called PALMA – tunes the parameters of the model such that true alignments score higher than other alignments. We study the accuracy of alignments of mRNAs containing artificially generated micro-exons to genomic DNA. In a carefully designed experiment, we show that our algorithm accurately identifies the intron boundaries as well as boundaries of the optimal local alignment. It outperforms all other methods: for 5702 artificially shortened EST sequences from C. elegans and human it correctly identifies the intron boundaries in all except two cases. The best other method is a recently proposed method called exalin which misaligns 37 of the sequences. Our method also demonstrates robustness to mutations, insertions and deletions, retaining accuracy even at high noise levels. Availability: Datasets for training, evaluation and testing, additional results and a stand-alone alignment tool implemented in C++ and python are available at http://www.fml.mpg.de/raetsch/projects/palma.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Training a Support Vector Machine in the Primal

Chapelle, O.

Neural Computation, 19(5):1155-1178, March 2007 (article)

Abstract
Most literature on Support Vector Machines (SVMs) concentrate on the dual optimization problem. In this paper, we would like to point out that the primal problem can also be solved efficiently, both for linear and non-linear SVMs, and that there is no reason for ignoring this possibilty. On the contrary, from the primal point of view new families of algorithms for large scale SVM training can be investigated.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning

Rätsch, G., Sonnenburg, S., Srinivasan, J., Witte, H., Müller, K., Sommer, R., Schölkopf, B.

PLoS Computational Biology, 3(2, e20):0313-0322, February 2007 (article)

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Statistical Consistency of Kernel Canonical Correlation Analysis

Fukumizu, K., Bach, F., Gretton, A.

Journal of Machine Learning Research, 8, pages: 361-383, February 2007 (article)

Abstract
While kernel canonical correlation analysis (CCA) has been applied in many contexts, the convergence of finite sample estimates of the associated functions to their population counterparts has not yet been established. This paper gives a mathematical proof of the statistical convergence of kernel CCA, providing a theoretical justification for the method. The proof uses covariance operators defined on reproducing kernel Hilbert spaces, and analyzes the convergence of their empirical estimates of finite rank to their population counterparts, which can have infinite rank. The result also gives a sufficient condition for convergence on the regularization coefficient involved in kernel CCA: this should decrease as n^{-1/3}, where n is the number of data.

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PDF [BibTex]

PDF [BibTex]


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Some observations on the pedestal effect

Henning, G., Wichmann, F.

Journal of Vision, 7(1:3):1-15, January 2007 (article)

Abstract
The pedestal or dipper effect is the large improvement in the detectability of a sinusoidal grating observed when it is added to a masking or pedestal grating of the same spatial frequency, orientation, and phase. We measured the pedestal effect in both broadband and notched noiseVnoise from which a 1.5-octave band centered on the signal frequency had been removed. Although the pedestal effect persists in broadband noise, it almost disappears in the notched noise. Furthermore, the pedestal effect is substantial when either high- or low-pass masking noise is used. We conclude that the pedestal effect in the absence of notched noise results principally from the use of information derived from channels with peak sensitivities at spatial frequencies different from that of the signal and the pedestal. We speculate that the spatial-frequency components of the notched noise above and below the spatial frequency of the signal and the pedestal prevent ‘‘off-frequency looking,’’ that is, prevent the use of information about changes in contrast carried in channels tuned to spatial frequencies that are very much different from that of the signal and the pedestal. Thus, the pedestal or dipper effect measured without notched noise appears not to be a characteristic of individual spatial-frequency-tuned channels.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Cue Combination and the Effect of Horizontal Disparity and Perspective on Stereoacuity

Zalevski, AM., Henning, GB., Hill, NJ.

Spatial Vision, 20(1):107-138, January 2007 (article)

Abstract
Relative depth judgments of vertical lines based on horizontal disparity deteriorate enormously when the lines form part of closed configurations (Westheimer, 1979). In studies showing this effect, perspective was not manipulated and thus produced inconsistency between horizontal disparity and perspective. We show that stereoacuity improves dramatically when perspective and horizontal disparity are made consistent. Observers appear to use unhelpful perspective cues in judging the relative depth of the vertical sides of rectangles in a way not incompatible with a form of cue weighting. However, 95% confidence intervals for the weights derived for cues usually exceed the a-priori [0-1] range.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


Frequency-domain displacement sensing with a fiber ring-resonator containing a variable gap
Frequency-domain displacement sensing with a fiber ring-resonator containing a variable gap

Vollmer, F., Fischer, P.

SENSORS AND ACTUATORS A-PHYSICAL, 134(2):410-413, 2007 (article)

Abstract
Ring-resonators are in general not amenable to strain-free (non-contact) displacement measurements. We show that this limitation may be overcome if the ring-resonator, here a fiber-loop, is designed to contain a gap, such that the light traverses a free-space part between two aligned waveguide ends. Displacements are determined with nanometer sensitivity by measuring the associated changes in the resonance frequencies. Miniaturization should increase the sensitivity of the ring-resonator interferometer. Ring geometries that contain an optical circulator can be used to profile reflective samples. (c) 2006 Elsevier B.V. All rights reserved.

pf

DOI [BibTex]

DOI [BibTex]


Observation of the Faraday effect via beam deflection in a longitudinal magnetic field
Observation of the Faraday effect via beam deflection in a longitudinal magnetic field

Ghosh, A., Hill, W., Fischer, P.

PHYSICAL REVIEW A, 76(5), 2007 (article)

Abstract
We show that magnetic-field-induced circular differential deflection of light can be observed in reflection or refraction at a single interface. The difference in the reflection or refraction angles between the two circular polarization components is a function of the magnetic-field strength and the Verdet constant, and permits the observation of the Faraday effect not via polarization rotation in transmission, but via changes in the propagation direction. Deflection measurements do not suffer from n-pi ambiguities and are shown to be another means to map magnetic fields with high axial resolution, or to determine the sign and magnitude of magnetic-field pulses in a single measurement.

pf

DOI [BibTex]