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2011


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Extraction of functional information from ongoing brain electrical activity: Extraction en temps-réel d’informations fonctionnelles à partir de l’activité électrique cérébrale

Besserve, M., Martinerie, J.

IRBM, 32(1):27-34, February 2011 (article)

Abstract
The modern analysis of multivariate electrical brain signals requires advanced statistical tools to automatically extract and quantify their information content. These tools include machine learning techniques and information theory. They are currently used both in basic neuroscience and challenging applications such as brain computer interfaces. We review here how these methods have been used at the Laboratoire d’Électroencéphalographie et de Neurophysiologie Appliquée (LENA) to develop a general tool for the real time analysis of functional brain signals. We then give some perspectives on how these tools can help understanding the biological mechanisms of information processing.

PDF DOI [BibTex]


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A graphical model framework for decoding in the visual ERP-based BCI speller

Martens, S., Mooij, J., Hill, N., Farquhar, J., Schölkopf, B.

Neural Computation, 23(1):160-182, January 2011 (article)

Abstract
We present a graphical model framework for decoding in the visual ERP-based speller system. The proposed framework allows researchers to build generative models from which the decoding rules are obtained in a straightforward manner. We suggest two models for generating brain signals conditioned on the stimulus events. Both models incorporate letter frequency information but assume different dependencies between brain signals and stimulus events. For both models, we derive decoding rules and perform a discriminative training. We show on real visual speller data how decoding performance improves by incorporating letter frequency information and using a more realistic graphical model for the dependencies between the brain signals and the stimulus events. Furthermore, we discuss how the standard approach to decoding can be seen as a special case of the graphical model framework. The letter also gives more insight into the discriminative approach for decoding in the visual speller system.

Web DOI [BibTex]

Web DOI [BibTex]


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Robust Control of Teleoperation Systems Interacting with Viscoelastic Soft Tissues

Cho, JH., Son, HI., Bhattacharjee, T., Lee, DG., Lee, DY.

IEEE Transactions on Control Systems Technology, January 2011 (article) In revision

[BibTex]

[BibTex]


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Effect of Control Parameters and Haptic Cues on Human Perception for Remote Operations

Son, HI., Bhattacharjee, T., Jung, H., Lee, DY.

Experimental Brain Research, January 2011 (article) Submitted

[BibTex]

[BibTex]


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Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes

Parts, L., Stegle, O., Winn, J., Durbin, R.

PLoS Genetics, 7(1):1-10, January 2011 (article)

Abstract
Even within a defined cell type, the expression level of a gene differs in individual samples. The effects of genotype, measured factors such as environmental conditions, and their interactions have been explored in recent studies. Methods have also been developed to identify unmeasured intermediate factors that coherently influence transcript levels of multiple genes. Here, we show how to bring these two approaches together and analyse genetic effects in the context of inferred determinants of gene expression. We use a sparse factor analysis model to infer hidden factors, which we treat as intermediate cellular phenotypes that in turn affect gene expression in a yeast dataset. We find that the inferred phenotypes are associated with locus genotypes and environmental conditions and can explain genetic associations to genes in trans. For the first time, we consider and find interactions between genotype and intermediate phenotypes inferred from gene expression levels, complementing and extending established results.

Web DOI [BibTex]

Web DOI [BibTex]


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Reinforcement Learning with Bounded Information Loss

Peters, J., Peters, J., Mülling, K., Altun, Y.

AIP Conference Proceedings, 1305(1):365-372, 2011 (article)

Abstract
Policy search is a successful approach to reinforcement learning. However, policy improvements often result in the loss of information. Hence, it has been marred by premature convergence and implausible solutions. As first suggested in the context of covariant or natural policy gradients, many of these problems may be addressed by constraining the information loss. In this paper, we continue this path of reasoning and suggest two reinforcement learning methods, i.e., a model‐based and a model free algorithm that bound the loss in relative entropy while maximizing their return. The resulting methods differ significantly from previous policy gradient approaches and yields an exact update step. It works well on typical reinforcement learning benchmark problems as well as novel evaluations in robotics. We also show a Bayesian bound motivation of this new approach [8].

Web DOI [BibTex]

2000


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Knowledge Discovery in Databases: An Information Retrieval Perspective

Ong, CS.

Malaysian Journal of Computer Science, 13(2):54-63, December 2000 (article)

Abstract
The current trend of increasing capabilities in data generation and collection has resulted in an urgent need for data mining applications, also called knowledge discovery in databases. This paper identifies and examines the issues involved in extracting useful grains of knowledge from large amounts of data. It describes a framework to categorise data mining systems. The author also gives an overview of the issues pertaining to data pre processing, as well as various information gathering methodologies and techniques. The paper covers some popular tools such as classification, clustering, and generalisation. A summary of statistical and machine learning techniques used currently is also provided.

PDF [BibTex]

2000

PDF [BibTex]


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A Simple Iterative Approach to Parameter Optimization

Zien, A., Zimmer, R., Lengauer, T.

Journal of Computational Biology, 7(3,4):483-501, November 2000 (article)

Abstract
Various bioinformatics problems require optimizing several different properties simultaneously. For example, in the protein threading problem, a scoring function combines the values for different parameters of possible sequence-to-structure alignments into a single score to allow for unambiguous optimization. In this context, an essential question is how each property should be weighted. As the native structures are known for some sequences, a partial ordering on optimal alignments to other structures, e.g., derived from structural comparisons, may be used to adjust the weights. To resolve the arising interdependence of weights and computed solutions, we propose a heuristic approach: iterating the computation of solutions (here, threading alignments) given the weights and the estimation of optimal weights of the scoring function given these solutions via systematic calibration methods. For our application (i.e., threading), this iterative approach results in structurally meaningful weights that significantly improve performance on both the training and the test data sets. In addition, the optimized parameters show significant improvements on the recognition rate for a grossly enlarged comprehensive benchmark, a modified recognition protocol as well as modified alignment types (local instead of global and profiles instead of single sequences). These results show the general validity of the optimized weights for the given threading program and the associated scoring contributions.

Web [BibTex]

Web [BibTex]


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Identification of Drug Target Proteins

Zien, A., Küffner, R., Mevissen, T., Zimmer, R., Lengauer, T.

ERCIM News, 43, pages: 16-17, October 2000 (article)

Web [BibTex]

Web [BibTex]


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Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites

Zien, A., Rätsch, G., Mika, S., Schölkopf, B., Lengauer, T., Müller, K.

Bioinformatics, 16(9):799-807, September 2000 (article)

Abstract
Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.

Web DOI [BibTex]

Web DOI [BibTex]


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A Meanfield Approach to the Thermodynamics of a Protein-Solvent System with Application to the Oligomerization of the Tumour Suppressor p53.

Noolandi, J., Davison, TS., Vokel, A., Nie, F., Kay, C., Arrowsmith, C.

Proceedings of the National Academy of Sciences of the United States of America, 97(18):9955-9960, August 2000 (article)

Web [BibTex]

Web [BibTex]


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New Support Vector Algorithms

Schölkopf, B., Smola, A., Williamson, R., Bartlett, P.

Neural Computation, 12(5):1207-1245, May 2000 (article)

Abstract
We propose a new class of support vector algorithms for regression and classification. In these algorithms, a parameter {nu} lets one effectively control the number of support vectors. While this can be useful in its own right, the parameterization has the additional benefit of enabling us to eliminate one of the other free parameters of the algorithm: the accuracy parameter {epsilon} in the regression case, and the regularization constant C in the classification case. We describe the algorithms, give some theoretical results concerning the meaning and the choice of {nu}, and report experimental results.

Web DOI [BibTex]

Web DOI [BibTex]


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Bounds on Error Expectation for Support Vector Machines

Vapnik, V., Chapelle, O.

Neural Computation, 12(9):2013-2036, 2000 (article)

Abstract
We introduce the concept of span of support vectors (SV) and show that the generalization ability of support vector machines (SVM) depends on this new geometrical concept. We prove that the value of the span is always smaller (and can be much smaller) than the diameter of the smallest sphere containing th e support vectors, used in previous bounds. We also demonstate experimentally that the prediction of the test error given by the span is very accurate and has direct application in model selection (choice of the optimal parameters of the SVM)

GZIP [BibTex]

GZIP [BibTex]

1995


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View-Based Cognitive Mapping and Path Planning

Schölkopf, B., Mallot, H.

Adaptive Behavior, 3(3):311-348, January 1995 (article)

Abstract
This article presents a scheme for learning a cognitive map of a maze from a sequence of views and movement decisions. The scheme is based on an intermediate representation called the view graph, whose nodes correspond to the views whereas the labeled edges represent the movements leading from one view to another. By means of a graph theoretical reconstruction method, the view graph is shown to carry complete information on the topological and directional structure of the maze. Path planning can be carried out directly in the view graph without actually performing this reconstruction. A neural network is presented that learns the view graph during a random exploration of the maze. It is based on an unsupervised competitive learning rule translating temporal sequence (rather than similarity) of views into connectedness in the network. The network uses its knowledge of the topological and directional structure of the maze to generate expectations about which views are likely to be encountered next, improving the view-recognition performance. Numerical simulations illustrate the network's ability for path planning and the recognition of views degraded by random noise. The results are compared to findings of behavioral neuroscience.

Web DOI [BibTex]

1995

Web DOI [BibTex]


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Suppression and creation of chaos in a periodically forced Lorenz system.

Franz, MO., Zhang, MH.

Physical Review, E 52, pages: 3558-3565, 1995 (article)

Abstract
Periodic forcing is introduced into the Lorenz model to study the effects of time-dependent forcing on the behavior of the system. Such a nonautonomous system stays dissipative and has a bounded attracting set which all trajectories finally enter. The possible kinds of attracting sets are restricted to periodic orbits and strange attractors. A large-scale survey of parameter space shows that periodic forcing has mainly three effects in the Lorenz system depending on the forcing frequency: (i) Fixed points are replaced by oscillations around them; (ii) resonant periodic orbits are created both in the stable and the chaotic region; (iii) chaos is created in the stable region near the resonance frequency and in periodic windows. A comparison to other studies shows that part of this behavior has been observed in simulations of higher truncations and real world experiments. Since very small modulations can already have a considerable effect, this suggests that periodic processes such as annual or diurnal cycles should not be omitted even in simple climate models.

[BibTex]

[BibTex]

1993


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Presynaptic and Postsynaptic Competition in models for the Development of Neuromuscular Connections

Rasmussen, CE., Willshaw, DJ.

Biological Cybernetics, 68, pages: 409-419, 1993 (article)

Abstract
The development of the nervous system involves in many cases interactions on a local scale rather than the execution of a fully specified genetic blueprint. The problem is to discover the nature of these interactions and the factors on which they depend. The withdrawal of polyinnervation in developing muscle is an example where such competitive interactions play an important role. We examine the possible types of competition in formal models that have plausible biological implementations. By relating the behaviour of the models to the anatomical and physiological findings we show that a model that incorporates two types of competition is superior to others. Analysis suggests that the phenomenon of intrinsic withdrawal is a side effect of the competitive mechanisms rather than a separate non-competitive feature. Full scale computer simulations have been used to confirm the capabilities of this model.

PostScript [BibTex]

1993

PostScript [BibTex]


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Cartesian Dynamics of Simple Molecules: X Linear Quadratomics (C∞v Symmetry).

Anderson, A., Davison, T., Nagi, N., Schlueter, S.

Spectroscopy Letters, 26, pages: 509-522, 1993 (article)

[BibTex]

[BibTex]