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Parallelized Agent-based Simulation on CPU and Graphics Hardware for Spatial and Stochastic Models in Biology

M. Falk, M. Klann, M. Ott, H. Koeppl, and T. Ertl. International Conference on Computational Methods in Systems Biology (CMSB 2011), ACM, (2011)
DOI: 10.1145/2037509.2037521

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Univ. -Prof. Dr. Heinz Kück University of Stuttgart

Pascal Heinzelmann University of Stuttgart

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A Local Nonlinear Model for the Approximation and Identification of a Class of Systems.H. Koeppl. IEEE Trans. on Circuits and Systems, 56-II (4): 315-319 (2009)Scalable inference using PMCMC and parallel tempering for high-throughput measurements of biomolecular reaction networks.L. Bronstein, and H. Koeppl. CDC, page 770-775. IEEE, (2016)Policy recognition via expectation maximization.A. Sosic, A. Zoubir, and H. Koeppl. ICASSP, page 4801-4805. IEEE, (2016)Collaborative Uploading in Heterogeneous Networks: Optimal and Adaptive Strategies.W. KhudaBukhsh, B. Alt, S. Kar, A. Rizk, and H. Koeppl. INFOCOM, page 1-9. IEEE, (2018)Collapsed Variational Inference for Nonparametric Bayesian Group Factor Analysis.S. Yang, and H. Koeppl. ICDM, page 687-696. IEEE Computer Society, (2018)A Variational Approach to Path Estimation and Parameter Inference of Hidden Diffusion Processes.T. Sutter, A. Ganguly, and H. Koeppl. J. Mach. Learn. Res., (2016)Finding invariant sets for biological systems using monomial domination.E. August, G. Craciun, and H. Koeppl. CDC, page 3001-3006. IEEE, (2012)Trajectory enclosures for nonlinear systems with uncertain initial conditions and parameters.E. August, J. Lu, and H. Koeppl. ACC, page 1488-1493. IEEE, (2012)From biochemical reaction networks to 3D dynamics in the cell: The ZigCell3D modeling, simulation and visualisation framework.P. de Heras Ciechomski, M. Klann, R. Mange, and H. Koeppl. BioVis, page 41-48. IEEE Computer Society, (2013)Optimal Kullback-Leibler Aggregation via Information Bottleneck.B. Geiger, T. Petrov, G. Kubin, and H. Koeppl. IEEE Trans. Automat. Contr., 60 (4): 1010-1022 (2015)