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2018


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Counterfactual Mean Embedding: A Kernel Method for Nonparametric Causal Inference

Muandet, K., Kanagawa, M., Saengkyongam, S., Marukata, S.

Arxiv e-prints, arXiv:1805.08845v1 [stat.ML], 2018 (article)

Abstract
This paper introduces a novel Hilbert space representation of a counterfactual distribution---called counterfactual mean embedding (CME)---with applications in nonparametric causal inference. Counterfactual prediction has become an ubiquitous tool in machine learning applications, such as online advertisement, recommendation systems, and medical diagnosis, whose performance relies on certain interventions. To infer the outcomes of such interventions, we propose to embed the associated counterfactual distribution into a reproducing kernel Hilbert space (RKHS) endowed with a positive definite kernel. Under appropriate assumptions, the CME allows us to perform causal inference over the entire landscape of the counterfactual distribution. The CME can be estimated consistently from observational data without requiring any parametric assumption about the underlying distributions. We also derive a rate of convergence which depends on the smoothness of the conditional mean and the Radon-Nikodym derivative of the underlying marginal distributions. Our framework can deal with not only real-valued outcome, but potentially also more complex and structured outcomes such as images, sequences, and graphs. Lastly, our experimental results on off-policy evaluation tasks demonstrate the advantages of the proposed estimator.

arXiv [BibTex]

2018

arXiv [BibTex]


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k–SVRG: Variance Reduction for Large Scale Optimization

Raj, A., Stich, S.

In 2018 (inproceedings) Submitted

[BibTex]

[BibTex]


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Distribution-Dissimilarities in Machine Learning

Simon-Gabriel, C. J.

Eberhard Karls Universität Tübingen, Germany, 2018 (phdthesis)

[BibTex]

[BibTex]


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Probabilistic Deep Learning using Random Sum-Product Networks

Peharz, R., Vergari, A., Stelzner, K., Molina, A., Trapp, M., Kersting, K., Ghahramani, Z.

2018 (conference) Submitted

arXiv [BibTex]

arXiv [BibTex]


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Autofocusing-based phase correction

Loktyushin, A., Ehses, P., Schölkopf, B., Scheffler, K.

Magnetic Resonance in Medicine, 80(3):958-968, 2018 (article)

DOI [BibTex]

DOI [BibTex]


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Generalized phase locking analysis of electrophysiology data

Safavi, S., Panagiotaropoulos, T., Kapoor, V., Logothetis, N. K., Besserve, M.

7th AREADNE Conference on Research in Encoding and Decoding of Neural Ensembles, 2018 (poster)

link (url) Project Page [BibTex]

link (url) Project Page [BibTex]


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Case series: Slowing alpha rhythm in late-stage ALS patients

Hohmann, M. R., Fomina, T., Jayaram, V., Emde, T., Just, J., Synofzik, M., Schölkopf, B., Schöls, L., Grosse-Wentrup, M.

Clinical Neurophysiology, 129(2):406-408, 2018 (article)

DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Inverse Reinforcement Learning via Nonparametric Spatio-Temporal Subgoal Modeling

Šošić, A., Rueckert, E., Peters, J., Zoubir, A., Koeppl, H.

Journal of Machine Learning Research, 19(69):1-45, 2018 (article)

link (url) Project Page [BibTex]

link (url) Project Page [BibTex]


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Grip Stabilization of Novel Objects using Slip Prediction

Veiga, F., Peters, J., Hermans, T.

IEEE Transactions on Haptics, 2018 (article) In press

DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Domain Adaptation Under Causal Assumptions

Lechner, T.

Eberhard Karls Universität Tübingen, Germany, 2018 (mastersthesis)

[BibTex]

[BibTex]


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A Differentially Private Kernel Two-Sample Test

Raj*, A., Law*, L., Sejdinovic*, D., Park, M.

2018, *equal contribution (conference) Submitted

[BibTex]

[BibTex]


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Electrophysiological correlates of neurodegeneration in motor and non-motor brain regions in amyotrophic lateral sclerosis—implications for brain–computer interfacing

Kellmeyer, P., Grosse-Wentrup, M., Schulze-Bonhage, A., Ziemann, U., Ball, T.

Journal of Neural Engineering, 15(4):041003, IOP Publishing, 2018 (article)

link (url) [BibTex]

link (url) [BibTex]


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Quantum machine learning: a classical perspective

Ciliberto, C., Herbster, M., Ialongo, A. D., Pontil, M., Rocchetto, A., Severini, S., Wossnig, L.

Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 474(2209):20170551, 2018 (article)

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Kernel-based tests for joint independence

Pfister, N., Bühlmann, P., Schölkopf, B., Peters, J.

Journal of the Royal Statistical Society: Series B (Statistical Methodology), 80(1):5-31, 2018 (article)

DOI [BibTex]

DOI [BibTex]


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Prediction of Glucose Tolerance without an Oral Glucose Tolerance Test

Babbar, R., Heni, M., Peter, A., Hrabě de Angelis, M., Häring, H., Fritsche, A., Preissl, H., Schölkopf, B., Wagner, R.

Frontiers in Endocrinology, 9, pages: 82, 2018 (article)

DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Invariant Models for Causal Transfer Learning

Rojas-Carulla, M., Schölkopf, B., Turner, R., Peters, J.

Journal of Machine Learning Research, 19(36):1-34, 2018 (article)

link (url) [BibTex]

link (url) [BibTex]


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MOABB: Trustworthy algorithm benchmarking for BCIs

Jayaram, V., Barachant, A.

Journal of Neural Engineering, 15(6):066011, 2018 (article)

link (url) DOI Project Page [BibTex]

link (url) DOI Project Page [BibTex]


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f-Divergence constrained policy improvement

Belousov, B., Peters, J.

Journal of Machine Learning Research, 2018 (article) Submitted

Project Page [BibTex]

Project Page [BibTex]


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Phylogenetic convolutional neural networks in metagenomics

Fioravanti*, D., Giarratano*, Y., Maggio*, V., Agostinelli, C., Chierici, M., Jurman, G., Furlanello, C.

BMC Bioinformatics, 19(2):49 pages, 2018, *equal contribution (article)

DOI [BibTex]

DOI [BibTex]


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Riemannian Adaptive Optimization Methods

Becigneul, G., Ganea, O.

ICLR 2019, 2018 (conference) Submitted

[BibTex]

[BibTex]


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Food specific inhibitory control under negative mood in binge-eating disorder: Evidence from a multimethod approach

Leehr, E. J., Schag, K., Dresler, T., Grosse-Wentrup, M., Hautzinger, M., Fallgatter, A. J., Zipfel, S., Giel, K. E., Ehlis, A.

International Journal of Eating Disorders, 51(2):112-123, Wiley Online Library, 2018 (article)

DOI [BibTex]

DOI [BibTex]


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Probabilistic Approaches to Stochastic Optimization

Mahsereci, M.

Eberhard Karls Universität Tübingen, Germany, 2018 (phdthesis)

link (url) Project Page [BibTex]

link (url) Project Page [BibTex]


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Reinforcement Learning for High-Speed Robotics with Muscular Actuation

Guist, S.

Ruprecht-Karls-Universität Heidelberg , 2018 (mastersthesis)

[BibTex]

[BibTex]


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Linking imaging to omics utilizing image-guided tissue extraction

Disselhorst, J. A., Krueger, M. A., Ud-Dean, S. M. M., Bezrukov, I., Jarboui, M. A., Trautwein, C., Traube, A., Spindler, C., Cotton, J. M., Leibfritz, D., Pichler, B. J.

Proceedings of the National Academy of Sciences, 115(13):E2980-E2987, 2018 (article)

DOI [BibTex]

DOI [BibTex]


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Methods in Psychophysics

Wichmann, F. A., Jäkel, F.

In Stevens’ Handbook of Experimental Psychology and Cognitive Neuroscience, 5 (Methodology), 7, 4th, John Wiley & Sons, Inc., 2018 (inbook)

[BibTex]

[BibTex]


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Discriminative Transfer Learning for General Image Restoration

Xiao, L., Heide, F., Heidrich, W., Schölkopf, B., Hirsch, M.

IEEE Transactions on Image Processing, 27(8):4091-4104, 2018 (article)

DOI [BibTex]

DOI [BibTex]


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Photorealistic Video Super Resolution

Pérez-Pellitero, E., Sajjadi, M. S. M., Hirsch, M., Schölkopf, B.

Workshop and Challenge on Perceptual Image Restoration and Manipulation (PIRM) at the 15th European Conference on Computer Vision (ECCV), 2018 (poster)

[BibTex]

[BibTex]


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Denotational Validation of Higher-order Bayesian Inference

Ścibior, A., Kammar, O., Vákár, M., Staton, S., Yang, H., Cai, Y., Ostermann, K., Moss, S. K., Heunen, C., Ghahramani, Z.

Proceedings of the ACM on Principles of Programming Languages (POPL), 2(Article No. 60):1-29, ACM, 2018 (conference)

DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Dissecting the synapse- and frequency-dependent network mechanisms of in vivo hippocampal sharp wave-ripples

Ramirez-Villegas, J. F., Willeke, K. F., Logothetis, N. K., Besserve, M.

Neuron, 100(5):1224-1240, 2018 (article)

link (url) DOI Project Page [BibTex]

link (url) DOI Project Page [BibTex]


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Two-qubit causal structures and the geometry of positive qubit-maps

Kübler, J. M., Braun, D.

New Journal of Physics, 20(8):083015, 2018 (article)

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Retinal image quality of the human eye across the visual field

Meding, K., Hirsch, M., Wichmann, F. A.

14th Biannual Conference of the German Society for Cognitive Science (KOGWIS 2018), 2018 (poster)

[BibTex]

[BibTex]


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In-Hand Object Stabilization by Independent Finger Control

Veiga, F. F., Edin, B. B., Peters, J.

IEEE Transactions on Robotics, 2018 (article) Submitted

Project Page [BibTex]

Project Page [BibTex]


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Visualizing and understanding Sum-Product Networks

Vergari, A., Di Mauro, N., Esposito, F.

Machine Learning, 2018 (article)

DOI [BibTex]

DOI [BibTex]


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Poincaré GloVe: Hyperbolic Word Embeddings

Tifrea*, A., Becigneul*, G., Ganea*, O.

ICLR 2019, 2018, *equal contribution (conference) Submitted

[BibTex]

[BibTex]


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Transfer Learning for BCIs

Jayaram, V., Fiebig, K., Peters, J., Grosse-Wentrup, M.

In Brain–Computer Interfaces Handbook, pages: 425-442, 22, (Editors: Chang S. Nam, Anton Nijholt and Fabien Lotte), CRC Press, 2018 (incollection)

Project Page [BibTex]

Project Page [BibTex]


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Probabilistic Ordinary Differential Equation Solvers — Theory and Applications

Schober, M.

Eberhard Karls Universität Tübingen, Germany, 2018 (phdthesis)

[BibTex]

[BibTex]


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A machine learning approach to taking EEG-based computer interfaces out of the lab

Jayaram, V.

Graduate Training Centre of Neuroscience, IMPRS, Eberhard Karls Universität Tübingen, Germany, 2018 (phdthesis)

[BibTex]

[BibTex]


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Non-Equilibrium Relations for Bounded Rational Decision-Making in Changing Environments

Grau-Moya, J, Krüger, M, Braun, DA

Entropy, 20(1:1):1-28, January 2018 (article)

Abstract
Living organisms from single cells to humans need to adapt continuously to respond to changes in their environment. The process of behavioural adaptation can be thought of as improving decision-making performance according to some utility function. Here, we consider an abstract model of organisms as decision-makers with limited information-processing resources that trade off between maximization of utility and computational costs measured by a relative entropy, in a similar fashion to thermodynamic systems undergoing isothermal transformations. Such systems minimize the free energy to reach equilibrium states that balance internal energy and entropic cost. When there is a fast change in the environment, these systems evolve in a non-equilibrium fashion because they are unable to follow the path of equilibrium distributions. Here, we apply concepts from non-equilibrium thermodynamics to characterize decision-makers that adapt to changing environments under the assumption that the temporal evolution of the utility function is externally driven and does not depend on the decision-maker’s action. This allows one to quantify performance loss due to imperfect adaptation in a general manner and, additionally, to find relations for decision-making similar to Crooks’ fluctuation theorem and Jarzynski’s equality. We provide simulations of several exemplary decision and inference problems in the discrete and continuous domains to illustrate the new relations.

DOI [BibTex]

DOI [BibTex]

2007


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HPLC analysis and pharmacokinetic study of quercitrin and isoquercitrin in rat plasma after administration of Hypericum japonicum thunb. extract.

Li, J., Wang, W., Zhang, L., Chen, H., Bi, S.

Biomedical Chromatography, 22(4):374-378, December 2007 (article)

Abstract
A simple HPLC method was developed for determination of quercitrin and isoquercitrin in rat plasma. Reversed-phase HPLC was employed for the quantitative analysis using kaempferol-3-O--d-glucopyranoside-7-O--l-rhamnoside as an internal standard. Following extraction from the plasma samples with ethyl acetate-isopropanol (95:5, v/v), these two compounds were successfully separated on a Luna C18 column (250 × 4.6 mm, 5 µm) with isocratic elution of acetonitrile-0.5% aqueous acetic acid (17:83, v/v) as the mobile phase. The flow-rate was set at 1 mL/min and the eluent was detected at 350 nm for both quercitrin and isoquercitrin. The method was linear over the studied ranges of 50-6000 and 50-5000 ng/mL for quercitrin and isoquercitrin, respectively. The intra- and inter-day precisions of the analysis were better than 13.1 and 13.2%, respectively. The lower limits of quantitation for quercitrin and isoquercitrin in plasma were both of 50 ng/mL. The mean extraction recoveries were 73 and 61% for quercitrin and i soquercitrin, respectively. The validated method was successfully applied to pharmacokinetic studies of the two analytes in rat plasma after the oral administration of Hypericum japonicum thunb. ethanol extract.

Web DOI [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.

Web [BibTex]

Web [BibTex]


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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.

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)

Web [BibTex]

Web [BibTex]


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Graph sharpening plus graph integration: a synergy that improves protein functional classification

Shin, HH., Lisewski, AM., Lichtarge, O.

Bioinformatics, 23(23):3217-3224, December 2007 (article)

Web DOI [BibTex]

Web DOI [BibTex]