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2019


Soft-magnetic coatings as possible sensors for magnetic imaging of superconductors
Soft-magnetic coatings as possible sensors for magnetic imaging of superconductors

Ionescu, A., Simmendinger, J., Bihler, M., Miksch, C., Fischer, P., Soltan, S., Schütz, G., Albrecht, J.

Supercond. Sci. and Tech., 33, pages: 015002, IOP, December 2019 (article)

Abstract
Magnetic imaging of superconductors typically requires a soft-magnetic material placed on top of the superconductor to probe local magnetic fields. For reasonable results the influence of the magnet onto the superconductor has to be small. Thin YBCO films with soft-magnetic coatings are investigated using SQUID magnetometry. Detailed measurements of the magnetic moment as a function of temperature, magnetic field and time have been performed for different heterostructures. It is found that the modification of the superconducting transport in these heterostructures strongly depends on the magnetic and structural properties of the soft-magnetic material. This effect is especially pronounced for an inhomogeneous coating consisting of ferromagnetic nanoparticles.

pf mms

link (url) DOI [BibTex]

2019


link (url) DOI [BibTex]


Acoustic hologram enhanced phased arrays for ultrasonic particle manipulation
Acoustic hologram enhanced phased arrays for ultrasonic particle manipulation

Cox, L., Melde, K., Croxford, A., Fischer, P., Drinkwater, B.

Phys. Rev. Applied, 12, pages: 064055, November 2019 (article)

Abstract
The ability to shape ultrasound fields is important for particle manipulation, medical therapeutics and imaging applications. If the amplitude and/or phase is spatially varied across the wavefront then it is possible to project ‘acoustic images’. When attempting to form an arbitrary desired static sound field, acoustic holograms are superior to phased arrays due to their significantly higher phase fidelity. However, they lack the dynamic flexibility of phased arrays. Here, we demonstrate how to combine the high-fidelity advantages of acoustic holograms with the dynamic control of phased arrays in the ultrasonic frequency range. Holograms are used with a 64-element phased array, driven with continuous excitation. Moving the position of the projected hologram via phase delays which steer the output beam is demonstrated experimentally. This allows the creation of a much more tightly focused point than with the phased array alone, whilst still being reconfigurable. It also allows the complex movement at a water-air interface of a “phase surfer” along a phase track or the manipulation of a more arbitrarily shaped particle via amplitude traps. Furthermore, a particle manipulation device with two emitters and a single split hologram is demonstrated that allows the positioning of a “phase surfer” along a 1D axis. This paper opens the door for new applications with complex manipulation of ultrasound whilst minimising the complexity and cost of the apparatus.

pf

link (url) DOI [BibTex]

link (url) DOI [BibTex]


Fast Feedback Control over Multi-hop Wireless Networks with Mode Changes and Stability Guarantees
Fast Feedback Control over Multi-hop Wireless Networks with Mode Changes and Stability Guarantees

Baumann, D., Mager, F., Jacob, R., Thiele, L., Zimmerling, M., Trimpe, S.

ACM Transactions on Cyber-Physical Systems, 4(2):18, November 2019 (article)

ics

arXiv PDF DOI [BibTex]

arXiv PDF DOI [BibTex]


A Helical Microrobot with an Optimized Propeller-Shape for Propulsion in Viscoelastic Biological Media
A Helical Microrobot with an Optimized Propeller-Shape for Propulsion in Viscoelastic Biological Media

Li., D., Jeong, M., Oren, E., Yu, T., Qiu, T.

Robotics, 8, pages: 87, MDPI, October 2019 (article)

Abstract
One major challenge for microrobots is to penetrate and effectively move through viscoelastic biological tissues. Most existing microrobots can only propel in viscous liquids. Recent advances demonstrate that sub-micron robots can actively penetrate nanoporous biological tissue, such as the vitreous of the eye. However, it is still difficult to propel a micron-sized device through dense biological tissue. Here, we report that a special twisted helical shape together with a high aspect ratio in cross-section permit a microrobot with a diameter of hundreds-of-micrometers to move through mouse liver tissue. The helical microrobot is driven by a rotating magnetic field and localized by ultrasound imaging inside the tissue. The twisted ribbon is made of molybdenum and a sharp tip is chemically etched to generate a higher pressure at the edge of the propeller to break the biopolymeric network of the dense tissue.

pf

link (url) DOI [BibTex]


Acoustic Holographic Cell Patterning in a Biocompatible Hydrogel
Acoustic Holographic Cell Patterning in a Biocompatible Hydrogel

Ma, Z., Holle, A., Melde, K., Qiu, T., Poeppel, K., Kadiri, V., Fischer, P.

Adv. Mat., October 2019 (article)

Abstract
Acoustophoresis is promising as a rapid, biocompatible, non-contact cell manipulation method, where cells are arranged along the nodes or antinodes of the acoustic field. Typically, the acoustic field is formed in a resonator, which results in highly symmetric regular patterns. However, arbitrary, non-symmetrically shaped cell assemblies are necessary to obtain the irregular cellular arrangements found in biological tissues. We show that arbitrarily shaped cell patterns can be obtained from the complex acoustic field distribution defined by an acoustic hologram. Attenuation of the sound field induces localized acoustic streaming and the resultant convection flow gently delivers the suspended cells to the image plane where they form the designed pattern. We show that the process can be implemented in a biocompatible collagen solution, which can then undergo gelation to immobilize the cell pattern inside the viscoelastic matrix. The patterned cells exhibit F-actin-based protrusions, which indicates that the cells grow and thrive within the matrix. Cell viability assays and brightfield imaging after one week confirm cell survival and that the patterns persist. Acoustophoretic cell manipulation by holographic fields thus holds promise for non-contact, long-range, long-term cellular pattern formation, with a wide variety of potential applications in tissue engineering and mechanobiology.

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link (url) DOI [BibTex]


A High-Fidelity Phantom for the Simulation and Quantitative Evaluation of Transurethral Resection of the Prostate
A High-Fidelity Phantom for the Simulation and Quantitative Evaluation of Transurethral Resection of the Prostate

Choi, E., Adams, F., Gengenbacher, A., Schlager, D., Palagi, S., Müller, P., Wetterauer, U., Miernik, A., Fischer, P., Qiu, T.

Annals of Biomed. Eng., October 2019 (article)

Abstract
Transurethral resection of the prostate (TURP) is a minimally invasive endoscopic procedure that requires experience and skill of the surgeon. To permit surgical training under realistic conditions we report a novel phantom of the human prostate that can be resected with TURP. The phantom mirrors the anatomy and haptic properties of the gland and permits quantitative evaluation of important surgical performance indicators. Mixtures of soft materials are engineered to mimic the physical properties of the human tissue, including the mechanical strength, the electrical and thermal conductivity, and the appearance under an endoscope. Electrocautery resection of the phantom closely resembles the procedure on human tissue. Ultrasound contrast agent was applied to the central zone, which was not detectable by the surgeon during the surgery but showed high contrast when imaged after the surgery, to serve as a label for the quantitative evaluation of the surgery. Quantitative criteria for performance assessment are established and evaluated by automated image analysis. We present the workflow of a surgical simulation on a prostate phantom followed by quantitative evaluation of the surgical performance. Surgery on the phantom is useful for medical training, and enables the development and testing of endoscopic and minimally invasive surgical instruments.

pf

link (url) DOI [BibTex]

link (url) DOI [BibTex]


Interactive Materials – Drivers of Future Robotic Systems
Interactive Materials – Drivers of Future Robotic Systems

Fischer, P.

Adv. Mat., October 2019 (article)

Abstract
A robot senses its environment, processes the sensory information, acts in response to these inputs, and possibly communicates with the outside world. Robots generally achieve these tasks with electronics-based hardware or by receiving inputs from some external hardware. In contrast, simple microorganisms can autonomously perceive, act, and communicate via purely physicochemical processes in soft material systems. A key property of biological systems is that they are built from energy-consuming ‘active’ units. Exciting developments in material science show that even very simple artificial active building blocks can show surprisingly rich emergent behaviors. Active non-equilibrium systems are therefore predicted to play an essential role to realize interactive materials. A major challenge is to find robust ways to couple and integrate the energy-consuming building blocks to the mechanical structure of the material. However, success in this endeavor will lead to a new generation of sophisticated micro- and soft-robotic systems that can operate autonomously.

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[BibTex]


Arrays of plasmonic nanoparticle dimers with defined nanogap spacers
Arrays of plasmonic nanoparticle dimers with defined nanogap spacers

Jeong, H., Adams, M. C., Guenther, J., Alarcon-Correa, M., Kim, I., Choi, E., Miksch, C., Mark, A. F. M., Mark, A. G., Fischer, P.

ACS Nano, September 2019 (article)

Abstract
Plasmonic molecules are building blocks of metallic nanostructures that give rise to intriguing optical phenomena with similarities to those seen in molecular systems. The ability to design plasmonic hybrid structures and molecules with nanometric resolution would enable applications in optical metamaterials and sensing that presently cannot be demonstrated, because of a lack of suitable fabrication methods allowing the structural control of the plasmonic atoms on a large scale. Here we demonstrate a wafer-scale “lithography-free” parallel fabrication scheme to realize nanogap plasmonic meta-molecules with precise control over their size, shape, material, and orientation. We demonstrate how we can tune the corresponding coupled resonances through the entire visible spectrum. Our fabrication method, based on glancing angle physical vapor deposition with gradient shadowing, permits critical parameters to be varied across the wafer and thus is ideally suited to screen potential structures. We obtain billions of aligned dimer structures with controlled variation of the spectral properties across the wafer. We spectroscopically map the plasmonic resonances of gold dimer structures and show that they not only are in good agreement with numerically modeled spectra, but also remain functional, at least for a year, in ambient conditions.

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link (url) DOI [BibTex]


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Convolutional neural networks: A magic bullet for gravitational-wave detection?

Gebhard, T., Kilbertus, N., Harry, I., Schölkopf, B.

Physical Review D, 100(6):063015, American Physical Society, September 2019 (article)

ei

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Data scarcity, robustness and extreme multi-label classification

Babbar, R., Schölkopf, B.

Machine Learning, 108(8):1329-1351, September 2019, Special Issue of the ECML PKDD 2019 Journal Track (article)

ei

DOI [BibTex]

DOI [BibTex]


Genetically modified M13 bacteriophage nanonets for enzyme catalysis and recovery
Genetically modified M13 bacteriophage nanonets for enzyme catalysis and recovery

Kadiri, V. M., Alarcon-Correa, M., Guenther, J. P., Ruppert, J., Bill, J., Rothenstein, D., Fischer, P.

Catalysts, 9, pages: 723, August 2019 (article)

Abstract
Enzyme-based biocatalysis exhibits multiple advantages over inorganic catalysts, including the biocompatibility and the unchallenged specificity of enzymes towards their substrate. The recovery and repeated use of enzymes is essential for any realistic application in biotechnology, but is not easily achieved with current strategies. For this purpose, enzymes are often immobilized on inorganic scaffolds, which could entail a reduction of the enzymes’ activity. Here, we show that immobilization to a nano-scaled biological scaffold, a nanonetwork of end-to-end cross-linked M13 bacteriophages, ensures high enzymatic activity and at the same time allows for the simple recovery of the enzymes. The bacteriophages have been genetically engineered to express AviTags at their ends, which permit biotinylation and their specific end-to-end self-assembly while allowing space on the major coat protein for enzyme coupling. We demonstrate that the phages form nanonetwork structures and that these so-called nanonets remain highly active even after re-using the nanonets multiple times in a flow-through reactor.

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link (url) DOI [BibTex]


Light-controlled micromotors and soft microrobots
Light-controlled micromotors and soft microrobots

Palagi, S., Singh, D. P., Fischer, P.

Adv. Opt. Mat., 7, pages: 1900370, August 2019 (article)

Abstract
Mobile microscale devices and microrobots can be powered by catalytic reactions (chemical micromotors) or by external fields. This report is focused on the role of light as a versatile means for wirelessly powering and controlling such microdevices. Recent advances in the development of autonomous micromotors are discussed, where light permits their actuation with unprecedented control and thereby enables advances in the field of active matter. In addition, structuring the light field is a new means to drive soft microrobots that are based on (photo‐) responsive polymers. The behavior of the two main classes of thermo‐ and photoresponsive polymers adopted in microrobotics (poly(N‐isopropylacrylamide) and liquid‐crystal elastomers) is analyzed, and recent applications are reported. The advantages and limitations of controlling micromotors and microrobots by light are reviewed, and some of the remaining challenges in the development of novel photo‐active materials for micromotors and microrobots are discussed.

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link (url) DOI [BibTex]


Learning Variable Impedance Control for Contact Sensitive Tasks
Learning Variable Impedance Control for Contact Sensitive Tasks

Bogdanovic, M., Khadiv, M., Righetti, L.

arXiv preprint, arXiv:1907.07500, July 2019 (article)

Abstract
Reinforcement learning algorithms have shown great success in solving different problems ranging from playing video games to robotics. However, they struggle to solve delicate robotic problems, especially those involving contact interactions. Though in principle a policy outputting joint torques should be able to learn these tasks, in practice we see that they have difficulty to robustly solve the problem without any structure in the action space. In this paper, we investigate how the choice of action space can give robust performance in presence of contact uncertainties. We propose to learn a policy that outputs impedance and desired position in joint space as a function of system states without imposing any other structure to the problem. We compare the performance of this approach to torque and position control policies under different contact uncertainties. Extensive simulation results on two different systems, a hopper (floating-base) with intermittent contacts and a manipulator (fixed-base) wiping a table, show that our proposed approach outperforms policies outputting torque or position in terms of both learning rate and robustness to environment uncertainty.

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[BibTex]


Resource-aware IoT Control: Saving Communication through Predictive Triggering
Resource-aware IoT Control: Saving Communication through Predictive Triggering

Trimpe, S., Baumann, D.

IEEE Internet of Things Journal, 6(3):5013-5028, June 2019 (article)

Abstract
The Internet of Things (IoT) interconnects multiple physical devices in large-scale networks. When the 'things' coordinate decisions and act collectively on shared information, feedback is introduced between them. Multiple feedback loops are thus closed over a shared, general-purpose network. Traditional feedback control is unsuitable for design of IoT control because it relies on high-rate periodic communication and is ignorant of the shared network resource. Therefore, recent event-based estimation methods are applied herein for resource-aware IoT control allowing agents to decide online whether communication with other agents is needed, or not. While this can reduce network traffic significantly, a severe limitation of typical event-based approaches is the need for instantaneous triggering decisions that leave no time to reallocate freed resources (e.g., communication slots), which hence remain unused. To address this problem, novel predictive and self triggering protocols are proposed herein. From a unified Bayesian decision framework, two schemes are developed: self triggers that predict, at the current triggering instant, the next one; and predictive triggers that check at every time step, whether communication will be needed at a given prediction horizon. The suitability of these triggers for feedback control is demonstrated in hardware experiments on a cart-pole, and scalability is discussed with a multi-vehicle simulation.

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PDF arXiv DOI [BibTex]

PDF arXiv DOI [BibTex]


Self-Assembled Phage-Based Colloids for High Localized Enzymatic Activity
Self-Assembled Phage-Based Colloids for High Localized Enzymatic Activity

Alarcon-Correa, M., Guenther, J., Troll, J., Kadiri, V. M., Bill, J., Fischer, P., Rothenstein, D.

ACS Nano, March 2019 (article)

Abstract
Catalytically active colloids are model systems for chemical motors and active matter. It is desirable to replace the inorganic catalysts and the toxic fuels that are often used, with biocompatible enzymatic reactions. However, compared to inorganic catalysts, enzyme-coated colloids tend to exhibit less activity. Here, we show that the self-assembly of genetically engineered M13 bacteriophages that bind enzymes to magnetic beads ensures high and localized enzymatic activity. These phage-decorated colloids provide a proteinaceous environment for directed enzyme immobilization. The magnetic properties of the colloidal carrier particle permit repeated enzyme recovery from a reaction solution, while the enzymatic activity is retained. Moreover, localizing the phage-based construct with a magnetic field in a microcontainer allows the enzyme-phage-colloids to function as an enzymatic micropump, where the enzymatic reaction generates a fluid flow. This system shows the fastest fluid flow reported to date by a biocompatible enzymatic micropump. In addition, it is functional in complex media including blood where the enzyme driven micropump can be powered at the physiological blood-urea concentration.

pf

link (url) DOI [BibTex]


Absolute diffusion measurements of active enzyme solutions by NMR
Absolute diffusion measurements of active enzyme solutions by NMR

Guenther, J., Majer, G., Fischer, P.

J. Chem. Phys., 150(124201), March 2019 (article)

Abstract
The diffusion of enzymes is of fundamental importance for many biochemical processes. Enhanced or directed enzyme diffusion can alter the accessibility of substrates and the organization of enzymes within cells. Several studies based on fluorescence correlation spectroscopy (FCS) report enhanced diffusion of enzymes upon interaction with their substrate or inhibitor. In this context, major importance is given to the enzyme fructose-bisphosphate aldolase, for which enhanced diffusion has been reported even though the catalysed reaction is endothermic. Additionally, enhanced diffusion of tracer particles surrounding the active aldolase enzymes has been reported. These studies suggest that active enzymes can act as chemical motors that self-propel and give rise to enhanced diffusion. However, fluorescence studies of enzymes can, despite several advantages, suffer from artefacts. Here we show that the absolute diffusion coefficients of active enzyme solutions can be determined with Pulsed Field Gradient Nuclear Magnetic Resonance (PFG-NMR). The advantage of PFG-NMR is that the motion of the molecule of interest is directly observed in its native state without the need for any labelling. Further, PFG-NMR is model-free and thus yields absolute diffusion constants. Our PFG-NMR experiments of solutions containing active fructose-bisphosphate aldolase from rabbit muscle do not show any diffusion enhancement for the active enzymes nor the surrounding molecules. Additionally, we do not observe any diffusion enhancement of aldolase in the presence of its inhibitor pyrophosphate.

pf

link (url) DOI [BibTex]


Chemical Nanomotors at the Gram Scale Form a Dense Active Optorheological Medium
Chemical Nanomotors at the Gram Scale Form a Dense Active Optorheological Medium

Choudhury, U., Singh, D. P., Qiu, T., Fischer, P.

Adv. Mat., (1807382), Febuary 2019 (article)

Abstract
The rheological properties of a colloidal suspension are a function of the concentration of the colloids and their interactions. While suspensions of passive colloids are well studied and have been shown to form crystals, gels, and glasses, examples of energy‐consuming “active” colloidal suspensions are still largely unexplored. Active suspensions of biological matter, such as motile bacteria or dense mixtures of active actin–motor–protein mixtures have, respectively, reveals superfluid‐like and gel‐like states. Attractive inanimate systems for active matter are chemically self‐propelled particles. It has so far been challenging to use these swimming particles at high enough densities to affect the bulk material properties of the suspension. Here, it is shown that light‐triggered asymmetric titanium dioxide that self‐propel, can be obtained in large quantities, and self‐organize to make a gram‐scale active medium. The suspension shows an activity‐dependent tenfold reversible change in its bulk viscosity.

pf

link (url) DOI [BibTex]


First Observation of Optical Activity in Hyper-Rayleigh Scattering
First Observation of Optical Activity in Hyper-Rayleigh Scattering

Collins, J., Rusimova, K., Hooper, D., Jeong, H. H., Ohnoutek, L., Pradaux-Caggiano, F., Verbiest, T., Carbery, D., Fischer, P., Valev, V.

Phys. Rev. X, 9(011024), January 2019 (article)

Abstract
Chiral nano- or metamaterials and surfaces enable striking photonic properties, such as negative refractive index and superchiral light, driving promising applications in novel optical components, nanorobotics, and enhanced chiral molecular interactions with light. In characterizing chirality, although nonlinear chiroptical techniques are typically much more sensitive than their linear optical counterparts, separating true chirality from anisotropy is a major challenge. Here, we report the first observation of optical activity in second-harmonic hyper-Rayleigh scattering (HRS). We demonstrate the effect in a 3D isotropic suspension of Ag nanohelices in water. The effect is 5 orders of magnitude stronger than linear optical activity and is well pronounced above the multiphoton luminescence background. Because of its sensitivity, isotropic environment, and straightforward experimental geometry, HRS optical activity constitutes a fundamental experimental breakthrough in chiral photonics for media including nanomaterials, metamaterials, and chemical molecules.

pf

link (url) DOI [BibTex]

link (url) DOI [BibTex]


Data-efficient Auto-tuning with Bayesian Optimization: An Industrial Control Study
Data-efficient Auto-tuning with Bayesian Optimization: An Industrial Control Study

Neumann-Brosig, M., Marco, A., Schwarzmann, D., Trimpe, S.

IEEE Transactions on Control Systems Technology, 2019 (article) Accepted

Abstract
Bayesian optimization is proposed for automatic learning of optimal controller parameters from experimental data. A probabilistic description (a Gaussian process) is used to model the unknown function from controller parameters to a user-defined cost. The probabilistic model is updated with data, which is obtained by testing a set of parameters on the physical system and evaluating the cost. In order to learn fast, the Bayesian optimization algorithm selects the next parameters to evaluate in a systematic way, for example, by maximizing information gain about the optimum. The algorithm thus iteratively finds the globally optimal parameters with only few experiments. Taking throttle valve control as a representative industrial control example, the proposed auto-tuning method is shown to outperform manual calibration: it consistently achieves better performance with a low number of experiments. The proposed auto-tuning framework is flexible and can handle different control structures and objectives.

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arXiv (PDF) DOI Project Page [BibTex]

arXiv (PDF) DOI Project Page [BibTex]


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A 32-channel multi-coil setup optimized for human brain shimming at 9.4T

Aghaeifar, A., Zhou, J., Heule, R., Tabibian, B., Schölkopf, B., Jia, F., Zaitsev, M., Scheffler, K.

Magnetic Resonance in Medicine, 2019, (Early View) (article)

ei

DOI [BibTex]

DOI [BibTex]


Multidimensional Contrast Limited Adaptive Histogram Equalization
Multidimensional Contrast Limited Adaptive Histogram Equalization

Stimper, V., Bauer, S., Ernstorfer, R., Schölkopf, B., Xian, R. P.

IEEE Access, 7, pages: 165437-165447, 2019 (article)

ei

arXiv link (url) DOI [BibTex]

arXiv link (url) DOI [BibTex]


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Enhancing Human Learning via Spaced Repetition Optimization

Tabibian, B., Upadhyay, U., De, A., Zarezade, A., Schölkopf, B., Gomez Rodriguez, M.

Proceedings of the National Academy of Sciences, 2019, PNAS published ahead of print January 22, 2019 (article)

ei

DOI Project Page Project Page [BibTex]

DOI Project Page Project Page [BibTex]


Learning to Control Highly Accelerated Ballistic Movements on Muscular Robots
Learning to Control Highly Accelerated Ballistic Movements on Muscular Robots

Büchler, D., Calandra, R., Peters, J.

2019 (article) Submitted

Abstract
High-speed and high-acceleration movements are inherently hard to control. Applying learning to the control of such motions on anthropomorphic robot arms can improve the accuracy of the control but might damage the system. The inherent exploration of learning approaches can lead to instabilities and the robot reaching joint limits at high speeds. Having hardware that enables safe exploration of high-speed and high-acceleration movements is therefore desirable. To address this issue, we propose to use robots actuated by Pneumatic Artificial Muscles (PAMs). In this paper, we present a four degrees of freedom (DoFs) robot arm that reaches high joint angle accelerations of up to 28000 °/s^2 while avoiding dangerous joint limits thanks to the antagonistic actuation and limits on the air pressure ranges. With this robot arm, we are able to tune control parameters using Bayesian optimization directly on the hardware without additional safety considerations. The achieved tracking performance on a fast trajectory exceeds previous results on comparable PAM-driven robots. We also show that our system can be controlled well on slow trajectories with PID controllers due to careful construction considerations such as minimal bending of cables, lightweight kinematics and minimal contact between PAMs and PAMs with the links. Finally, we propose a novel technique to control the the co-contraction of antagonistic muscle pairs. Experimental results illustrate that choosing the optimal co-contraction level is vital to reach better tracking performance. Through the use of PAM-driven robots and learning, we do a small step towards the future development of robots capable of more human-like motions.

ei

Arxiv Video [BibTex]


Autonomous Identification and Goal-Directed Invocation of Event-Predictive Behavioral Primitives
Autonomous Identification and Goal-Directed Invocation of Event-Predictive Behavioral Primitives

Gumbsch, C., Butz, M. V., Martius, G.

IEEE Transactions on Cognitive and Developmental Systems, 2019 (article)

Abstract
Voluntary behavior of humans appears to be composed of small, elementary building blocks or behavioral primitives. While this modular organization seems crucial for the learning of complex motor skills and the flexible adaption of behavior to new circumstances, the problem of learning meaningful, compositional abstractions from sensorimotor experiences remains an open challenge. Here, we introduce a computational learning architecture, termed surprise-based behavioral modularization into event-predictive structures (SUBMODES), that explores behavior and identifies the underlying behavioral units completely from scratch. The SUBMODES architecture bootstraps sensorimotor exploration using a self-organizing neural controller. While exploring the behavioral capabilities of its own body, the system learns modular structures that predict the sensorimotor dynamics and generate the associated behavior. In line with recent theories of event perception, the system uses unexpected prediction error signals, i.e., surprise, to detect transitions between successive behavioral primitives. We show that, when applied to two robotic systems with completely different body kinematics, the system manages to learn a variety of complex behavioral primitives. Moreover, after initial self-exploration the system can use its learned predictive models progressively more effectively for invoking model predictive planning and goal-directed control in different tasks and environments.

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arXiv PDF video link (url) DOI Project Page [BibTex]


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Inferring causation from time series with perspectives in Earth system sciences

Runge, J., Bathiany, S., Bollt, E., Camps-Valls, G., Coumou, D., Deyle, E., Glymour, C., Kretschmer, M., Mahecha, M., van Nes, E., Peters, J., Quax, R., Reichstein, M., Scheffer, M. S. B., Spirtes, P., Sugihara, G., Sun, J., Zhang, K., Zscheischler, J.

Nature Communications, 2019 (article) In revision

ei

[BibTex]

[BibTex]


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Machine Learning for Haptics: Inferring Multi-Contact Stimulation From Sparse Sensor Configuration

Sun, H., Martius, G.

Frontiers in Neurorobotics, 13, pages: 51, 2019 (article)

Abstract
Robust haptic sensation systems are essential for obtaining dexterous robots. Currently, we have solutions for small surface areas such as fingers, but affordable and robust techniques for covering large areas of an arbitrary 3D surface are still missing. Here, we introduce a general machine learning framework to infer multi-contact haptic forces on a 3D robot’s limb surface from internal deformation measured by only a few physical sensors. The general idea of this framework is to predict first the whole surface deformation pattern from the sparsely placed sensors and then to infer number, locations and force magnitudes of unknown contact points. We show how this can be done even if training data can only be obtained for single-contact points using transfer learning at the example of a modified limb of the Poppy robot. With only 10 strain-gauge sensors we obtain a high accuracy also for multiple-contact points. The method can be applied to arbitrarily shaped surfaces and physical sensor types, as long as training data can be obtained.

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link (url) DOI [BibTex]


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Quantum mean embedding of probability distributions

Kübler, J. M., Muandet, K., Schölkopf, B.

Physical Review Research, 1(3):033159, American Physical Society, 2019 (article)

ei

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Eigendecompositions of Transfer Operators in Reproducing Kernel Hilbert Spaces

Klus, S., Schuster, I., Muandet, K.

Journal of Nonlinear Science, 2019, First Online: 21 August 2019 (article)

ei

DOI [BibTex]

DOI [BibTex]

2008


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Modelling contrast discrimination data suggest both the pedestal effect and stochastic resonance to be caused by the same mechanism

Goris, R., Wagemans, J., Wichmann, F.

Journal of Vision, 8(15):1-21, November 2008 (article)

Abstract
Computational models of spatial vision typically make use of a (rectified) linear filter, a nonlinearity and dominant late noise to account for human contrast discrimination data. Linear–nonlinear cascade models predict an improvement in observers' contrast detection performance when low, subthreshold levels of external noise are added (i.e., stochastic resonance). Here, we address the issue whether a single contrast gain-control model of early spatial vision can account for both the pedestal effect, i.e., the improved detectability of a grating in the presence of a low-contrast masking grating, and stochastic resonance. We measured contrast discrimination performance without noise and in both weak and moderate levels of noise. Making use of a full quantitative description of our data with few parameters combined with comprehensive model selection assessments, we show the pedestal effect to be more reduced in the presence of weak noise than in moderate noise. This reduction rules out independent, additive sources of performance improvement and, together with a simulation study, supports the parsimonious explanation that a single mechanism underlies the pedestal effect and stochastic resonance in contrast perception.

ei

Web DOI [BibTex]


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gBoost: A Mathematical Programming Approach to Graph Classification and Regression

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

Machine Learning, 75(1):69-89, November 2008 (article)

Abstract
Graph mining methods enumerate frequently appearing subgraph patterns, which can be used as features for subsequent classification or regression. However, frequent patterns are not necessarily informative for the given learning problem. We propose a mathematical programming boosting method (gBoost) that progressively collects informative patterns. Compared to AdaBoost, gBoost can build the prediction rule with fewer iterations. To apply the boosting method to graph data, a branch-and-bound pattern search algorithm is developed based on the DFS code tree. The constructed search space is reused in later iterations to minimize the computation time. Our method can learn more efficiently than the simpler method based on frequent substructure mining, because the output labels are used as an extra information source for pruning the search space. Furthermore, by engineering the mathematical program, a wide range of machine learning problems can be solved without modifying the pattern search algorithm.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Machine Learning for Motor Skills in Robotics

Peters, J.

K{\"u}nstliche Intelligenz, 2008(4):41-43, November 2008 (article)

Abstract
Autonomous robots that can adapt to novel situations has been a long standing vision of robotics, artificial intelligence, and the cognitive sciences. Early approaches to this goal during the heydays of artificial intelligence research in the late 1980s, however, made it clear that an approach purely based on reasoning or human insights would not be able to model all the perceptuomotor tasks of future robots. Instead, new hope was put in the growing wake of machine learning that promised fully adaptive control algorithms which learn both by observation and trial-and-error. However, to date, learning techniques have yet to fulfill this promise as only few methods manage to scale into the high-dimensional domains of manipulator and humanoid robotics and usually scaling was only achieved in precisely pre-structured domains. We have investigated the ingredients for a general approach to motor skill learning in order to get one step closer towards human-like performance. For doing so, we study two major components for such an approach, i.e., firstly, a theoretically well-founded general approach to representing the required control structures for task representation and execution and, secondly, appropriate learning algorithms which can be applied in this setting.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Kernels, Regularization and Differential Equations

Steinke, F., Schölkopf, B.

Pattern Recognition, 41(11):3271-3286, November 2008 (article)

Abstract
Many common machine learning methods such as Support Vector Machines or Gaussian process inference make use of positive definite kernels, reproducing kernel Hilbert spaces, Gaussian processes, and regularization operators. In this work these objects are presented in a general, unifying framework, and interrelations are highlighted. With this in mind we then show how linear stochastic differential equation models can be incorporated naturally into the kernel framework. And vice versa, many kernel machines can be interpreted in terms of differential equations. We focus especially on ordinary differential equations, also known as dynamical systems, and it is shown that standard kernel inference algorithms are equivalent to Kalman filter methods based on such models. In order not to cloud qualitative insights with heavy mathematical machinery, we restrict ourselves to finite domains, implying that differential equations are treated via their corresponding finite difference equations.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Mixture Models for Protein Structure Ensembles

Hirsch, M., Habeck, M.

Bioinformatics, 24(19):2184-2192, October 2008 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Structure of the human voltage-dependent anion channel

Bayrhuber, M., Meins, T., Habeck, M., Becker, S., Giller, K., Villinger, S., Vonrhein, C., Griesinger, C., Zweckstetter, M., Zeth, K.

Proceedings of the National Academy of Sciences of the United States of America, 105(40):15370-15375, October 2008 (article)

Abstract
The voltage-dependent anion channel (VDAC), also known as mitochondrial porin, is the most abundant protein in the mitochondrial outer membrane (MOM). VDAC is the channel known to guide the metabolic flux across the MOM and plays a key role in mitochondrially induced apoptosis. Here, we present the 3D structure of human VDAC1, which was solved conjointly by NMR spectroscopy and x-ray crystallography. Human VDAC1 (hVDAC1) adopts a β-barrel architecture composed of 19 β-strands with an α-helix located horizontally midway within the pore. Bioinformatic analysis indicates that this channel architecture is common to all VDAC proteins and is adopted by the general import pore TOM40 of mammals, which is also located in the MOM.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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MRI-Based Attenuation Correction for PET/MRI: A Novel Approach Combining Pattern Recognition and Atlas Registration

Hofmann, M., Steinke, F., Scheel, V., Charpiat, G., Farquhar, J., Aschoff, P., Brady, M., Schölkopf, B., Pichler, B.

Journal of Nuclear Medicine, 49(11):1875-1883, October 2008 (article)

Abstract
For quantitative PET information, correction of tissue photon attenuation is mandatory. Generally in conventional PET, the attenuation map is obtained from a transmission scan, which uses a rotating radionuclide source, or from the CT scan in a combined PET/CT scanner. In the case of PET/MRI scanners currently under development, insufficient space for the rotating source exists; the attenuation map can be calculated from the MR image instead. This task is challenging because MR intensities correlate with proton densities and tissue-relaxation properties, rather than with attenuation-related mass density. METHODS: We used a combination of local pattern recognition and atlas registration, which captures global variation of anatomy, to predict pseudo-CT images from a given MR image. These pseudo-CT images were then used for attenuation correction, as the process would be performed in a PET/CT scanner. RESULTS: For human brain scans, we show on a database of 17 MR/CT image pairs that our method reliably enables e stimation of a pseudo-CT image from the MR image alone. On additional datasets of MRI/PET/CT triplets of human brain scans, we compare MRI-based attenuation correction with CT-based correction. Our approach enables PET quantification with a mean error of 3.2% for predefined regions of interest, which we found to be clinically not significant. However, our method is not specific to brain imaging, and we show promising initial results on 1 whole-body animal dataset. CONCLUSION: This method allows reliable MRI-based attenuation correction for human brain scans. Further work is necessary to validate the method for whole-body imaging.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Support Vector Machines and Kernels for Computational Biology

Ben-Hur, A., Ong, C., Sonnenburg, S., Schölkopf, B., Rätsch, G.

PLoS Computational Biology, 4(10: e1000173):1-10, October 2008 (article)

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PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Approximations for Binary Gaussian Process Classification

Nickisch, H., Rasmussen, C.

Journal of Machine Learning Research, 9, pages: 2035-2078, October 2008 (article)

Abstract
We provide a comprehensive overview of many recent algorithms for approximate inference in Gaussian process models for probabilistic binary classification. The relationships between several approaches are elucidated theoretically, and the properties of the different algorithms are corroborated by experimental results. We examine both 1) the quality of the predictive distributions and 2) the suitability of the different marginal likelihood approximations for model selection (selecting hyperparameters) and compare to a gold standard based on MCMC. Interestingly, some methods produce good predictive distributions although their marginal likelihood approximations are poor. Strong conclusions are drawn about the methods: The Expectation Propagation algorithm is almost always the method of choice unless the computational budget is very tight. We also extend existing methods in various ways, and provide unifying code implementing all approaches.

ei

PDF PDF [BibTex]

PDF PDF [BibTex]


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Accurate NMR Structures Through Minimization of an Extended Hybrid Energy

Nilges, M., Bernard, A., Bardiaux, B., Malliavin, T., Habeck, M., Rieping, W.

Structure, 16(9):1305-1312, September 2008 (article)

Abstract
The use of generous distance bounds has been the hallmark of NMR structure determination. However, bounds necessitate the estimation of data quality before the calculation, reduce the information content, introduce human bias, and allow for major errors in the structures. Here, we propose a new rapid structure calculation scheme based on Bayesian analysis. The minimization of an extended energy function, including a new type of distance restraint and a term depending on the data quality, results in an estimation of the data quality in addition to coordinates. This allows for the determination of the optimal weight on the experimental information. The resulting structures are of better quality and closer to the X–ray crystal structure of the same molecule. With the new calculation approach, the analysis of discrepancies from the target distances becomes meaningful. The strategy may be useful in other applications—for example, in homology modeling.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Similarity, Kernels, and the Triangle Inequality

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

Journal of Mathematical Psychology, 52(5):297-303, September 2008 (article)

Abstract
Similarity is used as an explanatory construct throughout psychology and multidimensional scaling (MDS) is the most popular way to assess similarity. In MDS, similarity is intimately connected to the idea of a geometric representation of stimuli in a perceptual space. Whilst connecting similarity and closeness of stimuli in a geometric representation may be intuitively plausible, Tversky and Gati [Tversky, A., Gati, I. (1982). Similarity, separability, and the triangle inequality. Psychological Review, 89(2), 123–154] have reported data which are inconsistent with the usual geometric representations that are based on segmental additivity. We show that similarity measures based on Shepard’s universal law of generalization [Shepard, R. N. (1987). Toward a universal law of generalization for psychologica science. Science, 237(4820), 1317–1323] lead to an inner product representation in a reproducing kernel Hilbert space. In such a space stimuli are represented by their similarity to all other stimuli. This representation, based on Shepard’s law, has a natural metric that does not have additive segments whilst still retaining the intuitive notion of connecting similarity and distance between stimuli. Furthermore, this representation has the psychologically appealing property that the distance between stimuli is bounded.

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PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Comparison of Pattern Recognition Methods in Classifying High-resolution BOLD Signals Obtained at High Magnetic Field in Monkeys

Ku, S., Gretton, A., Macke, J., Logothetis, N.

Magnetic Resonance Imaging, 26(7):1007-1014, September 2008 (article)

Abstract
Pattern recognition methods have shown that functional magnetic resonance imaging (fMRI) data can reveal significant information about brain activity. For example, in the debate of how object categories are represented in the brain, multivariate analysis has been used to provide evidence of a distributed encoding scheme [Science 293:5539 (2001) 2425–2430]. Many follow-up studies have employed different methods to analyze human fMRI data with varying degrees of success [Nature reviews 7:7 (2006) 523–534]. In this study, we compare four popular pattern recognition methods: correlation analysis, support-vector machines (SVM), linear discriminant analysis (LDA) and Gaussian naïve Bayes (GNB), using data collected at high field (7 Tesla) with higher resolution than usual fMRI studies. We investigate prediction performance on single trials and for averages across varying numbers of stimulus presentations. The performance of the various algorithms depends on the nature of the brain activity being categorized: for several tasks, many of the methods work well, whereas for others, no method performs above chance level. An important factor in overall classification performance is careful preprocessing of the data, including dimensionality reduction, voxel selection and outlier elimination.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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A Single-shot Measurement of the Energy of Product States in a Translation Invariant Spin Chain Can Replace Any Quantum Computation

Janzing, D., Wocjan, P., Zhang, S.

New Journal of Physics, 10(093004):1-18, September 2008 (article)

Abstract
In measurement-based quantum computation, quantum algorithms are implemented via sequences of measurements. We describe a translationally invariant finite-range interaction on a one-dimensional qudit chain and prove that a single-shot measurement of the energy of an appropriate computational basis state with respect to this Hamiltonian provides the output of any quantum circuit. The required measurement accuracy scales inverse polynomially with the size of the simulated quantum circuit. This shows that the implementation of energy measurements on generic qudit chains is as hard as the realization of quantum computation. Here, a ‘measurement‘ is any procedure that samples from the spectral measurement induced by the observable and the state under consideration. As opposed to measurement-based quantum computation, the post-measurement state is irrelevant.

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Voluntary Brain Regulation and Communication with ECoG-Signals

Hinterberger, T., Widmann, G., Lal, T., Hill, J., Tangermann, M., Rosenstiel, W., Schölkopf, B., Elger, C., Birbaumer, N.

Epilepsy and Behavior, 13(2):300-306, August 2008 (article)

Abstract
Brain–computer interfaces (BCIs) can be used for communication in writing without muscular activity or for learning to control seizures by voluntary regulation of brain signals such as the electroencephalogram (EEG). Three of five patients with epilepsy were able to spell their names with electrocorticogram (ECoG) signals derived from motor-related areas within only one or two training sessions. Imagery of finger or tongue movements was classified with support-vector classification of autoregressive coefficients derived from the ECoG signals. After training of the classifier, binary classification responses were used to select letters from a computer-generated menu. Offline analysis showed increased theta activity in the unsuccessful patients, whereas the successful patients exhibited dominant sensorimotor rhythms that they could control. The high spatial resolution and increased signal-to-noise ratio in ECoG signals, combined with short training periods, may offer an alternative for communication in complete paralysis, locked-in syndrome, and motor restoration.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Multi-class Common Spatial Pattern and Information Theoretic Feature Extraction

Grosse-Wentrup, M., Buss, M.

IEEE Transactions on Biomedical Engineering, 55(8):1991-2000, August 2008 (article)

Abstract
We address two shortcomings of the common spatial patterns (CSP) algorithm for spatial filtering in the context of brain--computer interfaces (BCIs) based on electroencephalography/magnetoencephalography (EEG/MEG): First, the question of optimality of CSP in terms of the minimal achievable classification error remains unsolved. Second, CSP has been initially proposed for two-class paradigms. Extensions to multiclass paradigms have been suggested, but are based on heuristics. We address these shortcomings in the framework of information theoretic feature extraction (ITFE). We show that for two-class paradigms, CSP maximizes an approximation of mutual information of extracted EEG/MEG components and class labels. This establishes a link between CSP and the minimal classification error. For multiclass paradigms, we point out that CSP by joint approximate diagonalization (JAD) is equivalent to independent component analysis (ICA), and provide a method to choose those independent components (ICs) that approximately maximize mutual information of ICs and class labels. This eliminates the need for heuristics in multiclass CSP, and allows incorporating prior class probabilities. The proposed method is applied to the dataset IIIa of the third BCI competition, and is shown to increase the mean classification accuracy by 23.4% in comparison to multiclass CSP.

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PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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At-TAX: A Whole Genome Tiling Array Resource for Developmental Expression Analysis and Transcript Identification in Arabidopsis thaliana

Laubinger, S., Zeller, G., Henz, S., Sachsenberg, T., Widmer, C., Naouar, N., Vuylsteke, M., Schölkopf, B., Rätsch, G., Weigel, D.

Genome Biology, 9(7: R112):1-16, July 2008 (article)

Abstract
Gene expression maps for model organisms, including Arabidopsis thaliana, have typically been created using gene-centric expression arrays. Here, we describe a comprehensive expression atlas, Arabidopsis thaliana Tiling Array Express (At-TAX), which is based on whole-genome tiling arrays. We demonstrate that tiling arrays are accurate tools for gene expression analysis and identified more than 1,000 unannotated transcribed regions. Visualizations of gene expression estimates, transcribed regions, and tiling probe measurements are accessible online at the At-TAX homepage.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Graphical Analysis of NMR Structural Quality and Interactive Contact Map of NOE Assignments in ARIA

Bardiaux, B., Bernard, A., Rieping, W., Habeck, M., Malliavin, T., Nilges, M.

BMC Structural Biology, 8(30):1-5, June 2008 (article)

Abstract
BACKGROUND: The Ambiguous Restraints for Iterative Assignment (ARIA) approach is widely used for NMR structure determination. It is based on simultaneously calculating structures and assigning NOE through an iterative protocol. The final solution consists of a set of conformers and a list of most probable assignments for the input NOE peak list. RESULTS: ARIA was extended with a series of graphical tools to facilitate a detailed analysis of the intermediate and final results of the ARIA protocol. These additional features provide (i) an interactive contact map, serving as a tool for the analysis of assignments, and (ii) graphical representations of structure quality scores and restraint statistics. The interactive contact map between residues can be clicked to obtain information about the restraints and their contributions. Profiles of quality scores are plotted along the protein sequence, and contact maps provide information of the agreement with the data on a residue pair level. CONCLUSIONS: The g raphical tools and outputs described here significantly extend the validation and analysis possibilities of NOE assignments given by ARIA as well as the analysis of the quality of the final structure ensemble. These tools are included in the latest version of ARIA, which is available at http://aria.pasteur.fr. The Web site also contains an installation guide, a user manual and example calculations.

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PDF DOI [BibTex]

PDF DOI [BibTex]


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Kernel Methods in Machine Learning

Hofmann, T., Schölkopf, B., Smola, A.

Annals of Statistics, 36(3):1171-1220, June 2008 (article)

Abstract
We review machine learning methods employing positive definite kernels. These methods formulate learning and estimation problems in a reproducing kernel Hilbert space (RKHS) of functions defined on the data domain, expanded in terms of a kernel. Working in linear spaces of function has the benefit of facilitating the construction and analysis of learning algorithms while at the same time allowing large classes of functions. The latter include nonlinear functions as well as functions defined on nonvectorial data.

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PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Cross-validation Optimization for Large Scale Structured Classification Kernel Methods

Seeger, M.

Journal of Machine Learning Research, 9, pages: 1147-1178, June 2008 (article)

Abstract
We propose a highly efficient framework for penalized likelihood kernel methods applied to multi-class models with a large, structured set of classes. As opposed to many previous approaches which try to decompose the fitting problem into many smaller ones, we focus on a Newton optimization of the complete model, making use of model structure and linear conjugate gradients in order to approximate Newton search directions. Crucially, our learning method is based entirely on matrix-vector multiplication primitives with the kernel matrices and their derivatives, allowing straightforward specialization to new kernels, and focusing code optimization efforts to these primitives only. Kernel parameters are learned automatically, by maximizing the cross-validation log likelihood in a gradient-based way, and predictive probabilities are estimated. We demonstrate our approach on large scale text classification tasks with hierarchical structure on thousands of classes, achieving state-of-the-art results in an order of magnitude less time than previous work.

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PDF PDF [BibTex]

PDF PDF [BibTex]