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Juggling revisited — A voxel based morphometry study with expert jugglers

Gerber, P., Schlaffke, L., Heba, S., Greenlee, M., Schultz, T., Schmidt-Wilcke, T.

NeuroImage, 95, pages: 320-325, 2014 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Assessing attention and cognitive function in completely locked-in state with event-related brain potentials and epidural electrocorticography

Bensch, M., Martens, S., Halder, S., Hill, J., Nijboer, F., Ramos, A., Birbaumer, N., Bodgan, M., Kotchoubey, B., Rosenstiel, W., Schölkopf, B., Gharabaghi, A.

Journal of Neural Engineering, 11(2):026006, 2014 (article)

Abstract
Objective. Patients in the completely locked-in state (CLIS), due to, for example, amyotrophic lateral sclerosis (ALS), no longer possess voluntary muscle control. Assessing attention and cognitive function in these patients during the course of the disease is a challenging but essential task for both nursing staff and physicians. Approach. An electrophysiological cognition test battery, including auditory and semantic stimuli, was applied in a late-stage ALS patient at four different time points during a six-month epidural electrocorticography (ECoG) recording period. Event-related cortical potentials (ERP), together with changes in the ECoG signal spectrum, were recorded via 128 channels that partially covered the left frontal, temporal and parietal cortex. Main results. Auditory but not semantic stimuli induced significant and reproducible ERP projecting to specific temporal and parietal cortical areas. N1/P2 responses could be detected throughout the whole study period. The highest P3 ERP was measured immediately after the patient's last communication through voluntary muscle control, which was paralleled by low theta and high gamma spectral power. Three months after the patient's last communication, i.e., in the CLIS, P3 responses could no longer be detected. At the same time, increased activity in low-frequency bands and a sharp drop of gamma spectral power were recorded. Significance. Cortical electrophysiological measures indicate at least partially intact attention and cognitive function during sparse volitional motor control for communication. Although the P3 ERP and frequency-specific changes in the ECoG spectrum may serve as indicators for CLIS, a close-meshed monitoring will be required to define the exact time point of the transition.

ei

DOI [BibTex]

DOI [BibTex]


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Identifiability of Gaussian Structural Equation Models with Equal Error Variances

Peters, J., Bühlman, P.

Biometrika, 101(1):219-228, 2014 (article)

ei

DOI [BibTex]


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Two numerical models designed to reproduce Saturn ring temperatures as measured by Cassini-CIRS

Altobelli, N., Lopez-Paz, D., Pilorz, S., Spilker, L., Morishima, R., Brooks, S., Leyrat, C., Deau, E., Edgington, S., Flandes, A.

Icarus, 238(0):205 - 220, 2014 (article)

ei

Web link (url) DOI [BibTex]

Web link (url) DOI [BibTex]


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Policy Evaluation with Temporal Differences: A Survey and Comparison

Dann, C., Neumann, G., Peters, J.

Journal of Machine Learning Research, 15, pages: 809-883, 2014 (article)

ei

PDF [BibTex]

PDF [BibTex]


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Uncovering the Structure and Temporal Dynamics of Information Propagation

Gomez Rodriguez, M., Leskovec, J., Balduzzi, D., Schölkopf, B.

Network Science, 2(1):26-65, 2014 (article)

Abstract
Time plays an essential role in the diffusion of information, influence, and disease over networks. In many cases we can only observe when a node is activated by a contagion—when a node learns about a piece of information, makes a decision, adopts a new behavior, or becomes infected with a disease. However, the underlying network connectivity and transmission rates between nodes are unknown. Inferring the underlying diffusion dynamics is important because it leads to new insights and enables forecasting, as well as influencing or containing information propagation. In this paper we model diffusion as a continuous temporal process occurring at different rates over a latent, unobserved network that may change over time. Given information diffusion data, we infer the edges and dynamics of the underlying network. Our model naturally imposes sparse solutions and requires no parameter tuning. We develop an efficient inference algorithm that uses stochastic convex optimization to compute online estimates of the edges and transmission rates. We evaluate our method by tracking information diffusion among 3.3 million mainstream media sites and blogs, and experiment with more than 179 million different instances of information spreading over the network in a one-year period. We apply our network inference algorithm to the top 5,000 media sites and blogs and report several interesting observations. First, information pathways for general recurrent topics are more stable across time than for on-going news events. Second, clusters of news media sites and blogs often emerge and vanish in a matter of days for on-going news events. Finally, major events, for example, large scale civil unrest as in the Libyan civil war or Syrian uprising, increase the number of information pathways among blogs, and also increase the network centrality of blogs and social media sites.

ei

DOI [BibTex]


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Causal discovery via reproducing kernel Hilbert space embeddings

Chen, Z., Zhang, K., Chan, L., Schölkopf, B.

Neural Computation, 26(7):1484-1517, 2014 (article)

ei

DOI Project Page [BibTex]


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A Brain-Computer Interface Based on Self-Regulation of Gamma-Oscillations in the Superior Parietal Cortex

Grosse-Wentrup, M., Schölkopf, B.

Journal of Neural Engineering, 11(5):056015, 2014 (article)

Abstract
Objective. Brain–computer interface (BCI) systems are often based on motor- and/or sensory processes that are known to be impaired in late stages of amyotrophic lateral sclerosis (ALS). We propose a novel BCI designed for patients in late stages of ALS that only requires high-level cognitive processes to transmit information from the user to the BCI. Approach. We trained subjects via EEG-based neurofeedback to self-regulate the amplitude of gamma-oscillations in the superior parietal cortex (SPC). We argue that parietal gamma-oscillations are likely to be associated with high-level attentional processes, thereby providing a communication channel that does not rely on the integrity of sensory- and/or motor-pathways impaired in late stages of ALS. Main results. Healthy subjects quickly learned to self-regulate gamma-power in the SPC by alternating between states of focused attention and relaxed wakefulness, resulting in an average decoding accuracy of 70.2%. One locked-in ALS patient (ALS-FRS-R score of zero) achieved an average decoding accuracy significantly above chance-level though insufficient for communication (55.8%). Significance. Self-regulation of gamma-power in the SPC is a feasible paradigm for brain–computer interfacing and may be preserved in late stages of ALS. This provides a novel approach to testing whether completely locked-in ALS patients retain the capacity for goal-directed thinking.

ei

Web DOI [BibTex]


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CAM: Causal Additive Models, high-dimensional order search and penalized regression

Bühlmann, P., Peters, J., Ernest, J.

Annals of Statistics, 42(6):2526-2556, 2014 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Unsupervised identification of neural events in local field potentials

Besserve, M., Schölkopf, B., Logothetis, N. K.

44th Annual Meeting of the Society for Neuroscience (Neuroscience), 2014 (talk)

ei

[BibTex]

[BibTex]


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Impact of Large-Scale Climate Extremes on Biospheric Carbon Fluxes: An Intercomparison Based on MsTMIP Data

Zscheischler, J., Michalak, A., Schwalm, M., Mahecha, M., Huntzinger, D., Reichstein, M., Berthier, G., Ciais, P., Cook, R., El-Masri, B., Huang, M., Ito, A., Jain, A., King, A., Lei, H., Lu, C., Mao, J., Peng, S., Poulter, B., Ricciuto, D., Shi, X., Tao, B., Tian, H., Viovy, N., Wang, W., Wei, Y., Yang, J., Zeng, N.

Global Biogeochemical Cycles, 2014 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Predicting Motor Learning Performance from Electroencephalographic Data

Meyer, T., Peters, J., Zander, T., Schölkopf, B., Grosse-Wentrup, M.

Journal of NeuroEngineering and Rehabilitation, 11:24, 2014 (article)

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Special issue on autonomous grasping and manipulation

Ben Amor, H., Saxena, A., Hudson, N., Peters, J.

Autonomous Robots, 36(1-2):1-3, 2014 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Evaluation of Positron Emission Tomographic Tracers for Imaging of Papillomavirus-Induced Tumors in Rabbits

Probst, S., Wiehr, S., Mantlik, F., Schmidt, H., Kolb, A., Münch, P., Delcuratolo, M., Stubenrauch, F., Pichler, B., Iftner, T.

Molecular Imaging, 13(1):1536-0121, 2014 (article)

ei

Web [BibTex]

Web [BibTex]


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Extreme events in gross primary production: a characterization across continents

Zscheischler, J., Reichstein, M., Harmeling, S., Rammig, A., Tomelleri, E., Mahecha, M.

Biogeosciences, 11, pages: 2909-2924, 2014 (article)

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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On power law distributions in large-scale taxonomies

Babbar, R., Metzig, C., Partalas, I., Gaussier, E., Amini, M.

SIGKDD Explorations, Special Issue on Big Data, 16(1):47-56, 2014 (article)

ei

[BibTex]

[BibTex]


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Quantifying statistical dependency

Besserve, M.

Research Network on Learning Systems Summer School, 2014 (talk)

ei

[BibTex]

[BibTex]


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Indirect Robot Model Learning for Tracking Control

Bocsi, B., Csató, L., Peters, J.

Advanced Robotics, 28(9):589-599, 2014 (article)

ei

PDF DOI [BibTex]


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An extended approach for spatiotemporal gapfilling: dealing with large and systematic gaps in geoscientific datasets

v Buttlar, J., Zscheischler, J., Mahecha, M.

Nonlinear Processes in Geophysics, 21(1):203-215, 2014 (article)

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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On the Quantification Accuracy, Homogeneity, and Stability of Simultaneous Positron Emission Tomography/Magnetic Resonance Imaging Systems

Schmidt, H., Schwenzer, N., Bezrukov, I., Mantlik, F., Kolb, A., Kupferschläger, J., Pichler, B.

Investigative Radiology, 49(6):373-381, 2014 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Natural Evolution Strategies

Wierstra, D., Schaul, T., Glasmachers, T., Sun, Y., Peters, J., Schmidhuber, J.

Journal of Machine Learning Research, 15, pages: 949-980, 2014 (article)

ei

PDF [BibTex]

PDF [BibTex]


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Factors controlling decomposition rates of fine root litter in temperate forests and grasslands

Solly, E., Schöning, I., Boch, S., Kandeler, E., Marhan, S., Michalzik, B., Müller, J., Zscheischler, J., Trumbore, S., Schrumpf, M.

Plant and Soil, 2014 (article)

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Causal Discovery with Continuous Additive Noise Models

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

Journal of Machine Learning Research, 15, pages: 2009-2053, 2014 (article)

ei

PDF Web [BibTex]

PDF Web [BibTex]


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A few extreme events dominate global interannual variability in gross primary production

Zscheischler, J., Mahecha, M., v Buttlar, J., Harmeling, S., Jung, M., Rammig, A., Randerson, J., Schölkopf, B., Seneviratne, S., Tomelleri, E., Zaehle, S., Reichstein, M.

Environmental Research Letters, 9(3):035001, 2014 (article)

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Kernel methods in system identification, machine learning and function estimation: A survey

Pillonetto, G., Dinuzzo, F., Chen, T., De Nicolao, G., Ljung, L.

Automatica, 50(3):657-682, 2014 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Development of a novel depth of interaction PET detector using highly multiplexed G-APD cross-strip encoding

Kolb, A., Parl, C., Mantlik, F., Liu, C., Lorenz, E., Renker, D., Pichler, B.

Medical Physics, 41(8), 2014 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Epidural electrocorticography for monitoring of arousal in locked-in state

Martens, S., Bensch, M., Halder, S., Hill, J., Nijboer, F., Ramos-Murguialday, A., Schölkopf, B., Birbaumer, N., Gharabaghi, A.

Frontiers in Human Neuroscience, 8(861), 2014 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Simultaneous Whole-Body PET/MR Imaging in Comparison to PET/CT in Pediatric Oncology: Initial Results

Schäfer, J. F., Gatidis, S., Schmidt, H., Gückel, B., Bezrukov, I., Pfannenberg, C. A., Reimold, M., M., E., Fuchs, J., Claussen, C. D., Schwenzer, N. F.

Radiology, 273(1):220-231, 2014 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Cost-Sensitive Active Learning With Lookahead: Optimizing Field Surveys for Remote Sensing Data Classification

Persello, C., Boularias, A., Dalponte, M., Gobakken, T., Naesset, E., Schölkopf, B.

IEEE Transactions on Geoscience and Remote Sensing, 10(52):6652 - 6664, 2014 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Principles of PET/MR Imaging

Disselhorst, J. A., Bezrukov, I., Kolb, A., Parl, C., Pichler, B. J.

Journal of Nuclear Medicine, 55(6, Supplement 2):2S-10S, 2014 (article)

ei

DOI [BibTex]

DOI [BibTex]


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IM3SHAPE: Maximum likelihood galaxy shear measurement code for cosmic gravitational lensing

Zuntz, J., Kacprzak, T., Voigt, L., Hirsch, M., Rowe, B., Bridle, S.

Astrophysics Source Code Library, 1, pages: 09013, 2014 (article)

ei

link (url) [BibTex]

link (url) [BibTex]


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Efficient nearest neighbors via robust sparse hashing

Cherian, A., Sra, S., Morellas, V., Papanikolopoulos, N.

IEEE Transactions on Image Processing, 23(8):3646-3655, 2014 (article)

ei

DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Sérsic galaxy models in weak lensing shape measurement: model bias, noise bias and their interaction

Kacprzak, T., Bridle, S., Rowe, B., Voigt, L., Zuntz, J., Hirsch, M., MacCrann, N.

Monthly Notices of the Royal Astronomical Society, 441(3):2528-2538, Oxford University Press, 2014 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Diminished White Matter Integrity in Patients with Systemic Lupus Erythematosus

Schmidt-Wilcke, T., Cagnoli, P., Wang, P., Schultz, T., Lotz, A., Mccune, W. J., Sundgren, P. C.

NeuroImage: Clinical, 5, pages: 291-297, 2014 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Information-Theoretic Bounded Rationality and ϵ-Optimality

Braun, DA, Ortega, PA

Entropy, 16(8):4662-4676, August 2014 (article)

Abstract
Bounded rationality concerns the study of decision makers with limited information processing resources. Previously, the free energy difference functional has been suggested to model bounded rational decision making, as it provides a natural trade-off between an energy or utility function that is to be optimized and information processing costs that are measured by entropic search costs. The main question of this article is how the information-theoretic free energy model relates to simple \(\epsilon\)-optimality models of bounded rational decision making, where the decision maker is satisfied with any action in an \(\epsilon\)-neighborhood of the optimal utility. We find that the stochastic policies that optimize the free energy trade-off comply with the notion of \(\epsilon\)-optimality. Moreover, this optimality criterion even holds when the environment is adversarial. We conclude that the study of bounded rationality based on \(\epsilon\)-optimality criteria that abstract away from the particulars of the information processing constraints is compatible with the information-theoretic free energy model of bounded rationality.

ei

DOI [BibTex]

DOI [BibTex]


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Occam’s Razor in sensorimotor learning

Genewein, T, Braun, D

Proceedings of the Royal Society of London B, 281(1783):1-7, May 2014 (article)

Abstract
A large number of recent studies suggest that the sensorimotor system uses probabilistic models to predict its environment and makes inferences about unobserved variables in line with Bayesian statistics. One of the important features of Bayesian statistics is Occam's Razor—an inbuilt preference for simpler models when comparing competing models that explain some observed data equally well. Here, we test directly for Occam's Razor in sensorimotor control. We designed a sensorimotor task in which participants had to draw lines through clouds of noisy samples of an unobserved curve generated by one of two possible probabilistic models—a simple model with a large length scale, leading to smooth curves, and a complex model with a short length scale, leading to more wiggly curves. In training trials, participants were informed about the model that generated the stimulus so that they could learn the statistics of each model. In probe trials, participants were then exposed to ambiguous stimuli. In probe trials where the ambiguous stimulus could be fitted equally well by both models, we found that participants showed a clear preference for the simpler model. Moreover, we found that participants’ choice behaviour was quantitatively consistent with Bayesian Occam's Razor. We also show that participants’ drawn trajectories were similar to samples from the Bayesian predictive distribution over trajectories and significantly different from two non-probabilistic heuristics. In two control experiments, we show that the preference of the simpler model cannot be simply explained by a difference in physical effort or by a preference for curve smoothness. Our results suggest that Occam's Razor is a general behavioural principle already present during sensorimotor processing.

ei

DOI [BibTex]

DOI [BibTex]


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Generalized Thompson sampling for sequential decision-making and causal inference

Ortega, PA, Braun, DA

Complex Adaptive Systems Modeling, 2(2):1-23, March 2014 (article)

Abstract
Purpose Sampling an action according to the probability that the action is believed to be the optimal one is sometimes called Thompson sampling. Methods Although mostly applied to bandit problems, Thompson sampling can also be used to solve sequential adaptive control problems, when the optimal policy is known for each possible environment. The predictive distribution over actions can then be constructed by a Bayesian superposition of the policies weighted by their posterior probability of being optimal. Results Here we discuss two important features of this approach. First, we show in how far such generalized Thompson sampling can be regarded as an optimal strategy under limited information processing capabilities that constrain the sampling complexity of the decision-making process. Second, we show how such Thompson sampling can be extended to solve causal inference problems when interacting with an environment in a sequential fashion. Conclusion In summary, our results suggest that Thompson sampling might not merely be a useful heuristic, but a principled method to address problems of adaptive sequential decision-making and causal inference.

ei

DOI [BibTex]

DOI [BibTex]


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Assessing randomness and complexity in human motion trajectories through analysis of symbolic sequences

Peng, Z, Genewein, T, Braun, DA

Frontiers in Human Neuroscience, 8(168):1-13, March 2014 (article)

Abstract
Complexity is a hallmark of intelligent behavior consisting both of regular patterns and random variation. To quantitatively assess the complexity and randomness of human motion, we designed a motor task in which we translated subjects' motion trajectories into strings of symbol sequences. In the first part of the experiment participants were asked to perform self-paced movements to create repetitive patterns, copy pre-specified letter sequences, and generate random movements. To investigate whether the degree of randomness can be manipulated, in the second part of the experiment participants were asked to perform unpredictable movements in the context of a pursuit game, where they received feedback from an online Bayesian predictor guessing their next move. We analyzed symbol sequences representing subjects' motion trajectories with five common complexity measures: predictability, compressibility, approximate entropy, Lempel-Ziv complexity, as well as effective measure complexity. We found that subjects’ self-created patterns were the most complex, followed by drawing movements of letters and self-paced random motion. We also found that participants could change the randomness of their behavior depending on context and feedback. Our results suggest that humans can adjust both complexity and regularity in different movement types and contexts and that this can be assessed with information-theoretic measures of the symbolic sequences generated from movement trajectories.

ei

DOI [BibTex]

DOI [BibTex]

2007


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Positional Oligomer Importance Matrices

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

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

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

ei

Web [BibTex]

2007


Web [BibTex]


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

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

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

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

ei

Web [BibTex]

Web [BibTex]


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Machine Learning Algorithms for Polymorphism Detection

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

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

ei

Web [BibTex]

Web [BibTex]


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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]

PDF PDF DOI [BibTex]


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An Automated Combination of Kernels for Predicting Protein Subcellular Localization

Zien, A., Ong, C.

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

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

ei

Web [BibTex]

Web [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]