Rebekka Burkholz

Helmholtz Center CISPA

Stuhlsatzenhaus 5

66123 Saarbrücken, Germany

burkholz (at) cispa (dot) de

I am a tenure-track faculty member at the Helmholtz Center CISPA. My research combines robust algorithm design with the quest for a theoretical understanding of deep neural networks. Cascade processes are fundamental to most of the problems I study, e.g., complex network inference, gene regulation, and systemic risk. More generally, I am interested in machine learning problems for high dimensional data as in gene regulation. In particular, I care about incorporating existing domain knowledge in machine learning approaches to alleviate the curse of dimensionality.

News

  • My paper on the existence of lottery tickets has been accepted at ICML 2022.

  • I am looking very forward to give a talk at John Hopkins' MINDS & CIS seminar in March. Many thanks for the invitation!

  • Two papers accepted at ICLR 2022!

  • Our paper on scaling up continuous-time Markov chains has been accepted at NeurIPS 2021!

  • I am excited to join the Helmholtz center CISPA as tenure-track faculty in September!

  • Glycowork is published in Glycobiology. Congratulations and thanks to my amazing coauthors Luc and Daniel!

  • Our paper on GCNs to represent glycans was accepted by Cell Reports!

  • Two papers accepted at AAAI 2021!

  • Welcome to a new NetZoo animal: OTTER. It introduces a general method to infer a bipartite network when we can only observe its noisy projections. This outperforms the state-of-the-art in gene regulatory network inference.


Publications

  • R. Burkholz (2022). Most Activation Functions Can Win the Lottery Without Excessive Depth. arXiv:2205.02321.

  • R. Burkholz (2022). Convolutional and Residual Networks Provably Contain Lottery Tickets. arXiv:2205.02343, ICML 2022.

  • M. Ben Guebila , D. Weighill, C.M. Lopes-Ramos, R. Burkholz, et al. (2022) An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nature Methods.

  • J. Fischer, R. Burkholz (2022). Plant 'n' Seek: Can You Find the Winning Ticket? arXiv:111.11153, ICLR 2022.

  • R. Burkholz, N. Laha, R. Mukherjee, A. Gotovos (2022). On the Existence of Universal Lottery Tickets. arXiv:2111.11146, ICLR 2022.

  • Laumer F, Di Vece D, Cammann VL, et al. (2022). Assessment of Artificial Intelligence in Echocardiography Diagnostics in Differentiating Takotsubo Syndrome From Myocardial Infarction. JAMA Cardiology.

  • J. Fischer, R. Burkholz (2021). Towards strong pruning for lottery tickets with non-zero biases. arXiv:2110.11150.

  • M. B. Guebila, C. Lopes-Ramos, D. Weighill, A. R. Sonawane, R. Burkholz, B. Shamsaei, J. Platig, K. Glass, M. L. Kuijjer, J. Quackenbush (2021). GRAND: A database of gene regulatory network models across human conditions. bioRxiv, Nucleic Acids Research.

  • A. Gotovos, R. Burkholz, J. Quackenbush, S. Jegelka. Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification (2021). arXiv:2107.02911, NeurIPS 2021.

  • D. Weighill*, R. Burkholz*, M. B. Guebila, H. U. Zacharias, J. Quackenbush**, M. Altenbuchinger** (2021). DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks. arXiv:2104.01690.

  • L. Thomés, R. Burkholz, D. Bojar. Glycowork: A Python package for glycan data science and machine learning (2021). bioRxiv, Glycobiology.

  • R. Burkholz, J. Quackenbush, D. Bojar (2021). Using Graph Convolutional Neural Networks to Learn a Representation of Glycans. Cell Reports 35(11), 109251.

  • S Weichwald, A Candreva*, R Burkholz*, R Klingenberg, L Räber, D Heg, R Manka, B Gencer, F Mach, D Nanchen, N Rodondi, S Windecker, R Laaksonen, SL Hazen, Av Eckardstein, F Ruschitzka, TF Lüscher, JM Buhmann, CM Matter (2021). Improving 1-year mortality prediction in ACS patients using machine learning. European Heart Journal: Acute Cardiovascular Care.

  • D. Weighill, M. B. Guebila, C. Lopes-Ramos, K. Glass, J. Quackenbush, J. Platig, R. Burkholz (2021). Gene regulatory network inference as relaxed graph matching. bioRxiv, AAAI 2021.

  • R. Burkholz, J. Quackenbush (2021). Cascade Size Distributions and Why They Matter. arXiv:1909.05416, AAAI 2021.

  • R. Burkholz, A. Dubatovka (2019). Initialization of ReLUs for Dynamical Isometry. arXiv:1806.06362. NeurIPS 2019. Code.

  • R. Burkholz (2019). Efficient message passing for cascade size distributions. arXiv:1811.06872. Scientific Reports 9, 6561.

  • R. Burkholz, F. Schweitzer (2019). International crop trade networks: The impact of shocks and cascades. arxiv:1901.05872. Environmental Research Letters.

  • R. Burkholz, F. Schweitzer (2018). Correlations between thresholds and degrees: An analytic approach to model attacks and failure cascades. arXiv:1706.04451. Phys. Rev. E 98, 022306.

  • R. Burkholz, F. Schweitzer (2018). Framework for cascade size calculations on random networks. arXiv:1701.06970. Phys. Rev. E 97, 042312.

  • R. Burkholz, H. J. Herrmann, F. Schweitzer (2018). Explicit size distributions of failure cascades redefine systemic risk on finite networks. arXiv:1802.03286. Scientific Reports 8 (1), 6878.

  • M. V. Tomasello, R. Burkholz, F. Schweitzer (2017). Modeling the formation of R&D alliances: an agent-based model with empirical validation. Economics E-Journal: No. 2017-107.

  • R. Burkholz, A. Garas, F. Schweitzer (2016). How damage diversification can reduce systemic risk. Physical Review E: 93: 042313.

  • R. Burkholz, M. V. Lecuc, A. Garas, F. Schweitzer (2016). Systemic risk in multiplex networks with asymmetric coupling and threshold feedback, Physica D: Nonlinear Phenomena 323-324, 64-72.

  • R. Burkholz (2016). Systemic Risk: From Generic Models to Food Trade Networks. PhD thesis.

Talks

  • 21/09/2021: Gene regulatory network inference as relaxed graph matching. Bio-IT World, Boston (USA), invited.

  • 07/07/2021: Gene regulatory network inference as relaxed graph matching. Networks 2021 (formerly NetSci), online.

  • 10/07/2020: International Crop Trade Networks: The impact of shocks and cascades. Graphs & Networks, Boston (USA), lightning talk.

  • 23/06/2020: Message passing for cascade size distributions. LSV seminar, École Normale Supérieure Paris-Sacley, Paris (France), invited.

  • 12/12/2019: Initialization of ReLUs for Dynamical Isometry. NeurIPS 2019, Vancouver (Canada), Poster.

  • 29/05/2019: Tree distribution approximation for finite networks. NetSci 2019, Burlington, Vermont. 2nd place at the NetSci Society YI for Best Talk Pitch.

  • 27/05/2019: Systemic risk in international crop trade. Network Science for Social Good. NetSci 2019 Satellite, Burlington, Vermont.

  • 23/05/2019: Non-invasive diagnosis of a rare heart disease by Machine Learning, 21st Future of Health Technology Summit, MIT, Boston.

  • 16/11/2018: Exact cascade size distributions redefine systemic risk on finite networks, MACSI seminar, University of Limerick (Ireland), invited.

  • 05/10/2018: How machines learn cardiology in three examples, ACS Plus, Berlin (Germany), invited.

  • 21/06/2018: How machines learn cardiology in three examples, Personalized Health Technologies and Translational Research Conference 2018, ETH Zurich (Switzerland), invited

  • 15/06/2018: Application of Temporal Multiplex Networks to Cascade Processes in Food Trade, NetSci 2018, Paris (France)

  • 12/06/2018: Correlations between thresholds and degrees: An analytic approach to model attacks and failure cascades, NetONets, NetSci18 Satellite, Paris (France).

  • 12/06/2018: Explicit size distributions of failure cascades redefine systemic risk on finite networks, Machine Learning in Network Science, NetSci18 Satellite, Paris (France).

  • 16/04/2018: Machine Learning for Cardiology. F. Hoffmann-La Roche Ltd., Diagnostics Division, Basel (Switzerland), invited.

  • 13/07/2017: A Framework To Calculate the Cascade Size Evolution on Random Networks, SIAM workshop on Network Science 2017, Pittsburgh (USA).

  • 05/07/2017: A Framework To Calculate the Cascade Size Evolution on Random Networks, PhD Seminar at Northeastern University, Boston (USA).

  • 23/06/2017: A Framework To Calculate the Cascade Size Evolution on Random Networks, NetSci 2017, Indianapolis (USA).

  • 21/06/2017: Application of Temporal Multiplex Networks to Cascade Processes in Food Trade, Lighthing talk at NetSci 2017, Indianapolis (USA).

  • 19/01/2017: A Framework for Cascade Processes on Random Networks, ETH48 Workshop on Cascade Processes: Mathematical Modeling and Applications, ETH Zurich (Switzerland).

  • 02/12/2016: A Framework for Cascade Size Calculations on Random Networks, Complex Networks 2016, Milan (Italy).

  • 03/10/2016: Systemic Risk: From Generic Models to Cascades in Food Trade, Computational Social Science seminar series, ETH Zurich (Switzerland), seminar talk.

  • 23/06/2016: Cascades in Food Trade Networks, WEHIA 2016, Castellò de la Plana (Spain).

  • 09/2015: Systemic Risk as Emergent Phenomenon, ETH Risk Center Advisory Board Meeting, ETH Zurich (Switzerland).

  • 23/06/2015: Cascades in Maize Trade Networks, Tackling World Food System Challenges: Across Disciplines, Sectors, and Scales, Ascona (Switzerland), poster presentation awarded with CSF Best Contribution Award by Young Scientist.

  • 03/06/2015: Cascades in Maize Trade Networks, NetSci 2015, Zaragoza (Spain), poster presentation.

  • 02/06/2015: Cascades on Multiplexes with Threshold Feedback, Satellite Workshop ‘NetONets2015’, NetSci 2015, Zaragoza, (Spain).

  • 01/06/2015: How Damage Diversification Can Reduce Systemic Risk, Satellite Workshop ‘Information, Self-Organizing Dynamics, and Synchronization on Complex Networks II’, NetSci 2015, Zaragoza (Spain).

  • 16/01/2015: Systemic Risk as Emergent Phenomenon, ETH Risk Center Dialogue Event, ETH Zurich (Switzerland).

  • 15/12/2014 - 19/12/2014:The Impact of Regulating Capital Buffers on Systemic Risk, Regulating Systemic Risk: insights from mathematical modeling, Newton In-stitute, Cambridge (UK), poster presentation.

  • 22/09/2014 - 26/09/2014: Modeling Systemic Risk and Risk Diversification, Monitoring Systemic Risk: Data, Models and Metrics, Newton Institute, Cambridge (UK), poster presentation.

  • 13/06/2012: A Stochastic FitzHugh-Nagumo Model, The 5th Japanese-German International Workshop on Mathematical Fluid Dynamics, Tokyo (Japan).

  • 06/06/2012 15th Internet Seminar 2011/12, Operator Semigroups for Numerical Analysis, Final Workshop, Blaubeuren (Germany), project, supervisor: Prof. Dr. Stig Larsson.

Academic service

  • On November 21st, 2018, the ETH Graduate Consulting Club had a panel discussion on "Data Science in Industry". It was a big pleasure to help organizing as content lead and to moderate through the discussion. The 5 speakers were amazing - super competent and engaging. Also big thanks to the participants (>160 ) and their insightful questions!

  • In was a pleasure to organize a workshop on cascade processes at the ETH Risk Center at ETH Zurich in January 2017. Thanks a lot to the great speakers!

  • I feel honored to review for ICLR, ICML, and NeurIPS. I also reviewed for ASONAM, Nature Communications, Physical Review Letters, Physical Review E, Journal of Economic Interaction and Coordination, Modern Physics C, Physica C, JSTAT, SocInfo16, Journal Social Network Analysis and Mining, ESREL 2015 in the past.

Short CV

From February 1st, 2019 to August 30th, 2021, I worked with John Quackenbush and a great interdisciplinary team at the Harvard T.H. Chan School of Public Health on inference of gene regulatory networks and machine learning. Our primary goal was to gain new insights into cancer.

From June 2017 - January 2019, I enjoyed doing postdoctoral research at the Institute for Machine Learning with Joachim Buhmann, where I had the pleasure to lead the efforts of ISE group to automate diagnosis and prognosis of carciovascular diseases in collaboration with cardiologists at UniversitySpital Zurich.

From June 2016 - May 2017, I was a PostDoc at the Chair of Systems Design headed by my doctoral father Frank Schweitzer at ETH Zurich.

From June 26th - July 12th, 2017, I felt honored to visit Asuman Ozdaglar and her group at MIT.

My PhD research about systemic risk (February 2013 - May 2016) was part of the ETH48 project at the ETH Risk Center, supervised by Frank Schweitzer and co-supervised by Hans J. Herrmann. My thesis has won the Zurich Dissertation Prize and my work on systemic risk in international maize trade won the CSF Best Contribution Award.

Before moving to Zurich, I interned at d-fine and Deutsche Bank in Frankfurt am Main (Germnay) to experience the fast moving financial industry. I am grateful for the many insights.

I enjoyed studying Physics (B.Sc.) and Mathematics (B.Sc.,M.Sc) at TU Darmstadt (Germany) from October 2006 to March 2011 and at Lund University from September 2008 - June 2009. I loved to explore the realms of stochastic as well as deterministic partial differential equations, fluid dynamics, numerical analysis, and optimization.

I am very grateful to Evangelisches Studienwerk Villigst for the academic and ideational scholarship and to Femtec for the soft skill trainings as well as the great network.