Biomedical Data Analysis Group

Publications

2021-present

• Physics-Informed Boundary Integral Networks (PIBI-Nets): A Data-Driven Approach for Solving Partial Differential Equations.
  Monika Nagy-Huber, Volker Roth.
  Journal of Computational Science, Elsevier, special issue "Machine Learning and Data Assimilation for Dynamical Systems", 2024.
  
• Lagrangian Flow Networks for Conservation Laws.
  Fabricio Arend Torres, Marcello Massimo Negri, Marco Inversi, Jonathan Aellen, Volker Roth.
  International Conference on Learning Representations (ICLR), 2024.
  
• Conditional Matrix Flows for Gaussian Graphical Models.
  Marcello Massimo Negri, Fabricio Arend Torres, Volker Roth.
  Advances in Neural Information Processing Systems, 2024.
  
• Altered Perception of Environmental Volatility During Social Learning in Emerging Psychosis.
  Daniel J. Hauke, Michelle Wobmann, Christina Andreou, Amatya J. Mackintosh, Renate de Bock, Povilas Karvelis, Rick A. Adams, Philipp Sterzer, Stefan Borgwardt, Volker Roth, Andreea O. Diaconescu.
  Computational Psychiatry, Ubiquity Press, Ltd., 2024.
  
• The effect of lysergic acid diethylamide (LSD) on whole-brain functional and effective connectivity.
  Peter Bedford, Daniel J. Hauke, Zheng Wang, Volker Roth, Monika Nagy-Huber, Friederike Holze, Laura Ley, Patrick Vizeli, Matthias E. Liechti, Stefan Borgwardt, Felix Müller, Andreea O. Diaconescu.
  Neuropsychopharmacology, Springer International Publishing Cham, 2023.
  
• Aberrant hierarchical prediction errors are associated with transition to psychosis: A computational single-trial analysis of the mismatch negativity.
  Daniel J. Hauke, Colleen E. Charlton, André Schmidt, John D. Griffiths, Scott W. Woods, Judith M. Ford, Vinod H. Srihari, Volker Roth, Andreea O. Diaconescu, Daniel H. Mathalon.
  Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, Elsevier, 2023.
  
• Machine Learning Facial Emotion Classifiers in Psychotherapy Research: A Proof-of-Concept Study.
  Martin Steppan, Ronan Zimmermann, Lukas Fürer, Matthew Southward, Julian Koenig, Michael Kaess, Johann Roland Kleinbub, Volker Roth, Klaus Schmeck.
  Psychopathology, Karger, 2023.
  
• Using Machine Learning–Based Algorithms to Identify and Quantify Exercise Limitations in Clinical Practice: Are We There Yet?.
  Fabian Schwendinger, Ann-Kathrin Biehler, Monika Nagy-Huber, Raphael Knaier, Volker Roth, Daniel Dumitrescu, F. Joachim Meyer, Alfred Hager, Arno Schmidt-Trucksäss.
  Medicine & Science in Sports & Exercise, 2023.
  
• Truly Mesh-free Eulerian Physics-Informed Neural Networks.
  Fabricio Arend Torres, Marcello Negri, Monika Nagy-Huber, Maxim Samarin, Volker Roth.
  arXiv preprint arXiv:2206.01545, 2022.
  
• Feature Learning and Random Features in Standard Finite-Width Convolutional Neural Networks: An Empirical Study.
  Maxim Samarin, Volker Roth, David Belius.
  Conference on Uncertainty in Artificial Intelligence (UAI), 2022.
• Learning Invariances with Generalised Input-Convex Neural Networks.
  Vitali Nesterov, Fabricio Arend Torres, Monika Nagy-Huber, Maxim Samarin, Volker Roth.
  arXiv preprint arXiv:2204.07009, 2022.
• Learning Conditional Invariance through Cycle Consistency.
  Maxim Samarin*, Vitali Nesterov*, Mario Wieser, Aleksander Wieczorek, Sonali Parbhoo, Volker Roth.
  Conference on Pattern Recognition (GCPR), 2021.
• Investigating Causal Factors of Shallow Landslides in Grassland Regions of Switzerland.
  Lauren Zweifel, Maxim Samarin, Katrin Meusburger, Christine Alewell.
  Natural Hazards and Earth System Sciences (NHESS), 2021.

2016-2020

• Cognitive Decline in Parkinson’s Disease is Associated with Reduced Complexity of EEG at Baseline.
  Sebastian M. Keller, Ute Gschwandtner, Antonia Meyer, Menorca Chaturvedi, Volker Roth, Peter Fuhr.
  Brain Communications, 2020.
  
• Learning Extremal Representations with Deep Archetypal Analysis.
  Sebastian M. Keller, Maxim Samarin, Fabricio Arend Torres, Mario Wieser, Volker Roth.
  International Journal on Computer Vision (IJCV), 2020.
• Identifying Soil Erosion Processes in Alpine Grasslands on Aerial Imagery with a U-Net Convolutional Neural Network.
  Maxim Samarin*, Lauren Zweifel*, Volker Roth, Christine Alewell.
  Remote Sensing, 2020.
• Inverse Learning of Symmetries.
  Mario Wieser, Sonali Parbhoo, Aleksander Wieczorek, Volker Roth.
  34th Conference on Neural Information Processing Systems, NeurIPS 2020.
• 3DMolNet: A Generative Network for Molecular Structures.
  Vitali Nesterov, Mario Wieser, Volker Roth.
  arXiv preprint arXiv:2010.06477, 2020.
• On the Empirical Neural Tangent Kernel of Standard Finite-Width Convolutional Neural Network Architectures.
  Maxim Samarin, Volker Roth, David Belius.
  arXiv preprint arXiv:2006.13645, 2020.
• On the Difference between the Information Bottleneck and the Deep Information Bottleneck.
  A Wieczorek, V Roth. Entropy 22 (2), 131, 2020.
• Regional Tree Regularization for Interpretability in Black Box Models.
  Mike Wu and Sonali Parbhoo and Michael C. Hughes and Ryan Kindle and Leo A. Celi and Maurizio Zazzi and Volker Roth and Finale Doshi-Velez.
  Proc. Thirty-Fourth AAAI Conference on Artificial Intelligence, 2020.
• Information Theoretic Causal Effect Quantification.
  A Wieczorek, V Roth.
  Entropy 21 (10), 975, 2019.
• Phase lag index and spectral power as QEEG features for identification of patients with mild cognitive impairment in Parkinson's disease.
  Menorca Chaturvedi, Jan Guy Bogaarts, Vitalii V Kozak, Florian Hatz, Ute Gschwandtner, Antonia Meyer, Peter Fuhr, Volker Roth.
  Clinical Neurophysiology 130 (10), 1937-1944, 2019.
• Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART.
  Nadine Bachmann, Chantal von Siebenthal, Valentina Vongrad, Teja Turk, Kathrin Neumann, Niko Beerenwinkel, Jasmina Bogojeska, Jaques Fellay, Volker Roth, Yik Lim Kok, Christian W Thorball, Alessandro Borghesi, Sonali Parbhoo, Mario Wieser, Jürg Böni, Matthieu Perreau, Thomas Klimkait, Sabine Yerly, Manuel Battegay, Andri Rauch, Matthias Hoffmann, Enos Bernasconi, Matthias Cavassini, Roger D Kouyos, Huldrych F Günthard, Karin J Metzner.
  Nature communications 10 (1), 1-11, 2019.
• Deep Archetypal Analysis.
  Sebastian Keller, Maxim Samarin, Mario Wieser, Volker Roth.
  German Conference on Pattern Recognition (GCPR), 2019.
• Cause-Effect Deep Information Bottleneck For Systematically Missing Covariates.
  Sonali Parbhoo, Mario Wieser, Aleksander Wieczorek, Volker Roth.
  Under review, 2019.
• Intelligent Policy Mixing for Improved HIV-1 Therapy Selection
  Sonali Parbhoo, Jasmina Bogojeska, Mario Wieser, Fabricio Arend Torres, Maur- izio Zazzi, Susana Posada Cespedes, Niko Beerenwinkel, Enos Bernasconi, Manuel Battegay, Alexander Calmy, Matthias Cavassini, Pietro Vernazza, Andri Rauch, Karin J. Metzner, Roger Kouyos, Huldrych Günthard, Finale Doshi-Velez, Volker Roth.
  Under review, 2019.
• Improving Counterfactual Reasoning with Kernelised Dynamic Mixing Models.
  Sonali Parbhoo, Omer Gottesman, Andrew Slavin Ross, Matthieu Komorowski, Aldo Faisal, Isabella Bon, Volker Roth, Finale Doshi-Velez.
  PLoS One, Volume 13, Number 11, 2018.
• Greedy Structure Learning of Hierarchical Compositional Models .
  Adam Kortylewski, Aleksander Wieczorek, Mario Wieser, Clemens Blumer, Sonali Parbhoo, Andreas Morel-Forster, Volker Roth, Thomas Vetter.
  IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2019.
• Informed MCMC with Bayesian Neural Networks for Facial Image Analysis.
  Adam Kortylewski, Mario Wieser, Andreas Morel-Forster, Aleksander Wieczorek, Sonali Parbhoo, Volker Roth, and Thomas Vetter.
  arXiv preprint arXiv:1811.07969 (2018).
• Learning Sparse Latent Representations with the Deep Copula Information Bottleneck.
  Mario Wieser, Aleksander Wieczorek, Damian Murezzan, Volker Roth.
  International Conference on Learning Representations (ICLR), 2018.
• Beyond Sparsity: Tree Regularization of Deep Models for Interpretability.
  Mike Wu, Michael C Hughes, Sonali Parbhoo, Maurizio Zazzi, Volker Roth, Finale Doshi-Velez.
  Thirty-Second AAAI Conference on Artificial Intelligence, 2018.
• Quantitative EEG (QEEG) Measures Differentiate Parkinson's Disease (PD) Patients from Healthy Controls (HC) .
  Chaturvedi, Menorca and Hatz, Florian and Gschwandtner, Ute and Bogaarts, Jan G. and Meyer, Antonia and Fuhr, Peter and Roth, Volker.
  Frontiers in Aging Neuroscience, Volume 9. 10.3389/fnagi.2017.00003, 2017
• Combining Kernel and Model-based Learning for HIV Therapy Selection.
  Sonali Parbhoo, Jasmina Bogojeska, Maurizio Zazzi, Volker Roth and Finale Doshi Velez.
  Proceedings of The American Medical Informatics Association (AMIA) Summit on Clinical Research Informatics (CRI), 2017
  A shortened version of the paper and a poster were presented at NIPS 2016 Machine Learning in Healthcare workshop.
• Quantitative proteomics and phosphoproteomics on serial tumor biopsies from a sorafenib-treated HCC patient.
  Eva Dazert, Marco Colombi, Tujana Boldanova, Suzette Moes, David Adametz, Luca Quagliata, Volker Roth, Luigi Terracciano, Markus Heim, Paul Jenoe, Michael N. Hall.
  PNAS, Proceedings of the National Academy of Sciences, Vol. 113, No. 5. (02 February 2016), pp. 1381-1386.
• Gene expression analysis of biopsy samples reveals critical limitations of transcriptome-based molecular classifications of hepatocellular carcinoma.
  Zuzanna Makowska, Tujana Boldanova, David Adametz, Luca Quagliata, Julia E. Vogt, Michael T. Dill, Mathias S. Matter, Volker Roth, Luigi Terracciano, Markus H. Heim.
  Journal of Pathology: Clinical Research, in press, 2016.
• Bayesian Markov Blanket Estimation.
  Dinu Kaufmann, Sonali Parbhoo, Aleksander Wieczorek, Sebastian Keller, David Adametz, Volker Roth.
  AI and Statistics -- AISTATS 2016, pp. 333-341, 2016.
• Copula Eigenfaces.
  Dinu Kaufmann, Sandro Schoenborn, Volker Roth and Thomas Vetter.
  Computer Graphics Theory and Applications--GRAPP 2016, in press, 2016.

2011-2015

• Copula Archetypal Analysis.
  Kaufmann, Dinu and Keller, Sebastian and Roth, Volker.
  In Pattern Recognition--GCPR 2015, pp 117--128, 2015.
  Erratum: Fig. 6, right panel should be this.
• Probabilistic clustering of time-evolving distance data.
  Vogt, Julia E.; Kloft, Marius; Stark, Stefan; Raman, Sudhir S.; Prabhakaran, Sandhya; Roth, Volker; Raetsch, Gunnar.
  Machine learning Vol 100, number 2-3, pages 635-654, 2015
• Power spectra for screening parkinsonian patients for mild cognitive impairment.
  Habib Bousleiman, Ronan Zimmermann, Shaheen Ahmed, Martin Hardmeier, Florian Hatz, Christian Schindler, Volker Roth, Ute Gschwandtner, Peter Fuhr.
  Annals of Clinical and Translational Neurology. Volume 1, Issue 11, pages 884-890, November 2014.
• Distance-based Network Recovery under Feature Correlation.
  David Adametz and Volker Roth.
  Advances in Neural Information Processing Systems--NIPS 2014, pages 775-783,2014.
• Information Bottleneck for Pathway-centric Gene Expression Analysis.
  David Adametz and Volker Roth.
  Proc. 36th German Conference on Pattern Recognition--GCPR 2014, pp 81-91, 2014.
• Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.
  Francesca Di Giallonardo, Armin Töpfer, Mélanie Rey, Sandhya Prabhakaran, Yannick Duport, Christine Leemann, Stefan Schmutz, Nottania K. Campbell, Beda Joos, Maria Rita Lecca, Andrea Patrignani, Martin Däumer, Christian Beisel, Peter Rusert, Alexandra Trkola, Huldrych F. Günthard, Volker Roth, Niko Beerenwinkel, Karin J. Metzner.
  Nucl Acids Res, First published online June 27, 2014, doi:10.1093/nar/gku537.
• Sparse meta-Gaussian information bottleneck.
  Mélanie Rey, Thomas J. Fuchs, Volker Roth.
  In Proceedings of the 31st International Conference on Machine Learning--ICML 2014, JMLR W&CP 32 (1) :910-918, 2014.
• Pegylated IFN-alpha regulates hepatic gene expression through transient Jak/STAT activation.
  Michael T. Dill, Zuzanna Makowska, Gaia Trincucci, Andreas J. Gruber, Julia E. Vogt, Magdalena Filipowicz, Diego Calabrese, Ilona Krol, Daryl T. Lau, Luigi Terracciano, Erik van Nimwegen, Volker Roth and Markus H. Heim.
  J Clin Invest 124(4):1568--1581, doi:10.1172/JCI70408, 2014.
• HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model.
  Sandhya Prabhakaran, Melanie Rey, Osvaldo Zagordi, Niko Beerenwinkel, Volker Roth.
  IEEE Transactions on Computational Biology and Bioinformatics, Jan.-Feb. 2014 (vol. 11 no. 1) pp. 182-191.
• Probabilistic Inference of Viral Quasispecies Subject to Recombination.
  Töpfer, Armin and Zagordi, Osvaldo and Prabhakaran, Sandhya and Roth, Volker and Halperin, Eran and Beerenwinkel, Niko.
  Journal of Computational Biology 20(2):113--123, 2013
• Malaria haplotype frequency estimation.
  Wigger, Leonore and Vogt, Julia E and Roth, Volker.
  Statistics in medicine, 2013.
• Recovering Networks from Distance Data.
  Sandhya Prabhakaran, Alex Boehm, Karin Metzner, Volker Roth.
  Machine Learning Journal, 10.1007/s10994-013-5370-7, 2013.
• Meta-Gaussian Information Bottleneck.
  Melanie Rey and Volker Roth.
  Advances in Neural Information Processing Systems 25:1925--1933, 2012
• Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.
  Niko Beerenwinkel, Huldrych F. Günthard, Volker Roth, and Karin J. Metzner.
  Frontiers in Microbiology, 3:329, 2012.
• Recovering Networks from Distance Data.
  Sandhya Prabhakaran, Alex Boehm, Karin Metzner, Volker Roth.
  Asian Conference on Machine Learning -- ACML 2012, Journal of Machine Learning Research, Workshop and Conference Proceedings 25:349--64, 2012.
• P139: Continuous exposure to PEG-IFN-Alpha only transiently activates JAK-stat signalling in human liver.
  Makowska, Z and Dill, MT and Vogt, JE and Filipowicz, M and Terraciano, L and Roth, V and Heim, MH.
  Cytokine 59(3):563--564, 2012.
• Sparse Point Estimation for Bayesian Regression via Simulated Annealing.
  Sudhir Raman, Volker Roth.
  Pattern Recognition: 34-th DAGM Symposium, volume 7476 of the Lecture Notes in Computer Science, pages 317-326, 2012.
• Automatic Model Selection in Archetype Analysis.
  Sandhya Prabhakaran, Sudhir Raman, Julia E. Vogt and Volker Roth.
  Pattern Recognition: 34-th DAGM Symposium, volume 7476 of the Lecture Notes in Computer Science, pages 458-467, 2012.
• A Complete Analysis of the l_{1,p} Group-Lasso.
  Julia Vogt, Volker Roth.
  ICML 2012.
• Copula Mixture Model for Dependency-seeking Clustering.
  Melanie Rey, Volker Roth.
  ICML 2012.
• A Seven-Marker Signature and Clinical Outcome in Malignant Melanoma: A Large-Scale Tissue-Microarray Study With Two Independent Patient Cohorts.
  Stefanie Meyer, Thomas J. Fuchs, Anja K. Bosserhoff, Ferdinand Hofstaedter, Armin Pauer, Volker Roth, Joachim M. Buhmann, Ingrid Moll, Nikos Anagnostou, Johanna Brandner, Kristian Ikenberg, Holger Moch, Michael Landthaler, Thomas Vogt, Peter J. Wild.
  PLoS ONE, 7:e38222, 2012.
• Probabilistic inference of viral quasispecies subject to recombination.
  Osvaldo Zagordi, Armin Toepfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin and Niko Beerenwinkel.
  RECOMB 2012:342-354.
• Bayesian Partitioning of Large-Scale Distance Data.
  David Adametz and Volker Roth.
  NIPS 2011:1368-1376, 2011.
• Proteome analysis in cardiovascular pathophysiology using Dahl rat model.
  Thomas Grussenmeyer, Silvia Meili-Butz, Volker Roth, Thomas Dieterle, Marijke Brink, Bernhard Winkler, Peter Matta, Thierry P. Carrela, Friedrich S. Eckstein, Ivan Lefkovits, and Martin T.R. Grapowa.
  Journal of Proteomics, 2011.
• Interferon Induced Gene Expression is a Stronger Predictor of Treatment Response in Hepatitis C than IL28B Genotype.
  Michael T. Dill, Francois H.T. Duong, Julia E. Vogt, Stephanie Bibert, Pierre-Yves Bochud, Luigi Terracciano, Andreas Papassotiropoulos, Volker Roth and Markus H. Heim.
  Gastroenterology, 2011 Mar;140(3):1021-1031.e10.

2006-2010

• Infinite mixture-of-experts model for sparse survival regression with application to breast cancer.
  Sudhir Raman, Thomas J Fuchs, Peter J Wild, Edgar Dahl, Joachim M Buhmann, Volker Roth.
  BMC Bioinformatics 2010, 11(Suppl 8):S8 (26 October 2010).
• The Group-Lasso: l_{1,\infty} Regularization versus l_{1,2} Regularization.
  Julia E. Vogt, Volker Roth.
  Pattern Recognition: 32-nd DAGM Symposium, Lecture Notes in Computer Science 6376:252-261, 2010. DAGM prize.
• Computational TMA Analysis and Cell Nucleus Classification of Renal Cell Carcinoma.
  Peter Schueffler, Thomas Fuchs, Cheng Soon Ong, Volker Roth, Joachim M. Buhmann.
  Pattern Recognition: 32-nd DAGM Symposium, Lecture Notes in Computer Science 6376:202-211, 2010.
• The Translation-invariant Wishart-Dirichlet Process for Clustering Distance Data.
  Julia E. Vogt, Sandhya Prabhakaran, Thomas J. Fuchs, Volker Roth.
  ICML 2010: Proceedings of the 27th international conference on Machine Learning. Best paper award runner up.
• Second messenger mediated adjustment of bacterial swimming velocity.
  Alex Boehm, Matthias Kaiser, Hui Li, Christian Spangler, Christoph Kasper, Martin Ackermann, Volkhard Kaever, Victor Sourjik, Volker Roth and Urs Jenal.
  Cell, Volume 141, Issue 1, 2 April 2010, Pages 107-116.
• Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction.
  Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel.
  Journal of Computational Biology. March 2010, Vol. 17, No. 3: 417-428.
• Sparse Bayesian Regression for Grouped Variables in Generalized Linear Models.
  Suhir Raman and Volker Roth.
  Pattern Recognition: 31st DAGM Symposium, Lecture Notes in Computer Science 5748, pages 242-251, 2009.
• The Bayesian Group-Lasso for Analyzing Contingency Tables.
  Sudhir Raman, Thomas Fuchs, Peter J. Wild, Edgar Dahl, Volker Roth.
  ICML'09: Proceedings of the 26th international conference on Machine Learning, pages 881-888, 2009.
• Detection of urothelial bladder cancer cells in voided urine can be improved by a combination of cytology and standardized microsatellite analysis.
  Peter J. Wild, Thomas Fuchs, Robert Stoehr, Dieter Zimmermann, Simona Frigerio, Barbara Padberg, Inbal Steiner, Ellen C. Zwarthoff, Maximilian Burger, Stefan Denzinger, Ferdinand Hofstaedter, Glen Kristiansen, T. Hermanns, Hans-Helge Seifert, Maurizio Provenzano, Tullio Sulser, Volker Roth, Joachim M. Buhmann, Holger Moch, Arndt Hartmann.
  Cancer Epidemiology, Biomarkers and Prevention, June 1, 2009, 18(6), page 1798-1806.