Publications

Structure-Aware Transformer for Graph Representation Learning

Dexiong Chen*, Leslie O'Bray*, and Karsten Borgwardt 
Proceedings of the 39th International Conference on Machine Learning (ICML 2022), 3469-3489
external page Online  |  external page ICML Presentation

Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients

Bowen Fan, Juliane Klatt, Michael M. Moor, Latasha A. Daniels, Swiss Pediatric Sepsis Study, Lazaro N. Sanchez-Pinto, Philipp K. A. Agyeman, Luregn J. Schlapbach, and Karsten M. Borgwardt
International Conference on Intelligent Systems for Molecular Biology (ISMB 2022) and Bioinformatics 2022, 38 (Supplement_1): i101–i108
external page Online  

Direct Antimicrobial Resistance Prediction from MALDI-TOF mass spectra profile in clinical isolates through Machine Learning

Caroline Weis, Aline Cuénod, Bastian Rieck, Olivier Dubuis, Susanne Graf, Claudia Lang, Michael Oberle, Kirstine K. Soegaard, Michael Osthoff, Karsten Borgwardt*, and Adrian Egli* (* = equal contribution)
Nature Medicine 2022, 28: 164–174
external page Online  |  external page arXiv  |  ETH News

Determinants of SARS-CoV-2 transmission to guide vaccination strategy in a city

Sarah C. Brüningk*, Juliane Klatt*, Madlen Stange*, Alfredo Mari, Myrta Brunner, Tim-Christoph Roloff, Helena M. B. Seth-Smith, Michael Schweitzer, Karoline Leuzinger, Kirstine K. Søgaard, Diana Albertos Torres, Alexander Gensch, Ann-Kathrin Schlotterbeck, Christian H. Nickel, Nicole Ritz, Ulrich Heininger, Julia Bielicki, Katharina Rentsch, Simon Fuchs, Roland Bingisser, Martin Siegemund, Hans Pargger, Diana Ciardo, Olivier Dubuis, Andreas Buser, Sarah Tschudin-Sutter, Manuel Battegay, Rita Schneider-Sliwa, Karsten M. Borgwardt°, Hans H. Hirsch°, and Adrian Egli° (* = equal contribution, ° = joint supervision)
Virus Evolution 2022, 8 (1): veac002
external page Online 

Evaluation Metrics for Graph Generative Models: Problems, Pitfalls, and Practical Solutions

Leslie O'Bray*, Max Horn*, Bastian Rieck*, and Karsten Borgwardt (* = equal contribution)
Tenth International Conference on Learning Representations (ICLR 2022)
external page OpenReview  |  external page arXiv  

Topological Graph Neural Networks

Max Horn*, Edward De Brouwer*, Michael Moor, Yves Moreau, Bastian Rieck°, and Karsten Borgwardt° (* = equal contribution)
Tenth International Conference on Learning Representations (ICLR 2022)
external page OpenReview  |  external page arXiv

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RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection

Kemal Avican, Jehad Aldahdooh, Matteo Togninalli, A. K. M. Firoj Mahmud, Jing Tang, Karsten M. Borgwardt, Mikael Rhen, and Maria Fällman
Nature Communications 2021, 12: 3282
external page Online 

Filtration Curves for Graph Representation

Leslie O’Bray*, Bastian Rieck* and Karsten Borgwardt (* = equal contribution)
In Proceedings of the 27th ACM SIGKDD Conference on Knowledge Discovery & Data Mining (KDD '21). Association for Computing Machinery, New York, NY, USA, 1267–1275.
external page Online   

Early Prediction of Sepsis in the ICU using Machine Learning: A Systematic Review

Michael Moor*, Bastian Rieck*, Max Horn, Catherine Jutzeler°, and Karsten Borgwardt° (* = equal contribution, ° = joint supervision)
Frontiers in Medicine 2021, 8:607952
external page Online  |  external page medRxiv

Biological network analysis with deep learning

Giulia Muzio*, Leslie O’Bray* and Karsten Borgwardt (* = equal contribution)
Briefings in Bioinformatics 2021, 22(2): 1515–1530
external page Online   

Network-guided search for genetic heterogeneity between gene pairs

Anja C. Gumpinger, Bastian Rieck, Dominik G. Grimm, International Headache Genetics Consortium, and Karsten M. Borgwardt
Bioinformatics 2021, 37(1): 57–65
external page Online  |  external page GitHub   

Using routine MRI data of depressed patients to predict individual responses to electroconvulsive therapy

Matti Gärtner, Elisabetta Ghisu, Ana L. Herrera-Melendez, Michael Koslowski, Sabine Aust, Patrick Asbach, Christian Otte, Francesca Regen, Isabella Heuser, Karsten Borgwardt, Malek Bajbouj and Simone Grimm
Experimental Neurology 2021, 335: 113505.
external page Online  |  external page Free version  

Ethnicity-based bias in clinical severity scores

Thomas Gumbsch and Karsten Borgwardt
The Lancet Digital Health 2021, 3(4): E209-E210
external page Online   

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Enhancing statistical power in temporal biomarker discovery through representative shapelet mining

Thomas Gumbsch, Christian Bock, Michael Moor, Bastian Rieck, and Karsten Borgwardt
ECCB and Bioinformatics 2020, 36(Supplement_2): i840–i848
external page Online 

Graph Kernels: State-of-the-Art and Future Challenges

Karsten Borgwardt, Elisabetta Ghisu, Felipe Llinares-López, Leslie O'Bray, and Bastian Rieck
Foundations and Trends® in Machine Learning 2020, 13 (5-6): 531-712.
external page Online  |  Project page  |  external page arXiv

Uncovering the Topology of Time-​Varying fMRI Data using Cubical Persistence

Bastian Rieck, Tristan Yates, Christian Bock, Karsten Borgwardt, Guy Wolf, Nicholas Turk-Browne, and Smita Krishnaswamy
Spotlight presentation at NeurIPS 2020 and Advances in Neural Information Processing Systems 33, 6900-6912
external page Online  |  external page arXiv  |  external page GitHub  |  external page Video

Comorbidities, clinical signs and symptoms, laboratory findings, imaging features, treatment strategies, and outcomes in adult and pediatric patients with COVID-19: A systematic review and meta-analysis

Catherine R. Jutzeler*, Lucie Bourguignon*, Caroline V. Weis, Bobo Tong, Cyrus Wong, Bastian Rieck, Hans Pargger, Sarah Tschudin-Sutter, Adrian Egli, Karsten Borgwardt° and Matthias Walter° (* = equal contribution, ° = joint supervision)
Travel Medicine and Infectious Disease 2020, 37: 101825
external page Online 

Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping

Simon Höllerer*, Laetitia Papaxanthos*, Anja Cathrin Gumpinger, Katrin Fischer, Christian Beisel, Karsten Borgwardt°, Yaakov Benenson° & Markus Jeschek° (* = equal contribution, ° = joint supervision)
Nature Communications 2020, 11: 3551
external page Online  |  external page Code (GitHub)  |  external page Data (GitHub)

SPHN/PHRT: Forming a Swiss-Wide Infrastructure for Data-Driven Sepsis Research

Adrian Egli, Manuel Battegay, Andrea C Büchler, Peter Bühlmann, Thierry Calandra, Philippe Eckert, Hansjakob Furrer, Gilbert Greub, Stephan M Jakob, Laurent Kaiser, Stephen L Leib, Stephan Marsch, Nicolai Meinshausen, Jean-Luc Pagani, Jerome Pugin, Gunnar Rätsch, Jacques Schrenzel, Reto Schüpbach, Martin Siegemund, Nicola Zamboni, Reinhard Zbinden, Annelies Zinkernagel, and Karsten Borgwardt
Studies in Health Technology and Informatics 2020, 270: 1163–1167
external page Online   

Machine Learning for Biomedical Time Series Classification: From Shapelets to Deep Learning

Christian Bock*, Michael Moor*, Catherine Jutzeler, Karsten Borgwardt (*=equal contribution)
In "Artificial Neural Networks", volume 2190 of Methods in Molecular Biology, 33-71
external page Online   

Set Functions for Time Series

Max Horn, Michael Moor, Christian Bock, Bastian Rieck and Karsten Borgwardt
Proceedings of the 37th International Conference on Machine Learning, PMLR 119:4353-4363, 2020.
external page Online  |  external page arXiv   

Topological Autoencoders

Michael Moor*, Max Horn*, Bastian Rieck° and Karsten Borgwardt° (*= equal contribution, °= equal contribution)
Proceedings of the 37th International Conference on Machine Learning, PMLR 119:7045-7054, 2020.
external page Online  | external page arXiv   

Machine learning for microbial identification and antimicrobial susceptibility testing on MALDI-TOF mass spectra: a systematic review

Caroline Weis*, Catherine Jutzeler* and Karsten Borgwardt (* = equal contribution)
Clinical Microbiology and Infection 2020, 26 (10): 1310-1317
external page Online  

Prediction of cancer driver genes through network-based moment propagation of mutation scores

Anja Gumpinger, Kasper Lage, Heiko Horn and Karsten Borgwardt
ISMB 2020 and Bioinformatics 2020, 36 (Supplement_1): i508–i515
external page Online  

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra

Caroline Weis, Max Horn, Bastian Rieck, Aline Cuenod, Adrian Egli and Karsten Borgwardt
ISMB 2020 and Bioinformatics 2020, 36 (Supplement_1): i30–i38
external page Online 

Early prediction of circulatory failure in the intensive care unit using machine learning

Stephanie L. Hyland*, Martin Faltys*, Matthias Hüser*, Xinrui Lyu*, Thomas Gumbsch*, Cristóbal Esteban, Christian Bock, Max Horn, Michael Moor, Bastian Rieck, Marc Zimmermann, Dean Bodenham, Karsten Borgwardt°, Gunnar Rätsch°, and Tobias M. Merz° (* = equal contribution, ° = joint supervision)
Nature Medicine 2020, 26:364–373
external page Online  |  external page Free, read-only version  |  ETH news  |  ETH Research Collection

AraPheno and the AraGWAS Catalog 2020: A major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana

Matteo Togninalli*, Ümit Seren*, Jan Freudenthal, J Grey Monroe, Meng Dazhe, Magnus Nordborg, Detlef Weigel, Karsten Borgwardt, Arthur Korte, Dominik Grimm (*=equal contributions)
Nucleic Acids Research 2020, 48 (D1): D1063–D1068
external page Online  |  ETH Research Collection  |  external page AraPheno  |  external page AraGWAS

Kernel Conditional Clustering and Kernel Conditional Semi-supervised Learning

Xiao He, Thomas Gumbsch, Damian Roqueiro and Karsten Borgwardt
Knowledge and Information Systems 2020, 62: 899–925.
external page Online  |  ETH Research Collection

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Pre-transplant kinetics of anti-HLA antibodies in patients on the waiting list for kidney transplantation

Matteo Togninalli, Daisuke Yoneoka, Antonios GA Kolios, Karsten Borgwardt and Jakob Nilsson
Journal of the American Society of Nephrology 2019, 30 (11) 2262-2274
external page Online  |  external page GitHub  |  ETH Research Collection

Wasserstein Weisfeiler-Lehman Graph Kernels

Matteo Togninalli*, Elisabetta Ghisu*, Felipe Llinares-Lopez, Bastian Rieck, and Karsten Borgwardt (*=equal contributions)
Advances in Neural Information Processing Systems 32 (NeurIPS 2019). Spotlight talk.
external page Online  |  external page GitHub  |  ETH Research Collection 

A Wasserstein Subsequence Kernel for Time Series

Christian Bock*, Matteo Togninalli*, Elisabetta Ghisu, Thomas Gumbsch, Bastian Rieck, and Karsten Borgwardt (*=equal contributions)
Proceedings of the 2019 IEEE International Conference on Data Mining (ICDM 2019), pp. 964-969.
external page Online  |  external page GitHub  | ETH Research Collection

Early Recognition of Sepsis with Gaussian Process Temporal Convolutional Networks and Dynamic Time Warping

Michael Moor, Max Horn, Bastian Rieck, Damian Roqueiro and Karsten Borgwardt
Machine Learning for Healthcare Conference (MLHC) 2019 and Proceedings of Machine Learning Research 106:2–26, 2019
external page Online  |  external page GitHub  |  ETH Research Collection

Finding Statistically Significant Interactions between Continuous Features

Mahito Sugiyama and Karsten Borgwardt
Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence (IJCAI-19), 3490-3498.
external page Online  |  external page GitHub  |  ETH Research Collection

A Persistent Weisfeiler–Lehman Procedure for Graph Classification

Bastian Rieck, Christian Bock and Karsten Borgwardt
Proceedings of the 36^th International Conference on Machine Learning (ICML 2019), PMLR 97: 5448-5458.
external page Online  |  external page GitHub  |  ETH Research Collection

Neural Persistence: A Complexity Measure for Deep Neural Networks Using Algebraic Topology

Bastian Rieck, Matteo Togninalli, Christian Bock, Michael Moor, Max Horn, Thomas Gumbsch and Karsten Borgwardt
International Conference on Learning Representations (ICLR) 2019.
external page OpenReview  |  external page GitHub  |  external page ETH Research Collection

CASMAP: Detection of statistically significant combinations of SNPs in association mapping

Felipe Llinares-Lopez*, Laetitia Papaxanthos*, Damian Roquiero, Dean Bodenham° and Karsten Borgwardt° (* = equal contribution, ° = joint supervision)
Bioinformatics 2019, 35 (15): 2680–2682
external page Online  |  external page Github  |  ETH Research Collection

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Association Mapping in Biomedical Time Series via Statistically Significant Shapelet Mining

Christian Bock, Thomas Gumbsch, Michael Moor, Bastian Rieck, Damian Roquiero and Karsten Borgwardt
ISMB 2018 and Bioinformatics 2018, 43 (13): i438–i446
external page Online  |  external page ETH Research Collection

Accurate and Adaptive Imputation of Summary Statistics in Mixed-Ethnicity Cohorts

Matteo Togninalli, Damian Roqueiro, COPDGene Investigators and Karsten M. Borgwardt
ECCB 2018 and Bioinformatics 2018, 35 (17): i687-i696
external page Online  |  external page ETH Research Collection

Aberrant working memory processing in major depression: evidence from multivoxel pattern classification

Matti Gärtner*, Elisabetta M. Ghisu*, Milan Scheidegger, Luisa Bönke, Yan Fan, Anna Stippl, Ana-Lucia Herrera-Melendez, Sophie Metz, Emilia Winnebeck, Maria Fissler, Anke Henning, Malek Bajbouj, Karsten Borgwardt, Thorsten Barnhofer and Simone Grimm (*=equal contributions)
Neuropsychopharmacology 2018, 43: 1972-1979
external page Online  |  ETH Research Collection

Multi-target drug repositioning by bipartite block-wise sparse multi-task learning

Limin Li, Xiao He and Karsten Borgwardt
BMC Systems Biology 2018, 12 (Suppl 4): 55
external page Online  |  external page ETH Research Collection

Kernelized rank learning for personalized drug recommendation

Xiao He, Lukas Folkman and Karsten Borgwardt
Bioinformatics 2018, 34 (16): 2808-2816
external page Online  |  external page ETH Research Collection

The AraGWAS Catalog: A curated and standardized Arabidopsis thaliana GWAS catalog

Matteo Togninalli*, Ümit Seren*, Dazhe Meng, Joffrey Fitz, Magnus Nordborg, Detlef Weigel, Karsten Borgwardt, Arthur Korte, Dominik Grimm (*=equal contributions)
Nucleic Acids Research 2018, 46 (D1): D1150-D1156
external page Online  |  external page ETH Research Collection

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graphkernels: R and Python packages for graph comparison

Mahito Sugiyama, Elisabetta Ghisu, Felipe Llinares-Lopez, Karsten Borgwardt
Bioinformatics 2018, 34 (3): 530-532
external page Online  |  ETH Reserach Collection  |  Project page

Kernel Conditional Clustering

Xiao He, Thomas Gumbsch, Damian Roqueiro and Karsten Borgwardt
IEEE International Conference on Data Mining (ICDM) 2017, 157-166
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

Multi-view Spectral Clustering on Conflicting Views

Xiao He, Limin Li, Damian Roqueiro and Karsten Borgwardt
European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD) 2017, 826-842
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

Genome-wide genetic heterogeneity discovery with categorical covariates

Felipe Llinares-Lopez*, Laetitia Papaxanthos*, Dean Bodenham, Damian Roqueiro, COPDGene Investigators and Karsten Borgwardt (*=equal contributions)
Bioinformatics 2017, 33 (12): 1820-1828
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

AraPheno: a public database for Arabidopsis thaliana phenotypes

Ümit Seren*, Dominik G. Grimm*, Joffrey Fitz, Detlef Weigel, Magnus Nordborg, Karsten Borgwardt and Arthur Korte (*=equal contributions)
Nucleic Acids Research 2017, 45(D1): D1054-D1059
external page Online  |  ETH Research Collection

easyGWAS: A Cloud-based Platform for Comparing the Results of Genome-wide Association Studies

Dominik G. Grimm, Damian Roqueiro, Patrice Salome, Stefan Kleeberger, Bastian Greshake, Wangsheng Zhu, Chang Liu, Christoph Lippert, Oliver Stegle, Bernhard Schölkopf, Detlef Weigel and Karsten Borgwardt
The Plant Cell 2017. 29(1): 5-19
external page Online  |  ETH Research Collection  |  Project page  |  easygwas.org

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The Genetic Architecture of Non-additive Inheritance in Arabidopsis thaliana Hybrids

Danelle Seymour*, Eunyoung Chae*, Dominik G. Grimm*, Carmen Martín, Anette Haring-Müller, François Vasseur, Barbara Rakitsch, Karsten M. Borgwardt, Daniel Koenig and Detlef Weigel (*=equal contributions)
Proceedings of the National Academy of Sciences (PNAS), 2016. 113(46): E7317-E7326
external page Online  |  ETH Research Collection    

Finding significant combinations of features in the presence of categorical covariates

Laetitia Papaxanthos*, Felipe Llinares-López*, Dean Bodenham and Karsten Borgwardt (*=equal contributions)
Advances in Neural Information Processing Systems 29 (NIPS 2016), 2271-2279.
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana

The 1001 Genomes Consortium*
Cell 2016, 166(2): 481-491
external page Online  |  ETH Research Collection

* Dominik G. Grimm and Karsten Borgwardt, as part of The 1001 Genomes Consortium

Genomic profiles of diversification and genotype-phenotype association in island nematode lineages,

Angela McGaughran, Christian Rödelsperger, Dominik G. Grimm, Jan Meyer, Katy Morgan, Mark Leaver, Vahan Serobyan, Barbara Rakitsch, Karsten Borgwardt and Ralf Sommer
Molecular Biology and Evolution 2016, 33(9): 2257-2272
external page Online  |  ETH Research Collection

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Prediction of human population responses to toxic compounds by a collaborative competition,

Federica Eduati, Lara M. Mangravite, Tao Wang, Hao Tang, J. Christopher Bare, Ruili Huang, Thea Norman, Mike Kellen, Michael P. Menden, Jichen Yang, Xiaowei Zhan, Rui Zhong, Guanghua Xiao, Menghang Xia, Nour Abdo, Oksana Kosyk, The NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Stephen Friend, Allen Dearry, Anton Simeonov, Raymond R. Tice, Ivan Rusyn, Fred A. Wright, Gustavo Stolovitzky and Yang Xie
Nature Biotechnology 2015 Sep, 33(9): 933-40
external page Online  |  external page ETH Research Collection

Halting in Random Walk Kernels

Mahito Sugiyama and Karsten Borgwardt
Advances in Neural Information Processing Systems 28 (NIPS 2015), 1639-1647
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

Fast and Memory-Efficient Significant Pattern Mining via Permutation Testing

Felipe Llinares-López, Mahito Sugiyama, Laetitia Papaxanthos and Karsten Borgwardt
Proceedings of the 21st ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD2015), 2015, 725-734
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

In silico phenotyping via co-training for improved phenotype prediction from genotype

Damian Roqueiro, Menno Witteveen, Verneri Anttila, Gisela Terwindt, Arn van den Maagdenberg and Karsten Borgwardt
ISMB 2015 and Bioinformatics 2015, 31 (12): i303-i310
external page Online  | ETH Research Collection  |  Project page with code

Genome-wide detection of intervals of genetic heterogeneity associated with complex traits

Felipe Llinares-López, Dominik G. Grimm, Dean A. Bodenham, Udo Gieraths, Mahito Sugiyama, Beth Rowan and Karsten Borgwardt
ISMB 2015 and Bioinformatics 2015, 31 (12): i240-i249
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

The Evaluation of Tools Used to Predict the Impact of Missense Variants is Hindered by Two Types of Circularity

Dominik G. Grimm, Chloé-Agathe Azencott, Fabian Aicheler, Udo Gieraths, Daniel G. MacArthur, Kaitlin E. Samocha, David N. Cooper, Peter D. Stenson, Mark J. Daly, Jordan W. Smoller, Laramie E. Duncan and Karsten Borgwardt
Human Mutation 2015, 36(5): 513-523
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

Significant Subgraph Mining with Multiple Testing Correction

Mahito Sugiyama, Felipe Llinares López, Niklas Kasenburg and Karsten Borgwardt
Proceedings of the 2015 SIAM International Conference on Data Mining 2015, 37-45
external page Online  |  ETH Research Collection   

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage

Jörg Hagmann, Claude Becker, Jonas Müller, Oliver Stegle, R.C. Meyer, George Wang, Korbinian Schneeberger, Joffrey Fitz, T. Altmann, Joy Bergelson, Karsten Borgwardt and Detlef Weigel
PLoS Genetics 2015 Jan 8, 11(1): 1-18
external page Online  |  ETH Research Collection 

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

Congmao Wang, Chang Liu, Damian Roqueiro, Dominik G. Grimm, Rebecca Schwab, Claude Becker, Christa Lanz and Detlef Weigel
Genome Research 2015, 25(2): 246-256
external page Online  

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Multi-Task Feature Selection on Multiple Networks via Maximum Flows

Mahito Sugiyama, Chloé-Agathe Azencott, Dominik G. Grimm, Yoshinobu Kawahara and Karsten Borgwardt
Proceedings of the 2014 SIAM International Conference on Data Mining 2014, 199-207
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub  |  Supplement

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Efficient network-guided multi-locus association mapping with graph cuts

Chloé-Agathe Azencott, Dominik G. Grimm, Mahito Sugiyama, Yoshinobu Kawahara and Karsten Borgwardt
ISMB 2013 and Bioinformatics 2013, 29 (13): i171-i179
external page Online  |  ETH Research Collection  |  Project page including code

A Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction

Barbara Rakitsch, Christoph Lippert, Oliver Stegle and Karsten Borgwardt
Bioinformatics 2013, 29(2): 206-214
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

Accurate indel prediction using paired-end short reads

Dominik G. Grimm, Jörg Hagmann, Daniel Koenig, Detlef Weigel and Karsten Borgwardt
BMC Genomics 2013, 14(1): 132-141
external page Online  |  external page ETH Research Collection  |  Project page  |  external page GitHub

Accurate Detection of Differential RNA Processing

Philipp Drewe, Oliver Stegle, Lisa Hartmann, Andre Kahles, Regina Bohnert, Andreas Wachter, Karsten Borgwardt and Gunnar Rätsch
Nucleic Acids Research 2013, 41(10): 5189-5198
external page Online  |  ETH Research Collection   

Geometric tree kernels: Classification of COPD from airway tree geometry

Aasa Feragen, Jens Petersen, Dominik G. Grimm, Asger Dirksen, Jesper Holst Pedersen, Karsten Borgwardt and Marleen de Bruijne
Lecture Notes in Computer Science, Volume 7917: Information Processing in Medical Imaging 2013, 171–183
external page Online  |  ETH Research Collection   

Detecting regulatory gene-environment interactions with unmeasured environmental factors

Nicolo Fusi, Christoph Lippert, Karsten Borgwardt, Neil Lawrence and Oliver Stegle
Bioinformatics 2013, 29(11): 1382-9
external page Online  |  ETH Research Collection   

Rapid Distance-Based Outlier Detection via Sampling

Mahito Sugiyama and Karsten Borgwardt
Advances in Neural Information Processing Systems 26 (NIPS 2013), 467-475
external page Online  |  ETH Research Collection  |  Project page including code

Scalable kernels for graphs with continuous attributes

Aasa Feragen, Niklas Kasenburg, Jens Petersen, Marleen de Bruijne and Karsten Borgwardt
Advances in Neural Information Processing Systems 26 (NIPS 2013), 216-224
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

It is all in the noise: Efficient multi-task Gaussian process inference with structured residuals

Barbara Rakitsch, Christoph Lippert, Karsten Borgwardt* and Oliver Stegle* (*=equal contributions)
Advances in Neural Information Processing Systems 26 (NIPS 2013), 1466-1474
external page Online  |  ETH Research Collection

Measuring Statistical Dependence via the Mutual Information Dimension

Mahito Sugiyama and Karsten Borgwardt
Proceedings of the 23rd International Joint Conference on Artificial Intelligence (IJCAI 2013), 1692-1698
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

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GLIDE: GPU-based linear regression for detection of epistasis

Tony Kam-Thong, Chloé-Agathe Azencott, Lawrence Cayton, Benno Pütz, Andre Altmann, Philipp G. Sämann, Bernhard Schölkopf, Bertram Müller-Myhsok, Karsten M. Borgwardt
Human Heredity 2012, 73: 220-236
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis

Oliver Windram, Priyadharshini Madhou, Stuart McHattie, Claire Hill, Richard Hickman, Emma Cooke, Dafyd J. Jenkins, Christopher A. Penfold, Laura Baxter, Emily Breeze, Steven J. Kiddle, Johanna Rhodes, Susanna Atwell, Daniel J. Kliebenstein, Youn-sung Kima, Oliver Stegle, Karsten Borgwardt, Cunjin Zhang, Alex Tabrett, Roxane Legaie, Jonathan Moore, Bärbel Finkenstadt, David L. Wild, Andrew Mead, David Rand, Jim Beynon, Sascha Ott, Vicky Buchanan-Wollaston and Katherine J. Denby
Plant Cell 2012, 24(9): 3530-57
external page Online  |  ETH Research Collection

Feature Selection via Dependence Maximization

Le Song, Alex Smola, Arthur Gretton, Justin Bedo and Karsten Borgwardt
Journal of Machine Learning Research (JMLR) 2012, 13(1): 1393−1434
external page Online  |  ETH Research Collection

ShapePheno: Unsupervised extraction of shape phenotypes from biological image collections

Theofanis Karaletsos, Oliver Stegle, Christine Dreyer, John Winn and Karsten Borgwardt
Bioinformatics 2012, 28 (7): 1001-1008
external page Online  |  ETH Research Collection

A Kernel Two-Sample Test

Arthur Gretton, Karsten Borgwardt, Malte Rasch, Bernhard Schölkopf and Alexander Smola
Journal of Machine Learning Research (JMLR) 2012, 13:723−773
external page Online  |  ETH Research Collection

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Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Claude Becker, Jörg Hagmann, Jonas Müller, Daniel Koenig, Oliver Stegle, Karsten Borgwardt and Detlef Weigel
Nature 2011, 480: 245–249
external page Online  |  ETH Research Collection

Whole-genome sequencing of multiple Arabidopsis thaliana populations

Jun Cao, Korbinian Schneeberger, Stephan Ossowski, Torsten Günther, Sebastian Bender, Joffrey Fitz, Daniel Koenig, Christa Lanz, Oliver Ste- gle, Christoph Lippert, Xi Wang, Felix Ott, Jonas Müller, Carlos Alonso-Blanco, Karsten Borgwardt, Karl J Schmid and Detlef Weigel
Nature Genetics 2011, 43(10):956–963
external page Online  |  ETH Research Collection

Weisfeiler-Lehman Graph Kernels

Nino Shervashidze, Pascal Schweitzer, Erik Jan van Leeuwen, Kurt Mehlhorn and Karsten M. Borgwardt
Journal of Machine Learning Research (JMLR) 2011, 12: 2539−2561
external page Online | ETH Research Collection | Project page including code

Efficient inference in matrix-variate Gaussian models with iid observation noise

Oliver Stegle, Christoph Lippert, Joris Mooij, Neil Lawrence and Karsten Borgwardt
Advances in Neural Information Processing Systems 24 (NIPS 2011), 630-638
external page Online  |  ETH Research Collection

ccSVM: Correcting Support Vector Machines for confounding factors in biological data classification

Limin Li, Barbara Rakitsch and Karsten Borgwardt
ISMB 2011 and Bioinformatics 2011, 27 (13): i342-i348
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs

Tony Kam-Thong, Benno Pütz, Nazanin Karbalai, Bertram Müller-Myhsok and Karsten Borgwardt
ISMB 2011 and Bioinformatics 2011, 27 (13): i214-i221
external page Online   |  ETH Research Collection

Two-locus association mapping in subquadratic runtime

Panagiotis Achlioptas, Bernhard Schölkopf and Karsten Borgwardt
Proceedings of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2011), 727-734
external page Online  |  ETH Research Collection  |  Project page  |  external page GitHub

EPIBLASTER-Fast exhaustive two-locus epistasis detection strategy using graphical processing units

Tony Kam-Thong, Darina Czamara, Koji Tsuda, Karsten Borgwardt, Cathryn M. Lewis, Angelika Erhardt-Lehmann, Bernhard Hemmer, Peter Rieckmann, Markus Daake, Frank Weber, Christiane Wolf, Andreas Ziegler, Benno Pütz, Florian Holsboer, Bernhard Schölkopf and Bertram Müller-Myhsok
European Journal of Human Genetics 2011, 19: 465–471
external page Online  |  ETH Research Collection   

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Spatio-spectral remote sensing image classification with graph kernels

Gustavo Camps-Valls, Nino Shervashidze and Karsten Borgwardt
IEEE Geoscience and Remote Sensing Letters 2010, 99: 741-745
external page Online  |  ETH Research Collection

Discriminative frequent subgraph mining with optimality guarantees

Marisa Thoma, Hong Cheng, Arthur Gretton, Jiawei Han, Hans-Peter Kriegel, Alexander J. Smola, Le Song, Philip S. Yu, Xifeng Yan and Karsten M. Borgwardt
Journal of Statistical Analysis and Data Mining 2010, 3(5): 302–318
external page Online  |  ETH Research Collection

A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series

Oliver Stegle, Katherine Denby, Emma Cooke, David Wild, Zoubin Ghahramani and Karsten Borgwardt
Journal of Computational Biology 2010, 17(3): 355-367
external page Online  |  ETH Research Collection

Gene function prediction from synthetic lethality networks via ranking on demand

Christoph Lippert, Zoubin Ghahramani and Karsten Borgwardt
Bioinformatics 2010, 26(7): 912-918
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Graph Kernels

SVN Vishwanathan, Nic Schraudolph, Risi Kondor and Karsten M. Borgwardt
Journal of Machine Learning Research (JMLR) 2010, 11: 1201−1242
external page Online  |  ETH Research Collection  |  Project page including code  

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Fast subtree kernels on graphs

Nino Shervashidze and Karsten M. Borgwardt
Advances in Neural Information Processing Systems 22 (NIPS 2009), 1660-1668
NIPS Outstanding Student Paper Award Winner
external page Online  |  ETH Research Collection

A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series

Oliver Stegle, Katherine Denby, David L. Wild, Zoubin Ghahramani and Karsten Borgwardt
In Lecture Notes in Computer Science 5541 "Research in Computational Molecular Biology. RECOMB 2009" , 201-216
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Discovering temporal patterns of differential gene expression in microarray time series

Oliver Stegle, Katherine Denby, David Wild, Stuart McHattie, Andrew Mead, Zoubin Ghahramani and Karsten Borgwardt
In Lecture Notes in Informatics 157 "German Conference on Bioinformatics 2009", 133-142
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The Graphlet Spectrum

Risi Kondor, Nino Shervashidze and Karsten M. Borgwardt
Proceedings of the 26th Annual International Conference on Machine Learning (ICML 2009), 529-536
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A kernel method for unsupervised structured network inference

Christoph Lippert, Oliver Stegle, Zoubin Ghahramani, Karsten Borgwardt
Artificial Intelligence and Statistics (AISTATS) 2009, 5: 368-375
Full oral presentation
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Efficient Graphlet Kernels for Large Graph Comparison

Nino Shervashidze, SVN Vishwanathan, Tobias Petri, Kurt Mehlhorn, Karsten Borgwardt
Artificial Intelligence and Statistics (AISTATS) 2009, 5: 488-495
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Near-optimal supervised feature selection among frequent subgraphs

Marisa Thoma, Hong Cheng, Arthur Gretton, Jiawei Han, Hans-Peter Kriegel, Alexander J. Smola, Le Song, Philip S. Yu, Xifeng Yan and Karsten M. Borgwardt
SIAM Data Mining (SDM) 2009, 1076-1087
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The genome of the simian and human malaria parasite Plasmodium knowlesi

A. Pain, U. Böhme, A.E. Berry, K. Mungall, R.D. Finn, A.P. Jackson, T. Mourier, J. Mistry, E.M. Pasini, M.A. Aslett, S. Balasubrammaniam, K. Borgwardt, K. Brooks, C. Carret, T.J. Carver, I. Cherevach, T. Chillingworth, T. Clarke, M.R. Galinski, N. Hall, D. Harper, D. Harris, H. Hauser, A. Ivens, C.S. Janssen, T. Keane, N. Larke, S. Lapp , M. Marti, S. Moule, I.M. Meyer, D. Ormond, N. Peters, M. Sanders, S. Sanders, T.J. Sergeant, M. Simmonds, F. Smith, R. Squares, S. Thurston, A.R. Tivey, D. Walker, B. White, E. Zuiderwijk, C. Churcher, M.A. Quail, A.F. Cowman, C.M.R. Turner, M.A. Rajandream , C.H.M. Kocken, A.W. Thomas, C. Newbold, B.G. Barrell and M. Berriman
Nature 2008, 455: 799-803
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Predicting phenotypic effects of gene perturbations in C.elegans using an integrated network model

Karsten Borgwardt
Bioessays 2008, 30(8): 707-710
external page Online  |  ETH Research Collection

Metropolis Algorithms for Representative Subgraph Sampling

Christian Hübler, Karsten Borgwardt, Hans-Peter Kriegel and Zoubin Ghahramani
Eighth IEEE International Conference on Data Mining (ICDM) 2008, 283-292
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The skew spectrum of graphs

Risi Kondor and Karsten Borgwardt
Proceedings of the 25th International Conference on Machine Learning (ICML 2008), 496-503
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Future trends in data mining

Hans-Peter Kriegel, Karsten M. Borgwardt, Peer Kröger, Alexey Pryakhin, Matthias Schubert and Arthur Zimek
Data Mining and Knowledge Discorvery 2007, 15 (1): 87-97
external page Online  |  ETH Research Collection

Gene Selection via the BAHSIC Family of Algorithms

Le Song, Justin Bedo, Karsten Borgwardt, Arthur Gretton and Alexander Smola
ISMB 2007 and Bioinformatics 2007, 23(13): i490-i498
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Colored Maximum Variance Unfolding

Le Song, Alexander Smola, Karsten Borgwardt and Arthur Gretton
Advances in Neural Information Processing Systems 20 (NIPS 2007), 1385-1392
Full oral presentation
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A Kernel Approach to Comparing Distributions

Arthur Gretton, Karsten Borgwardt, Malte Rasch, Bernhard Schölkopf and Alexander Smola
Proceedings of the 22nd National Conference on Artificial Intelligence (AAAI 2007), 2: 1637-1641
Highlights Track
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A Dependence Maximization View of Clustering

Le Song, Alexander Smola, Arthur Gretton and Karsten Borgwardt
Proceedings of the 24th International Conference on Machine Learning (ICML 2007), 815-822
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Supervised Feature Selection via Dependence Estimation

Le Song, Arthur Gretton, Alexander Smola, Karsten Borgwardt and Justin Bedo
Proceedings of the 24th International Conference on Machine Learning (ICML 2007), 823-830
external page Online  |  ETH Research Collection

Graph kernels for disease outcome prediction from protein-protein interaction networks

Karsten Borgwardt, S.V.N. Vishwanathan, Nicol Schraudolph and Hans-Peter Kriegel
In Biocomputing 2007: Proceedings of the Pacific Symposium (PSB 2007), 12: 4-15
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Integrating structured biological data by Kernel Maximum Mean Discrepancy

Karsten Borgwardt, Arthur Gretton, Malte Rasch, Hans-Peter Kriegel, Bernhard Schölkopf and Alexander Smola
ISMB 2006 and Bioinformatics 2006, 22(14): e49-e57
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Kernel Extrapolation

S.V.N. Vishwanathan, Karsten Borgwardt, Omri Guttman and Alexander Smola
Neurocomputing 2006, 69(7-9): 721-729
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Pattern Mining in Frequent Dynamic Subgraphs

Karsten Borgwardt, Hans-Peter Kriegel and Peter Wackersreuther
In Proceedings of 6th International Conference on Data Mining (ICDM '06), 818-822
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Correcting Sample Selection Bias by Unlabeled Data

Jiayuan Huang, Alexander Smola, Arthur Gretton, Karsten Borgwardt and Bernhard Schölkopf
Advances in Neural Information Processing Systems 20 (NIPS 2006), 601-608
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A Kernel Method for the Two-Sample-Problem

Arthur Gretton, Karsten Borgwardt, Malte Rasch, Bernhard Schölkopf and Alexander Smola
Advances in Neural Information Processing Systems 19 (NIPS 2006), 513-520
Full oral presentation
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Fast Computation of Graph Kernels

S.V.N. Vishwanathan, Karsten Borgwardt, Nicol Schraudolph
Advances in Neural Information Processing Systems 19 (NIPS 2006), 1449-1456
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3DString: A Feature String Kernel for 3D Object Classification on Voxelized Data

Johannes Aßfalg, Karsten Borgwardt and Hans-Peter Kriegel
Proceedings of the 15th ACM International Conference on Information and Knowledge Management (CIKM 2006), 198-207
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Class prediction from time series gene expression profiles using dynamical systems kernels

Karsten Borgwardt, S.V.N. Vishwanathan and Hans-Peter Kriegel
Biocomputing 2006: Proceedings of the Pacific Symposium (PSB 2006), 547-558
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Protein Function Prediction via Graph Kernels

Karsten Borgwardt, Cheng S. Ong, Stefan Schönauer, S.V.N. Vishwanathan, Alexander Smola and Hans-Peter Kriegel
ISMB 2005 and Bioinformatics 2005, 21(suppl_1): i47-i56
external page Online  |  ETH Research Collection  |  Project page

Shortest-path kernels on graphs

Karsten Borgwardt and Hans-Peter Kriegel
Proceedings of the 5th IEEE International Conference on Data Mining (ICDM 2005)
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Joint Regularization

Karsten Borgwardt, Omri Guttman, S.V.N. Vishwanathan and Alexander Smola
Proceedings of the 13th European Symposium on Artificial Neural Networks (ESANN 2005), 455-460
ETH Research Collection  |  Download Download (PDF, 298 KB)