Publications

Authors that equally contributed to a publication are marked with a †.

2026 Link to heading

SpIDER: Spatially Informed Dense Embedding Retrieval for Software Issue Localization
Shravan Chaudhari, Rahul Thomas Jacob, Mononito Goswami, Jiajun Cao, Shihab Rashid, Christian Bock
Preprint, arXiv:2512.16956

SWE-PolyBench: A multi-language benchmark for repository level evaluation of coding agents
Muhammad Shihab Rashid^†, Christian Bock^†, Yuan Zhuang, Alexander Buchholz, Tim Esler, Simon Valentin, Luca Franceschi, Martin Wistuba, Prabhu Teja Sivaprasad, Woo Jung Kim, Anoop Deoras, Giovanni Zappella, Laurent Callot
Preprint, arXiv:2504.08703

Textual Gradients are a Flawed Metaphor for Automatic Prompt Optimization
Daniel Melcer, Qi Chen, Wen-Hao Chiang, Shweta Garg, Pranav Garg, Christian Bock
Preprint, arXiv:2512.13598

2024 Link to heading

Enhancing the diagnosis of functionally relevant coronary artery disease with machine learning
Christian Bock, Joan Elias Walter, Bastian Rieck, Ivo Strebel, Klara Rumora, Ibrahim Schaefer, Michael J. Zellweger, Karsten Borgwardt, Christian Mueller
Nature Communications, 15(1), 5034, 2024.

2022 Link to heading

Online Time Series Anomaly Detection with State Space Gaussian Processes
Christian Bock^†, François-Xavier Aubet^†, Jan Gasthaus, Andrey Kan, Ming Chen, Laurent Callot
Preprint, arXiv:2201.06763

2021 Link to heading

Motifs and Manifolds: Statistical and Topological Machine Learning for Characterising and Classifying Biomedical Time Series
Christian Bock
Ph.D. Dissertation

2020 Link to heading

Enhancing statistical power in temporal biomarker discovery through representative shapelet mining
Thomas Gumbsch, Christian Bock, Michael Moor, Bastian Rieck, Karsten Borgwardt
Bioinformatics, Volume 36, pp. i840–i848, 2020

Set functions for time series
Max Horn, Michael Moor, Christian Bock, Bastian Rieck, Karsten Borgwardt
Proceedings of the 37th International Conference on Machine Learning (ICML), PMLR 119:4353-4363, 2020

Uncovering the topology of time-varying fmri data using cubical persistence
Bastian Rieck^†, Tristan Yates^†, Christian Bock, Karsten Borgwardt, Guy Wolf, Nicholas Turk-Browne, Smita Krishnaswamy
Advances in Neural Information Processing Systems (NeurIPS), Volume 33, 2020

Machine Learning for Biomedical Time Series Classification: From Shapelets to Deep Learning
Christian Bock^†, Michael Moor^†, Catherine R. Jutzeler, Karsten Borgwardt
Book chapter in: Artificial Neural Networks. Methods in Molecular Biology

Path Imputation Strategies for Signature Models
Michael Moor, Max Horn, Christian Bock, Karsten Borgwardt, Bastian Rieck
Preprint, arXiv:2005.12359, 2020.

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
Nature Medicine, Volume 26, Issue 3, pp. 364–373, March 2020.

2019 Link to heading

Set Functions for Time Series
Max Horn, Michael Moor, Christian Bock, Bastian Rieck, and Karsten Borgwardt
Preprint, arXiv:1909.12064, 2019.

A Wasserstein Subsequence Kernel for Time Series
Christian Bock^†, Matteo Togninalli^†, Elisabetta Ghisu, Thomas Gumbsch, Bastian Rieck, and Karsten Borgwardt
Proceedings of The 19th IEEE International Conference on Data Mining (ICDM 2019).

A Persistent Weisfeiler–Lehman Procedure for Graph Classification
Bastian Rieck^†, Christian Bock^†, Karsten Borgwardt
Proceedings of the 36th International Conference on Machine Learning (ICML), Volume 97 of Proceedings of Machine Learning Research, pp. 5448–5458, June 2019.
Poster

Neural Persistence: A Complexity Measure for Deep Neural Networks Using Algebraic Topology
Bastian Rieck^†, Matteo Togninalli^†, Christian Bock^†, Michael Moor, Max Horn, Thomas Gumbsch, Karsten Borgwardt
Proceedings of the International Conference on Learning Representations (ICLR), 2019.
Poster

2018 Link to heading

Association Mapping in Biomedical Time Series via Statistically Significant Shapelet Mining
Christian Bock, Thomas Gumbsch, Michael Moor, Bastian Rieck, Damian Roqueiro, Karsten Borgwardt Bioinformatics, Volume 34, Issue 13, pp. i438–i446, July 2018.
Slides

Biological and Functional Relevance of CASP Predictions
Tianyun Liu, Shirbi Ish‐Shalom, Wen Torng, Aleix Lafita, Christian Bock, Matthew Mort, David N Cooper, Spencer Bliven, Guido Capitani, Sean D. Mooney, Russ B. Altman
Proteins 86, 374-386.

2017 Link to heading

Mapping Genetic Variations to Three-dimensional Protein Structures to Enhance Variant Interpretation: A Proposed Framework
Gustavo Glusman, Peter W Rose, Andreas Prlić, Jennifer Dougherty, José M Duarte, Andrew S Hoffman, Geoffrey J Barton, Emøke Bendixen, Timothy Bergquist, Christian Bock, Elizabeth Brunk, Marija Buljan, Stephen K Burley, Binghuang Cai, Hannah Carter, JianJiong Gao, Adam Godzik, Michael Heuer, Michael Hicks, Thomas Hrabe, Rachel Karchin, Julia Koehler Leman, Lydie Lane, David L Masica, Sean D Mooney, John Moult, Gilbert S Omenn, Frances Pearl, Vikas Pejaver, Sheila M Reynolds, Ariel Rokem, Torsten Schwede, Sicheng Song, Hagen Tilgner, Yana Valasatava, Yang Zhang, Eric W Deutsch
Genome Med., 9(1), 113.

Solving Interoperability in Translational Health
Anne M. Turner, Julio C. Facelli, Monique Jaspers, Thomas Wetter, Daniel Pfeifer, Laël Cranmer Gatewood, Terry Adam, YuChuan Li, Ming-Chin Lin, R. Scott Evans, Anna Beukenhorst, Hugo Johan Theodoore van Mens, Esmée Tensen, Christian Bock, Laura Fendrich, Peter Seitz, Julian Suleder, Ranyah Aldekhyyel, Kent Bridgeman, Zhen Hu, Aaron Sattler, Shin-Yi Guo, Islam Md. Mohaimenul, Dina Nur Anggraini Ningrum, Hsin-Ru Tung, Jiantao Bian, Joseph M. Plasek, Casey Rommel, Juandalyn Burke, Harkirat Sohi
Applied clinical informatics, 8(02), 651-659.