2024

Cui, Kai ; Tahir, Anam ; Sinzger, Mark ; Koeppl, Heinz (2024)
Discrete-Time Mean Field Control with Environment States.
2021 60th IEEE Conference on Decision and Control (CDC). Austin, TX, USA (14.12.2021-17.12.2021)
doi: 10.26083/tuprints-00028856
Conference or Workshop Item, Secondary publication, Postprint

Fabian, Christian ; Cui, Kai ; Koeppl, Heinz (2024)
Learning Sparse Graphon Mean Field Games.
International Conference on Artificial Intelligence and Statistics. Palau de Congressos, Valencia, Spain (25.04.2023 - 27.04.2023)
doi: 10.26083/tuprints-00028917
Conference or Workshop Item, Secondary publication, Publisher's Version

Fabian, Christian ; Cui, Kai ; Koeppl, Heinz (2024)
Mean Field Games on Weighted and Directed Graphs via Colored Digraphons.
In: IEEE Control Systems Letters, 2023, 7
doi: 10.26083/tuprints-00026543
Article, Secondary publication, Publisher's Version

Ourari, Ramzi ; Cui, Kai ; Elshamanhory, Ahmed ; Koeppl, Heinz (2024)
Nearest-Neighbor-based Collision Avoidance for Quadrotors via Reinforcement Learning.
2022 IEEE International Conference on Robotics and Automation (ICRA). Philadelphia, PA, USA (23.05.2022-27.05.2022)
doi: 10.26083/tuprints-00028926
Conference or Workshop Item, Secondary publication, Postprint

Cui, Kai ; Yilmaz, Mustafa Burak ; Tahir, Anam ; Klein, Anja ; Koeppl, Heinz (2024)
Optimal Offloading Strategies for Edge-Computing via Mean-Field Games and Control.
GLOBECOM 2022 - 2022 IEEE Global Communications Conference. Rio de Janeiro, Brazil (04.12.2022-08.12.2022)
doi: 10.26083/tuprints-00028855
Conference or Workshop Item, Secondary publication, Postprint

Cui, Kai ; Li, Mengguang ; Fabian, Christian ; Koeppl, Heinz (2024)
Scalable Task-Driven Robotic Swarm Control via Collision Avoidance and Learning Mean-Field Control.
2023 IEEE International Conference on Robotics and Automation (ICRA). London, United Kingdom (29.05.2023-02.06.2023)
doi: 10.1109/ICRA48891.2023.10161498
Conference or Workshop Item, Secondary publication, Postprint

Cui, Kai ; Baumgärtner, Lars ; Yilmaz, Mustafa Burak ; Li, Mengguang ; Fabian, Christian ; Becker, Benjamin ; Xiang, Lin ; Bauer, Maximilian ; Koeppl, Heinz (2024)
UAV Swarms for Joint Data Ferrying and Dynamic Cell Coverage via Optimal Transport Descent and Quadratic Assignment.
2023 IEEE 48th Conference on Local Computer Networks (LCN). Daytona Beach, FL, USA (02.10.2023-05.10.2023)
doi: 10.26083/tuprints-00028857
Conference or Workshop Item, Secondary publication, Postprint

Kruk, Nikita ; Carrillo, José A. ; Koeppl, Heinz (2024)
A finite volume method for continuum limit equations of nonlocally interacting active chiral particles.
In: Journal of Computational Physics, 2021, 440
doi: 10.26083/tuprints-00026629
Article, Secondary publication, Publisher's Version

Klann, Michael ; Ganguly, Arnab ; Koeppl, Heinz (2024)
Hybrid spatial Gillespie and particle tracking simulation.
In: Bioinformatics, 2012, 28 (18)
doi: 10.26083/tuprints-00026937
Article, Secondary publication, Publisher's Version

Cui, Kai ; Dayanıklı, Gökçe ; Laurière, Mathieu ; Geist, Matthieu ; Pietquin, Olivier ; Koeppl, Heinz (2024)
Learning Discrete-Time Major-Minor Mean Field Games.
38th AAAI Conference on Artificial Intelligence. Vancouver, Canada (20.02.2024 - 27.02.2024)
doi: 10.26083/tuprints-00028687
Conference or Workshop Item, Secondary publication, Postprint

Cui, Kai ; KhudaBukhsh, Wasiur R. ; Koeppl, Heinz (2024)
Motif-based mean-field approximation of interacting particles on clustered networks.
In: Physical Review E, 2022, 105 (4)
doi: 10.26083/tuprints-00028854
Article, Secondary publication, Publisher's Version

Reich, Christoph ; Prangemeier, Tim ; Ozdemir, Cetin ; Koeppl, Heinz (2024)
OSS-Net: Memory Efficient High Resolution Semantic Segmentation of 3D Medical Data.
32nd British Machine Vision Conference. Virtual Conference (22.11.2021-25.11.2021)
doi: 10.26083/tuprints-00028914
Conference or Workshop Item, Secondary publication, Publisher's Version

Sreedhara, Akash Kopparam ; Padala, Deepesh ; Mahesh, Shashank ; Cui, Kai ; Li, Mengguang ; Koeppl, Heinz (2024)
Optimal Collaborative Transportation for Under-Capacitated Vehicle Routing Problems using Aerial Drone Swarms.
2024 IEEE International Conference on Robotics and Automation (ICRA). Yokohama, Japan (13.05.2024-17.05.2024)
doi: 10.26083/tuprints-00028686
Conference or Workshop Item, Secondary publication, Postprint

Sharifian, Hoda ; Lampert, Fabienne ; Stojanovski, Klement ; Regot, Sergi ; Vaga, Stefania ; Buser, Raymond ; Lee, Sung Sik ; Koeppl, Heinz ; Posas, Francesc ; Pelet, Serge ; Peter, Matthias (2024)
Parallel feedback loops control the basal activity of the HOG MAPK signaling cascade.
In: Integrative Biology, 2015, 7 (4)
doi: 10.26083/tuprints-00026924
Article, Secondary publication, Publisher's Version

Ermentrout, Bard ; Zechner, Christoph ; Koeppl, Heinz (2024)
Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments.
In: PLoS Computational Biology, 2014, 10 (12)
doi: 10.26083/tuprints-00026931
Article, Secondary publication, Publisher's Version

Eich, Yannick ; Alt, Bastian ; Koeppl, Heinz (2024)
Approximate Control for Continuous-Time POMDPs.
International Conference on Artificial Intelligence and Statistics. Valencia, Spain (02.05.2024 - 04.05.2024)
doi: 10.26083/tuprints-00028690
Conference or Workshop Item, Secondary publication, Publisher's Version

Kubaczka, Erik ; Gehringer, Maximilian ; Marlhens, Jérémie J. M. ; Schwarz, Tobias ; Molderings, Maik ; Engelmann, Nicolai ; Garcia, Hernan G. ; Hochberger, Christian ; Koeppl, Heinz (2024)
Energy Aware Technology Mapping of Genetic Logic Circuits.
In: ACS Synthetic Biology, 2024, 13 (10)
doi: 10.26083/tuprints-00028688
Article, Secondary publication, Publisher's Version

Cui, Kai ; Hauck, Sascha ; Fabian, Christian ; Koeppl, Heinz (2024)
Learning Decentralized Partially Observable Mean Field Control for Artificial Collective Behavior.
International Conference on Learning Representations. Vienna, Austria (07.05.2024 - 11.05.2024)
doi: 10.26083/tuprints-00028689
Conference or Workshop Item, Secondary publication, Publisher's Version

Fabian, Christian ; Cui, Kai ; Koeppl, Heinz (2024)
Learning Mean Field Games on Sparse Graphs: A Hybrid Graphex Approach.
International Conference on Learning Representations. Vienna, Austria (07.05.2024 - 11.05.2024)
doi: 10.26083/tuprints-00028691
Conference or Workshop Item, Secondary publication, Postprint

Engelmann, Nicolai ; Schwarz, Tobias ; Kubaczka, Erik ; Hochberger, Christian ; Koeppl, Heinz (2024)
Context-Aware Technology Mapping in Genetic Design Automation.
In: ACS Synthetic Biology, 2023, 12 (2)
doi: 10.26083/tuprints-00026517
Article, Secondary publication, Publisher's Version

Tahir, Anam ; Alt, Bastian ; Rizk, Amr ; Koeppl, Heinz (2024)
Load Balancing in Compute Clusters With Delayed Feedback.
In: IEEE Transactions on Computers, 2023, 72 (6)
doi: 10.26083/tuprints-00026536
Article, Secondary publication, Publisher's Version

Schladt, Tobias ; Engelmann, Nicolai ; Kubaczka, Erik ; Hochberger, Christian ; Koeppl, Heinz (2024)
Automated Design of Robust Genetic Circuits: Structural Variants and Parameter Uncertainty.
In: ACS Synthetic Biology, 2021, 10 (12)
doi: 10.26083/tuprints-00026627
Article, Secondary publication, Publisher's Version

Sporns, Olaf ; Hafner, Marc ; Koeppl, Heinz ; Gonze, Didier (2024)
Effect of Network Architecture on Synchronization and Entrainment Properties of the Circadian Oscillations in the Suprachiasmatic Nucleus.
In: PLoS Computational Biology, 2012, 8 (3)
doi: 10.26083/tuprints-00026934
Article, Secondary publication, Publisher's Version

Papin, Jason A. ; Hafner, Marc ; Koeppl, Heinz ; Hasler, Martin ; Wagner, Andreas (2024)
‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators.
In: PLoS Computational Biology, 2009, 5 (10)
doi: 10.26083/tuprints-00026926
Article, Secondary publication, Publisher's Version

Altıntan, Derya ; Koeppl, Heinz (2024)
Hybrid master equation for jump-diffusion approximation of biomolecular reaction networks.
In: BIT Numerical Mathematics, 2020, 60 (2)
doi: 10.26083/tuprints-00027079
Article, Secondary publication, Publisher's Version

Johannes, Ludger ; Klann, Michael ; Koeppl, Heinz ; Reuss, Matthias (2024)
Spatial Modeling of Vesicle Transport and the Cytoskeleton: The Challenge of Hitting the Right Road.
In: PLoS ONE, 2012, 7 (1)
doi: 10.26083/tuprints-00026930
Article, Secondary publication, Publisher's Version

Kramat, Janice ; Kraus, Leon ; Gunawan, Vincent J. ; Smyej, Elias ; Froehlich, Philipp ; Weber, Tim E. ; Spiehl, Dieter ; Koeppl, Heinz ; Blaeser, Andreas ; Suess, Beatrix (2024)
Sensing Levofloxacin with an RNA Aptamer as a Bioreceptor.
In: Biosensors, 2024, 14 (1)
doi: 10.26083/tuprints-00027255
Article, Secondary publication, Publisher's Version

Camporesi, Ferdinanda ; Feret, Jérôme ; Koeppl, Heinz ; Petrov, Tatjana (2024)
Combining Model Reductions.
In: Electronic Notes in Theoretical Computer Science, 2010, 265
doi: 10.26083/tuprints-00026719
Article, Secondary publication, Publisher's Version

Benenson, Yaakov ; Dalchau, Neil ; Koeppl, Heinz ; Maler, Oded (2024)
Formal Methods for the Synthesis of Biomolecular Circuits.
In: Dagstuhl Reports, 2018, 8 (2)
doi: 10.26083/tuprints-00026921
Article, Secondary publication, Publisher's Version

Hiroi, Noriko ; Klann, Michael ; Iba, Keisuke ; Heras Ciechomski, Pablo de ; Yamashita, Shuji ; Tabira, Akito ; Okuhara, Takahiro ; Kubojima, Takeshi ; Okada, Yasunori ; Oka, Kotaro ; Mange, Robin ; Unger, Michael ; Funahashi, Akira ; Koeppl, Heinz (2024)
From microscopy data to in silico environments for in vivo-oriented simulations.
In: EURASIP Journal on Bioinformatics and Systems Biology, 2012, 1 (7)
doi: 10.26083/tuprints-00026938
Article, Secondary publication, Publisher's Version

Sulaimanov, Nurgazy ; Koeppl, Heinz (2024)
Graph reconstruction using covariance-based methods.
In: EURASIP Journal on Bioinformatics and Systems Biology, 2016
doi: 10.26083/tuprints-00026979
Article, Secondary publication, Publisher's Version

Cui, Kai ; KhudaBukhsh, Wasiur R. ; Koeppl, Heinz (2024)
Hypergraphon mean field games.
In: Chaos: An Interdisciplinary Journal of Nonlinear Science, 2022, 32 (11)
doi: 10.26083/tuprints-00026621
Article, Secondary publication, Publisher's Version

Šošić, Adrian ; Rueckert, Elmar ; Peters, Jan ; Zoubir, Abdelhak M. ; Koeppl, Heinz (2024)
Inverse Reinforcement Learning via Nonparametric Spatio-Temporal Subgoal Modeling.
In: Journal of Machine Learning Research, 2018, 19 (69)
doi: 10.26083/tuprints-00026700
Article, Secondary publication, Publisher's Version

Koeppl, Heinz ; Hafner, Marc ; Lu, James (2024)
Mapping behavioral specifications to model parameters in synthetic biology.
In: BMC Bioinformatics, 2013, 14 (S10)
doi: 10.26083/tuprints-00026717
Article, Secondary publication, Publisher's Version

Petrov, Tatjana ; Ganguly, Arnab ; Koeppl, Heinz (2024)
Model Decomposition and Stochastic Fragments.
In: Electronic Notes in Theoretical Computer Science, 2012, 284
doi: 10.26083/tuprints-00026720
Article, Secondary publication, Publisher's Version

Danos, Vincent ; Koeppl, Heinz (2024)
Self-assembly and Self-organization in Computer Science and Biology.
In: Dagstuhl Reports, 2016, 5 (9)
doi: 10.26083/tuprints-00026922
Article, Secondary publication, Publisher's Version

Klann, Michael ; Koeppl, Heinz (2024)
Spatial Simulations in Systems Biology: From Molecules to Cells.
In: International Journal of Molecular Sciences, 2012, 13 (6)
doi: 10.26083/tuprints-00026923
Article, Secondary publication, Publisher's Version

Koeppl, Heinz ; Petrov, Tatjana (2024)
Stochastic Semantics of Signaling as a Composition of Agent-view Automata.
In: Electronic Notes in Theoretical Computer Science, 2011, 272
doi: 10.26083/tuprints-00026721
Article, Secondary publication, Publisher's Version

Ion, Ion Gabriel ; Wildner, Christian ; Loukrezis, Dimitrios ; Koeppl, Heinz ; De Gersem, Herbert (2024)
Tensor-train approximation of the chemical master equation and its application for parameter inference.
In: The Journal of Chemical Physics, 2021, 155 (3)
doi: 10.26083/tuprints-00026628
Article, Secondary publication, Publisher's Version

Hill, Steven M. ; Heiser, Laura M. ; Cokelaer, Thomas ; Unger, Michael ; Nesser, Nicole K. ; Carlin, Daniel E. ; Zhang, Yang ; Sokolov, Artem ; Paull, Evan O. ; Wong, Chris K. ; Graim, Kiley ; Bivol, Adrian ; Wang, Haizhou ; Zhu, Fan ; Afsari, Bahman ; Danilova, Ludmila V. ; Favorov, Alexander V. ; Lee, Wai Shing ; Taylor, Dane ; Hu, Chenyue W. ; Long, Byron L. ; Noren, David P. ; Bisberg, Alexander J. ; Mills, Gordon B. ; Gray, Joe W. ; Kellen, Michael ; Norman, Thea ; Friend, Stephen ; Qutub, Amina A. ; Fertig, Elana J. ; Guan, Yuanfang ; Song, Mingzhou ; Stuart, Joshua M. ; Spellman, Paul T. ; Koeppl, Heinz ; Stolovitzky, Gustavo ; Saez-Rodriguez, Julio ; Mukherjee, Sach (2024)
Inferring causal molecular networks: empirical assessment through a community-based effort.
In: Nature Methods, 2016, 13 (4)
doi: 10.26083/tuprints-00027016
Article, Secondary publication, Publisher's Version

Nandy, Preetam ; Unger, Michael ; Zechner, Christoph ; Dey, Kushal K. ; Koeppl, Heinz (2024)
Learning diagnostic signatures from microarray data using L1-regularized logistic regression.
In: Systems Biomedicine, 2013, 1 (4)
doi: 10.26083/tuprints-00027017
Article, Secondary publication, Publisher's Version

Alkhalili, Yassin ; Weil, Jannis ; Tahir, Anam ; Meuser, Tobias ; Koldehofe, Boris ; Mauthe, Andreas ; Koeppl, Heinz ; Steinmetz, Ralf (2024)
Towards QoE-Driven Optimization of Multi-Dimensional Content Streaming.
In: Electronic Communications of the EASST, 2021, 80
doi: 10.26083/tuprints-00027018
Article, Secondary publication, Publisher's Version

Kuebert, Thomas ; Puder, Henning ; Koeppl, Heinz (2024)
Daily Routine Recognition for Hearing Aid Personalization.
In: SN Computer Science, 2021, 2 (3)
doi: 10.26083/tuprints-00023594
Article, Secondary publication, Publisher's Version

Tahir, Anam ; Cui, Kai ; Koeppl, Heinz (2024)
Learning Mean-Field Control for Delayed Information Load Balancing in Large Queuing Systems.
51st International Conference on Parallel Processing (ICPP ’22). Bordeaux, France (29.08.2022-01.09.2022)
doi: 10.26083/tuprints-00026518
Conference or Workshop Item, Secondary publication, Publisher's Version

2023

Linzner, Dominik ; Koeppl, Heinz (2023)
Active Learning of Continuous-time Bayesian Networks through Interventions.
Thirty-eighth International Conference on Machine Learning. Virtual (18.07.2021-24.07.2021)
doi: 10.26083/tuprints-00023308
Conference or Workshop Item, Secondary publication, Publisher's Version

Alt, Bastian ; Schultheis, Matthias ; Koeppl, Heinz (2023)
POMDPs in Continuous Time and Discrete Spaces.
34th Conference on Neural Information Processing Systems. virtual (06.12.2020-12.12.2020)
doi: 10.26083/tuprints-00023309
Conference or Workshop Item, Secondary publication, Publisher's Version

2022

Köhs, Lukas ; Kukovetz, Kerri ; Rauh, Oliver ; Koeppl, Heinz (2022)
Nonparametric Bayesian inference for meta-stable conformational dynamics.
In: Physical Biology, 2022, 19 (5)
doi: 10.26083/tuprints-00022096
Article, Secondary publication, Publisher's Version

Sinzger, Mark ; Gehri, Maximilian ; Koeppl, Heinz (2022)
Poisson channel with binary Markov input and average sojourn time constraint.
ISIT'20 - International Symposium on Information Theory. Online (21.06.2020-26.06.2020)
doi: 10.26083/tuprints-00021525
Conference or Workshop Item, Secondary publication, Postprint

Cui, Kai ; Koeppl, Heinz (2022)
Approximately Solving Mean Field Games via Entropy-Regularized Deep Reinforcement Learning.
24th International Conference on Artificial Intelligence and Statistics (AISTATS) 2021. Virtual (13.04.2021-15.04.2021)
doi: 10.26083/tuprints-00021511
Conference or Workshop Item, Secondary publication, Publisher's Version

Prangemeier, Tim ; Reich, Christoph ; Koeppl, Heinz (2022)
Attention-Based Transformers for Instance Segmentation of Cells in Microstructures.
IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2020). virtual Conference (16.12.2020-19.12.2020)
doi: 10.26083/tuprints-00021666
Conference or Workshop Item, Secondary publication, Postprint

Engelmann, Nicolai ; Linzner, Dominik ; Koeppl, Heinz (2022)
Continuous Time Bayesian Networks with Clocks.
37th International Conference on Machine Learning. Online (12.07.2020-18.07.2020)
doi: 10.26083/tuprints-00021516
Conference or Workshop Item, Secondary publication, Publisher's Version

Khuda Bukhsh, Wasiur R. ; Kar, Sounak ; Alt, Bastian ; Rizk, Amr ; Koeppl, Heinz (2022)
Generalized Cost-Based Job Scheduling in Very Large Heterogeneous Cluster Systems.
In: IEEE Transactions on Parallel and Distributed Systems, 2020, 31 (11)
doi: 10.26083/tuprints-00021667
Article, Secondary publication, Postprint

Yang, Sikun ; Koeppl, Heinz (2022)
The Hawkes Edge Partition Model for Continuous-time Event-based Temporal Networks.
Conference on Uncertainty in Artificial Intelligence (UAI). Online (03.08.2020-06.08.2020)
doi: 10.26083/tuprints-00021515
Conference or Workshop Item, Secondary publication, Publisher's Version

Wildner, Christian ; Koeppl, Heinz (2022)
Moment-Based Variational Inference for Stochastic Differential Equations.
24th International Conference on Artificial Intelligence and Statistics (AISTATS) 2021. Virtual (13.04.2021-15.04.2021)
doi: 10.26083/tuprints-00021512
Conference or Workshop Item, Secondary publication, Publisher's Version

Prangemeier, Tim ; Wildner, Christian ; Françani, André O. ; Reich, Christoph ; Koeppl, Heinz (2022)
Multiclass Yeast Segmentation in Microstructured Environments with Deep Learning.
IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB). Online (27.10.2020-29.10.2020)
doi: 10.26083/tuprints-00021524
Conference or Workshop Item, Secondary publication, Postprint

Kar, Sounak ; Rehrmann, Robin ; Mukhopadhyay, Arpan ; Alt, Bastian ; Ciucu, Florin ; Koeppl, Heinz ; Binnig, Carsten ; Rizk, Amr (2022)
On the Throughput Optimization in Large-scale Batch-processing Systems.
In: Performance Evaluation, 2020, 144
doi: 10.26083/tuprints-00021522
Article, Secondary publication, Postprint

Kruk, Nikita ; Maistrenko, Yuriy ; Koeppl, Heinz (2022)
Solitary states in the mean-field limit.
In: Chaos: An Interdisciplinary Journal of Nonlinear Science, 2020, 30 (11)
doi: 10.26083/tuprints-00021568
Article, Secondary publication, Publisher's Version

Kumar, Sunil ; Lun, Xiao-Kang ; Bodenmiller, Bernd ; Rodríguez Martínez, María ; Koeppl, Heinz (2022)
Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data.
In: Scientific Reports, 2020, (1)
doi: 10.26083/tuprints-00021513
Article, Secondary publication, Publisher's Version

Kruk, Nikita ; Carrillo, José A. ; Koeppl, Heinz (2022)
Traveling bands, clouds, and vortices of chiral active matter.
In: Physical Review E, 2020, 102 (2)
doi: 10.26083/tuprints-00021567
Article, Secondary publication, Publisher's Version

2019

Hofmann, Anja ; Falk, Johannes ; Prangemeier, Tim ; Happel, Dominic ; Köber, Adrian ; Christmann, Andreas ; Koeppl, Heinz ; Kolmar, Harald (2019)
A tightly regulated and adjustable CRISPR-dCas9 based AND gate in yeast.
In: Nucleic Acids Research, 2018, 47 (1)
Article, Secondary publication, Publisher's Version