**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

**s****caling 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. Ne****tworks 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,**21^{st}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,**P**ersonalized**He**alth**T**echnologies and**T**ranslational**R**esearch Conference 2018, ETH Zurich (Switzerland), invited15/06/2018: 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.