Publications | Max Planck Institute for Intelligent Systems

245 results (View BibTeX file of all listed publications)

2007

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

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.

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2007

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

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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.

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

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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)

Web [BibTex]

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

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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.

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ei von Luxburg, U. A Tutorial on Spectral Clustering Statistics and Computing, 17(4):395-416, December 2007 (article)

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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.

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

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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 conceptsthe so-called kernel trick, the representer theorem and regularizationwhich may open up the possibility that insights from machine learning can feed back into psychology.

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ei Jäkel, F., Schölkopf, B., Wichmann, F. A Tutorial on Kernel Methods for Categorization Journal of Mathematical Psychology, 51(6):343-358, December 2007 (article)

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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.

PDF DOI [BibTex]

ei Sonnenburg, S., Schweikert, G., Philips, P., Behr, J., Rätsch, G. Accurate Splice site Prediction Using Support Vector Machines BMC Bioinformatics, 8(Supplement 10):1-16, December 2007 (article)

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

Hill, NJ.

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

Abstract

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

[BibTex]

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

[BibTex]

Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models

Steinke, F., Seeger, M., Tsuda, K.

BMC Systems Biology, 1(51):1-15, November 2007 (article)

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ei Steinke, F., Seeger, M., Tsuda, K. Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models BMC Systems Biology, 1(51):1-15, November 2007 (article)

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Policy Learning for Robotics

Peters, J.

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

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

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A unifying framework for robot control with redundant DOFs

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

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

Abstract

Recently, Udwadia (Proc. R. Soc. Lond. A 2003:17831800, 2003) suggested to derive tracking controllers for mechanical systems with redundant degrees-of-freedom (DOFs) using a generalization of Gauss principle of least constraint. This method allows reformulating control problems as a special class of optimal controllers. In this paper, we take this line of reasoning one step further and demonstrate that several well-known and also novel nonlinear robot control laws can be derived from this generic methodology. We show experimental verifications on a Sarcos Master Arm robot for some of the derived controllers. The suggested approach offers a promising unification and simplification of nonlinear control law design for robots obeying rigid body dynamics equations, both with or without external constraints, with over-actuation or underactuation, as well as open-chain and closed-chain kinematics.

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ei Peters, J., Mistry, M., Udwadia, F., Nakanishi, J., Schaal, S. A unifying framework for robot control with redundant DOFs Autonomous Robots, 24(1):1-12, October 2007 (article)

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The Need for Open Source Software in Machine Learning

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

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

Abstract

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

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ei Sonnenburg, S., Braun, M., Ong, C., Bengio, S., Bottou, L., Holmes, G., LeCun, Y., Müller, K., Pereira, F., Rasmussen, C., Rätsch, G., Schölkopf, B., Smola, A., Vincent, P., Weston, J., Williamson, R. The Need for Open Source Software in Machine Learning Journal of Machine Learning Research, 8, pages: 2443-2466, October 2007 (article)

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Hilbert Space Representations of Probability Distributions

Gretton, A.

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

Abstract

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

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

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Regression with Intervals

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

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

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

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Some observations on the masking effects of Mach bands

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

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

Abstract

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

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ei Curnow, T., Cowie, DA., Henning, GB., Hill, NJ. Some observations on the masking effects of Mach bands Journal of the Optical Society of America A, 24(10):3233-3241, October 2007 (article)

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MR-Based PET Attenuation Correction: Method and Validation

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

Joint Molecular Imaging Conference, September 2007 (talk)

Abstract

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

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

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Mining complex genotypic features for predicting HIV-1 drug resistance

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

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

Abstract

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

Web DOI [BibTex]

ei Saigo, H., Uno, T., Tsuda, K. Mining complex genotypic features for predicting HIV-1 drug resistance Bioinformatics, 23(18):2455-2462, September 2007 (article)

Web DOI [BibTex]

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

Schölkopf, B., Platt, J., Hofmann, T.

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

Abstract

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

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ei Schölkopf, B., Platt, J., Hofmann, T. Advances in Neural Information Processing Systems 19: Proceedings of the 2006 Conference Proceedings of the Twentieth Annual Conference on Neural Information Processing Systems (NIPS 2006), pages: 1690, MIT Press, Cambridge, MA, USA, 20th Annual Conference on Neural Information Processing Systems (NIPS), September 2007 (proceedings)

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Bayesian methods for NMR structure determination

Habeck, M.

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

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

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

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

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

Abstract

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

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ei Waldert, S., Bensch, M., Bogdan, M., Rosenstiel, W., Schölkopf, B., Lowery, C., Eswaran, H., Preissl, H. Real-Time Fetal Heart Monitoring in Biomagnetic Measurements Using Adaptive Real-Time ICA IEEE Transactions on Biomedical Engineering, 54(10):1867-1874, September 2007 (article)

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Book Review: Computational Intelligence: Principles, Techniques and Applications by Amit Konar

Peters, J.

The Computer Journal, 50(6):758-758, September 2007 (article)

Web DOI [BibTex]

ei Peters, J. Book Review: Computational Intelligence: Principles, Techniques and Applications by Amit Konar The Computer Journal, 50(6):758-758, September 2007 (article)

Web DOI [BibTex]

Collaborative Filtering via Ensembles of Matrix Factorizations

Wu, M.

KDD Cup and Workshop, August 2007 (talk)

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ei Wu, M. Collaborative Filtering via Ensembles of Matrix Factorizations KDD Cup and Workshop, August 2007 (talk)

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Thinking Out Loud: Research and Development of Brain Computer Interfaces

Hill, NJ.

Invited keynote talk at the Max Planck Society‘s PhDNet Workshop., July 2007 (talk)

Abstract

My principal interest is in applying machine-learning methods to the development of Brain-Computer Interfaces (BCI). This involves the classification of a user‘s intentions or mental states, or regression against some continuous intentional control signal, using brain signals obtained for example by EEG, ECoG or MEG. The long-term aim is to develop systems that a completely paralysed person (such as someone suffering from advanced Amyotrophic Lateral Sclerosis) could use to communicate. Such systems have the potential to improve the lives of many people who would be otherwise completely unable to communicate, but they are still very much in the research and development stages.

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ei Hill, NJ. Thinking Out Loud: Research and Development of Brain Computer Interfaces Invited keynote talk at the Max Planck Society‘s PhDNet Workshop., July 2007 (talk)

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Feature Selection for Trouble Shooting in Complex Assembly Lines

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

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

Abstract

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

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ei Pfingsten, T., Herrmann, D., Schnitzler, T., Feustel, A., Schölkopf, B. Feature Selection for Trouble Shooting in Complex Assembly Lines IEEE Transactions on Automation Science and Engineering, 4(3):465-469, July 2007 (article)

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Local Learning Algorithms for Transductive Classification, Clustering and Data Projection

Wu, M.

Yahoo Inc., July 2007 (talk)

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ei Wu, M. Local Learning Algorithms for Transductive Classification, Clustering and Data Projection Yahoo Inc., July 2007 (talk)

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Gene selection via the BAHSIC family of algorithms

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

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

Abstract

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

Web DOI [BibTex]

ei Song, L., Bedo, J., Borgwardt, K., Gretton, A., Smola, A. Gene selection via the BAHSIC family of algorithms Bioinformatics, 23(13: ISMB/ECCB 2007 Conference Proceedings):i490-i498, July 2007 (article)

Web DOI [BibTex]

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

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

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

Abstract

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

DOI [BibTex]

ei Zien, A., Gebhard, P., Fundel, K., Aigner, T. Phenotyping of Chondrocytes In Vivo and In Vitro Using cDNA Array Technology Clinical Orthopaedics and Related Research, 460, pages: 226-233, July 2007 (article)

DOI [BibTex]

Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

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

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

Abstract

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

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ei Clark, R., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T., Fu, G., Hinds, D., Chen, H., Frazer, K., Huson, D., Schölkopf, B., Nordborg, M., Rätsch, G., Ecker, J., Weigel, D. Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana Science, 317(5836):338-342, July 2007 (article)

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Graph Laplacians and their Convergence on Random Neighborhood Graphs

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

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

Abstract

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

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ei Hein, M., Audibert, J., von Luxburg, U. Graph Laplacians and their Convergence on Random Neighborhood Graphs Journal of Machine Learning Research, 8, pages: 1325-1370, June 2007 (article)

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Dirichlet Process Mixtures of Factor Analysers

Görür, D., Rasmussen, C.

Fifth Workshop on Bayesian Inference in Stochastic Processes (BSP5), June 2007 (talk)

Abstract

Mixture of factor analysers (MFA) is a well-known model that combines the dimensionality reduction technique of Factor Analysis (FA) with mixture modeling. The key issue in MFA is deciding on the latent dimension and the number of mixture components to be used. The Bayesian treatment of MFA has been considered by Beal and Ghahramani (2000) using variational approximation and by Fokoué and Titterington (2003) using birth-and death Markov chain Monte Carlo (MCMC). Here, we present the nonparametric MFA model utilizing a Dirichlet process (DP) prior on the component parameters (that is, the factor loading matrix and the mean vector of each component) and describe an MCMC scheme for inference. The clustering property of the DP provides automatic selection of the number of mixture components. The latent dimensionality of each component is inferred by automatic relevance determination (ARD). Identifying the action potentials of individual neurons from extracellular recordings, known as spike sorting, is a challenging clustering problem. We apply our model for clustering the waveforms recorded from the cortex of a macaque monkey.

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ei Görür, D., Rasmussen, C. Dirichlet Process Mixtures of Factor Analysers Fifth Workshop on Bayesian Inference in Stochastic Processes (BSP5), June 2007 (talk)

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New BCI approaches: Selective Attention to Auditory and Tactile Stimulus Streams

Hill, N., Raths, C.

Invited talk at the PASCAL Workshop on Methods of Data Analysis in Computational Neuroscience and Brain Computer Interfaces, June 2007 (talk)

Abstract

When considering Brain-Computer Interface (BCI) development for patients in the most severely paralysed states, there is considerable motivation to move away from BCI systems based on either motor cortex activity, or on visual stimuli. Together these account for most of current BCI research. I present the results of our recent exploration of new auditory- and tactile-stimulus-driven BCIs. The talk includes a tutorial on the construction and interpretation of classifiers which extract spatio-temporal features from event-related potential data. The effects and implications of whitening are discussed, and preliminary results on the effectiveness of a low-rank constraint (Tomioka and Aihara 2007) are shown.

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ei Hill, N., Raths, C. New BCI approaches: Selective Attention to Auditory and Tactile Stimulus Streams Invited talk at the PASCAL Workshop on Methods of Data Analysis in Computational Neuroscience and Brain Computer Interfaces, June 2007 (talk)

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Towards Motor Skill Learning in Robotics

Peters, J.

Interactive Robot Learning - RSS workshop, June 2007 (talk)

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ei Peters, J. Towards Motor Skill Learning in Robotics Interactive Robot Learning - RSS workshop, June 2007 (talk)

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Transductive Support Vector Machines for Structured Variables

Zien, A., Brefeld, U., Scheffer, T.

International Conference on Machine Learning (ICML), June 2007 (talk)

Abstract

We study the problem of learning kernel machines transductively for structured output variables. Transductive learning can be reduced to combinatorial optimization problems over all possible labelings of the unlabeled data. In order to scale transductive learning to structured variables, we transform the corresponding non-convex, combinatorial, constrained optimization problems into continuous, unconstrained optimization problems. The discrete optimization parameters are eliminated and the resulting differentiable problems can be optimized efficiently. We study the effectiveness of the generalized TSVM on multiclass classification and label-sequence learning problems empirically.

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ei Zien, A., Brefeld, U., Scheffer, T. Transductive Support Vector Machines for Structured Variables International Conference on Machine Learning (ICML), June 2007 (talk)

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Bayesian Reconstruction of the Density of States

Habeck, M.

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

Abstract

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

Web DOI [BibTex]

ei Habeck, M. Bayesian Reconstruction of the Density of States Physical Review Letters, 98(20, 200601):1-4, May 2007 (article)

Web DOI [BibTex]

PALMA: mRNA to Genome Alignments using Large Margin Algorithms

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

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

Abstract

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

Web DOI [BibTex]

ei Schulze, U., Hepp, B., Ong, C., Rätsch, G. PALMA: mRNA to Genome Alignments using Large Margin Algorithms Bioinformatics, 23(15):1892-1900, May 2007 (article)

Web DOI [BibTex]

Impact of target-to-target interval on classification performance in the P300 speller

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

Scientific Meeting "Applied Neuroscience for Healthy Brain Function", May 2007 (talk)

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ei Martens, S., Hill, J., Farquhar, J., Schölkopf, B. Impact of target-to-target interval on classification performance in the P300 speller Scientific Meeting "Applied Neuroscience for Healthy Brain Function", May 2007 (talk)

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Texture and object motion in slant discrimination: Failure of reliability-based weighting of cues may be evidence for strong fusion

Rosas, P., Wichmann, F., Wagemans, J.

Journal of Vision, 7(6:3):1-21, April 2007 (article)

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ei Rosas, P., Wichmann, F., Wagemans, J. Texture and object motion in slant discrimination: Failure of reliability-based weighting of cues may be evidence for strong fusion Journal of Vision, 7(6:3):1-21, April 2007 (article)

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Training a Support Vector Machine in the Primal

Chapelle, O.

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

Abstract

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

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ei Chapelle, O. Training a Support Vector Machine in the Primal Neural Computation, 19(5):1155-1178, March 2007 (article)

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Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning

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

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

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ei Rätsch, G., Sonnenburg, S., Srinivasan, J., Witte, H., Müller, K., Sommer, R., Schölkopf, B. Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning PLoS Computational Biology, 3(2, e20):0313-0322, February 2007 (article)

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Quantum broadcasting problem in classical low-power signal processing

Janzing, D., Steudel, B.

Physical Review A, 75(2):11, February 2007 (article)

Web DOI [BibTex]

ei Janzing, D., Steudel, B. Quantum broadcasting problem in classical low-power signal processing Physical Review A, 75(2):11, February 2007 (article)

Web DOI [BibTex]

Statistical Consistency of Kernel Canonical Correlation Analysis

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

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

Abstract

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

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ei Fukumizu, K., Bach, F., Gretton, A. Statistical Consistency of Kernel Canonical Correlation Analysis Journal of Machine Learning Research, 8, pages: 361-383, February 2007 (article)

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New Margin- and Evidence-Based Approaches for EEG Signal Classification

Hill, N., Farquhar, J.

Invited talk at the FaSor Jahressymposium, February 2007 (talk)

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ei Hill, N., Farquhar, J. New Margin- and Evidence-Based Approaches for EEG Signal Classification Invited talk at the FaSor Jahressymposium, February 2007 (talk)

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Some observations on the pedestal effect

Henning, G., Wichmann, F.

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

Abstract

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

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ei Henning, G., Wichmann, F. Some observations on the pedestal effect Journal of Vision, 7(1:3):1-15, January 2007 (article)

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

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

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

Abstract

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

PDF PDF DOI [BibTex]

ei Zalevski, AM., Henning, GB., Hill, NJ. Cue Combination and the Effect of Horizontal Disparity and Perspective on Stereoacuity Spatial Vision, 20(1):107-138, January 2007 (article)

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

Vollmer, F., Fischer, P.

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

Abstract

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

DOI [BibTex]

pf Vollmer, F., Fischer, P. Frequency-domain displacement sensing with a fiber ring-resonator containing a variable gap SENSORS AND ACTUATORS A-PHYSICAL, 134(2):410-413, 2007 (article)

DOI [BibTex]

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

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

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

Abstract

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

DOI [BibTex]

pf Ghosh, A., Hill, W., Fischer, P. Observation of the Faraday effect via beam deflection in a longitudinal magnetic field PHYSICAL REVIEW A, 76(5), 2007 (article)

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Comment on “negative refraction at optical frequencies in nonmagnetic two-component molecular media” - Reply

Chen, Y., Fischer, P., Wise, F. W.

PHYSICAL REVIEW LETTERS, 98(5), 2007 (article)

DOI [BibTex]

pf Chen, Y., Fischer, P., Wise, F. W. Comment on “negative refraction at optical frequencies in nonmagnetic two-component molecular media” - Reply PHYSICAL REVIEW LETTERS, 98(5), 2007 (article)

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Circular differential double diffraction in chiral media

Ghosh, A., Fazal, F. M., Fischer, P.

OPTICS LETTERS, 32(13):1836-1838, 2007 (article)

Abstract

In an optically active liquid the diffraction angle depends on the circular polarization state of the incident light beam. We report the observation of circular differential diffraction in an isotropic chiral medium, and we demonstrate that double diffraction is an alternate means to determine the handedness (enantiomeric excess) of a solution. (c) 2007 Optical Society of America.

DOI [BibTex]

pf Ghosh, A., Fazal, F. M., Fischer, P. Circular differential double diffraction in chiral media OPTICS LETTERS, 32(13):1836-1838, 2007 (article)

DOI [BibTex]