TY - GEN A1 - Gupta, Pooja A1 - Gramatke, Annika A1 - Einspanier, Ralf A1 - Schütte, Christof A1 - von Kleist, Max A1 - Sharbati, Jutta T1 - In silicio cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements N2 - Early and reliable identification of chemical toxicity is of utmost importance. At the same time, reduction of animal testing is paramount. Therefore, methods that improve the interpretability and usability of in vitro assays are essential. xCELLigence’s real-time cell analyzer (RTCA) provides a novel, fast and cost effective in vitro method to probe compound toxicity. We developed a simple mathematical framework for the qualitative and quantitative assessment of toxicity for RTCA measurements. Compound toxicity, in terms of its 50% inhibitory concentration IC_{50} on cell growth, and parameters related to cell turnover were estimated on cultured IEC-6 cells exposed to 10 chemicals at varying concentrations. Our method estimated IC50 values of 113.05, 7.16, 28.69 and 725.15 μM for the apparently toxic compounds 2-acetylamino-fluorene, aflatoxin B1, benzo-[a]-pyrene and chloramphenicol in the tested cell line, in agreement with literature knowledge. IC_{50} values of all apparent in vivo non-toxic compounds were estimated to be non-toxic by our method. Corresponding estimates from RTCA’s in-built model gave false positive (toxicity) predictions in 5/10 cases. Taken together, our proposed method reduces false positive predictions and reliably identifies chemical toxicity based on impedance measurements. The source code for the developed method including instructions is available at https://git.zib.de/bzfgupta/toxfit/tree/master. T3 - ZIB-Report - 17-08 KW - Real-time cell analyzer KW - Toxicity KW - Mathematical modeling KW - IC_{50} Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62666 SN - 1438-0064 ER - TY - CHAP A1 - Gupta, Pooja A1 - Krause, Carola A1 - Rikeit, Paul A1 - Röblitz, Susanna A1 - Knaus, Petra A1 - Schütte, Christof T1 - Modeling of the BMP mediated co-regulation of the Smad and Non-Smad pathways in the context of cell density T2 - 10th International BMP conference, 2014, Berlin, Germany Y1 - 2014 ER - TY - JOUR A1 - Gupta, Pooja A1 - Peter, Sarah A1 - Jung, Markus A1 - Lewin, Astrid A1 - Hemmrich-Stanisak, Georg A1 - Franke, Andre A1 - von Kleist, Max A1 - Schütte, Christof A1 - Einspanier, Ralf A1 - Sharbati, Soroush A1 - zur Bruegge, Jennifer T1 - Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel 2 aspects of Mycobacterium avium subspecies paratuberculosis infections JF - Scientific Reports in Nature N2 - Paratuberculosis is a major disease in cattle that severely affects animal welfare and causes huge economic losses worldwide. Development of alternative diagnostic methods is of urgent need to control the disease. Recent studies suggest that long non-coding RNAs (lncRNAs) play a crucial role in regulating immune function and may confer valuable information about the disease. However, their role has not yet been investigated in cattle with respect to infection towards Paratuberculosis. Therefore, we investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq. We identified 397 potentially novel lncRNA candidates in macrophages of which 38 were differentially regulated by the infection. A total of 820 coding genes were also significantly altered by the infection. Co-expression analysis of lncRNAs and their neighbouring coding genes suggest regulatory functions of lncRNAs in pathways related to immune response. For example, this included protein coding genes such as TNIP3, TNFAIP3 and NF-κB2 that play a role in NF-κB2 signalling, a pathway associated with immune response. This study advances our understanding of lncRNA roles during Paratuberculosis infection. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-018-38141-x VL - 9 ER - TY - GEN A1 - Gupta, Pooja A1 - Röblitz, Susanna A1 - Krause, Carola A1 - Knaus, Petra A1 - Schütte, Christof T1 - Mathematical modeling of the Smad and Non-Smad BMP signaling pathways in context of cell density T2 - Computational Models in biology and medicine, 2013, Dresden, Germany Y1 - 2013 ER - TY - GEN A1 - Hartmann, Carsten A1 - Banisch, Ralf A1 - Sarich, Marco A1 - Badowski, Thomas A1 - Schütte, Christof T1 - Characterization of Rare Events in Molecular Dynamics N2 - A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski's equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods. T3 - ZIB-Report - 13-51 KW - rare events KW - moleculare dynamics KW - optimal pathways KW - stochastic control KW - dynamic programming KW - change of measure KW - cumulant generating function Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42410 SN - 1438-0064 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Banisch, Ralf A1 - Sarich, Marco A1 - Badowski, Thomas A1 - Schütte, Christof T1 - Characterization of Rare Events in Molecular Dynamics JF - Entropy (Special Issue) Y1 - 2013 U6 - https://doi.org/10.3390/e16010350 VL - 16 IS - 1 SP - 350 EP - 376 ER - TY - GEN A1 - Hartmann, Carsten A1 - Richter, Lorenz A1 - Schütte, Christof A1 - Zhang, Wei T1 - Variational characterization of free energy: Theory and algorithms N2 - The article surveys and extends variational formulations of the thermodynamic free energy and discusses their information-theoretic content from the perspective of mathematical statistics. We revisit the well-known Jarzynski equality for nonequilibrium free energy sampling within the framework of importance sampling and Girsanov change-of-measure transformations. The implications of the different variational formulations for designing efficient stochastic optimization and nonequilibrium simulation algorithms for computing free energies are discussed and illustrated. T3 - ZIB-Report - 17-52 KW - Importance sampling KW - Donsker-Varadhan principle KW - thermodynamic free energy KW - nonequilibrium molecular dynamics KW - stochastic approximation KW - cross-entropy method Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65045 SN - 1438-0064 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Richter, Lorenz A1 - Schütte, Christof A1 - Zhang, Wei T1 - Variational characterization of free energy: theory and algorithms JF - Entropy Y1 - 2017 U6 - https://doi.org/10.3390/e19110626 VL - 19 IS - 11 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Efficient rare event simulation by optimal nonequilibrium forcing JF - J. Stat. Mech. Theor. Exp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1153/ U6 - https://doi.org/10.1088/1742-5468/2012/11/P11004 VL - 2012 SP - P11004 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Geometric Approach to Constrained Molecular Dynamics and Free Energy JF - Comm. Math. Sci. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/48/ VL - 3 IS - 1 SP - 1 EP - 20 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Balancing of partially-observed stochastic differential equations JF - 47th IEEE Conference on Decision and Control Y1 - 2008 UR - http://publications.imp.fu-berlin.de/16/ U6 - https://doi.org/10.1109/CDC.2008.4739161 SP - 4867 EP - 4872 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Comment on Two Distinct Notions of Free Energy JF - Physica D Y1 - 2007 UR - http://publications.imp.fu-berlin.de/30/ U6 - https://doi.org/10.1016/j.physd.2007.02.006 VL - 228 IS - 1 SP - 59 EP - 63 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables JF - Z. Angew. Math. Mech. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/47/ U6 - https://doi.org/10.1002/zamm.200410218 VL - 85 IS - 10 SP - 700 EP - 710 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Ciccotti, Giovanni T1 - On the linear response of mechanical systems with constraints JF - J. Chem. Phys. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/794/ U6 - https://doi.org/10.1063/1.3354126 VL - 132 IS - 11 SP - 111103 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Kalibaeva, G. A1 - Pierro, M. A1 - Ciccotti, Giovanni T1 - Fast Simulation of Polymer Chains JF - J. Chem. Phys. Y1 - 2009 UR - http://publications.imp.fu-berlin.de/18/ U6 - https://doi.org/10.1063/1.3110603 VL - 130 SP - 144101 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Weber, Marcus A1 - Zhang, Wei T1 - Importance sampling in path space for diffusion processes with slow-fast variables JF - Probability Theory and Related Fields N2 - Importance sampling is a widely used technique to reduce the variance of a Monte Carlo estimator by an appropriate change of measure. In this work, we study importance sampling in the framework of diffusion process and consider the change of measure which is realized by adding a control force to the original dynamics. For certain exponential type expectation, the corresponding control force of the optimal change of measure leads to a zero-variance estimator and is related to the solution of a Hamilton–Jacobi–Bellmann equation. We focus on certain diffusions with both slow and fast variables, and the main result is that we obtain an upper bound of the relative error for the importance sampling estimators with control obtained from the limiting dynamics. We demonstrate our approximation strategy with an illustrative numerical example. Y1 - 2017 UR - http://rdcu.be/oA51 U6 - https://doi.org/10.1007/s00440-017-0755-3 N1 - If you are not subscribing to the journal please use the http link below as part of the Springer Nature SharedIt initiative SP - 1 EP - 52 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Zhang, Wei T1 - Jarzynski's equality, fluctuation theorems, and variance reduction: Mathematical analysis and numerical algorithms JF - Journal of Statistical Physics N2 - In this paper, we study Jarzynski's equality and fluctuation theorems for diffusion processes. While some of the results considered in the current work are known in the (mainly physics) literature, we review and generalize these nonequilibrium theorems using mathematical arguments, therefore enabling further investigations in the mathematical community. On the numerical side, variance reduction approaches such as importance sampling method are studied in order to compute free energy differences based on Jarzynski's equality. Y1 - 2018 U6 - https://doi.org/10.1007/s10955-019-02286-4 VL - 175 IS - 6 SP - 1214 EP - 1261 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Zhang, Wei T1 - Model reduction algorithms for optimal control and importance sampling of diffusions JF - Nonlinearity N2 - We propose numerical algorithms for solving optimal control and importance sampling problems based on simplified models. The algorithms combine model reduction techniques for multiscale diffusions and stochastic optimization tools, with the aim of reducing the original, possibly high-dimensional problem to a lower dimensional representation of the dynamics, in which only a few relevant degrees of freedom are controlled or biased. Specifically, we study situations in which either a reaction coordinate onto which the dynamics can be projected is known, or situations in which the dynamics shows strongly localized behavior in the small noise regime. No explicit assumptions about small parameters or scale separation have to be made. We illustrate the approach with simple, but paradigmatic numerical examples. Y1 - 2016 U6 - https://doi.org/10.1088/0951-7715/29/8/2298 VL - 29 IS - 8 SP - 2298 EP - 2326 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Vulcanov, V.-M. A1 - Schütte, Christof T1 - Balanced Truncation of Second Order Systems JF - Multiscale Model. Simul. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/28/ U6 - https://doi.org/10.1137/080732717 VL - 8 IS - 4 SP - 1348 EP - 1367 ER - TY - CHAP A1 - Held, M. A1 - Meerbach, E. A1 - Hinderlich, S. A1 - Reutter, W. A1 - Schütte, Christof ED - Hansmann, U. ED - Meinke, J. ED - Mohanty, S. ED - Zimmermann, O. T1 - Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity T2 - From Computational Biophysics to Systems Biology Y1 - 2007 UR - http://publications.imp.fu-berlin.de/113/ VL - 36 SP - 145 EP - 148 PB - John von Neumann Institut for Computing ER - TY - JOUR A1 - Helfmann, Luzie A1 - Conrad, Natasa Djurdjevac A1 - Lorenz-Spreen, Philipp A1 - Schütte, Christof T1 - Modelling opinion dynamics under the impact of influencer and media strategies JF - Scientific Reports N2 - Digital communication has made the public discourse considerably more complex, and new actors and strategies have emerged as a result of this seismic shift. Aside from the often-studied interactions among individuals during opinion formation, which have been facilitated on a large scale by social media platforms, the changing role of traditional media and the emerging role of "influencers" are not well understood, and the implications of their engagement strategies arising from the incentive structure of the attention economy even less so. Here we propose a novel opinion dynamics model that accounts for these different roles, namely that media and influencers change their own positions on slower time scales than individuals, while influencers dynamically gain and lose followers. Numerical simulations show the importance of their relative influence in creating qualitatively different opinion formation dynamics: with influencers, fragmented but short-lived clusters emerge, which are then counteracted by more stable media positions. Mean-field approximations by partial differential equations reproduce this dynamic. Based on the mean-field model, we study how strategies of influencers to gain more followers can influence the overall opinion distribution. We show that moving towards extreme positions can be a beneficial strategy for influencers to gain followers. Finally, we demonstrate that optimal control strategies allow other influencers or media to counteract such attempts and prevent further fragmentation of the opinion landscape. Our modelling framework contributes to better understanding the different roles and strategies in the increasingly complex information ecosystem and their impact on public opinion formation. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-46187-9 VL - 13 SP - 19375 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Djurdjevac Conrad, Natasa A1 - Djurdjevac, Ana A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - From interacting agents to density-based modeling with stochastic PDEs JF - Communications in Applied Mathematics and Computational Science N2 - Many real-world processes can naturally be modeled as systems of interacting agents. However, the long-term simulation of such agent-based models is often intractable when the system becomes too large. In this paper, starting from a stochastic spatio-temporal agent-based model (ABM), we present a reduced model in terms of stochastic PDEs that describes the evolution of agent number densities for large populations. We discuss the algorithmic details of both approaches; regarding the SPDE model, we apply Finite Element discretization in space which not only ensures efficient simulation but also serves as a regularization of the SPDE. Illustrative examples for the spreading of an innovation among agents are given and used for comparing ABM and SPDE models. Y1 - 2021 U6 - https://doi.org/10.2140/camcos.2021.16.1 VL - 16 IS - 1 SP - 1 EP - 32 ER - TY - GEN A1 - Helfmann, Luzie A1 - Djurdjevac Conrad, Natasa A1 - Djurdjevac, Ana A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - From interacting agents to density-based modeling with stochastic PDEs N2 - Many real-world processes can naturally be modeled as systems of interacting agents. However, the long-term simulation of such agent-based models is often intractable when the system becomes too large. In this paper, starting from a stochastic spatio-temporal agent-based model (ABM), we present a reduced model in terms of stochastic PDEs that describes the evolution of agent number densities for large populations. We discuss the algorithmic details of both approaches; regarding the SPDE model, we apply Finite Element discretization in space which not only ensures efficient simulation but also serves as a regularization of the SPDE. Illustrative examples for the spreading of an innovation among agents are given and used for comparing ABM and SPDE models. T3 - ZIB-Report - 19-21 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73456 SN - 1438-0064 ER - TY - GEN A1 - Helfmann, Luzie A1 - Djurdjevac Conrad, Natasa A1 - Lorenz-Spreen, Philipp A1 - Schütte, Christof T1 - Supplementary code for the paper Modelling opinion dynamics under the impact of influencer and media strategies N2 - This repository contains the Julia code accompanying the paper "Modelling opinion dynamics under the impact of influencer and media strategies", Scientific Reports, Vol.13, p. 19375, 2023. Y1 - 2023 U6 - https://doi.org/10.12752/9267 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Heitzig, Jobst A1 - Koltai, Péter A1 - Kurths, Jürgen A1 - Schütte, Christof T1 - Statistical analysis of tipping pathways in agent-based models JF - Eur. Phys. J. Spec. Top. N2 - Agent-based models are a natural choice for modeling complex social systems. In such models simple stochastic interaction rules for a large population of individuals on the microscopic scale can lead to emergent dynamics on the macroscopic scale, for instance a sudden shift of majority opinion or behavior. Here we are introducing a methodology for studying noise-induced tipping between relevant subsets of the agent state space representing characteristic configurations. Due to a large number of interacting individuals, agent-based models are high-dimensional, though usually a lower-dimensional structure of the emerging collective behaviour exists. We therefore apply Diffusion Maps, a non-linear dimension reduction technique, to reveal the intrinsic low-dimensional structure. We characterize the tipping behaviour by means of Transition Path Theory, which helps gaining a statistical understanding of the tipping paths such as their distribution, flux and rate. By systematically studying two agent-based models that exhibit a multitude of tipping pathways and cascading effects, we illustrate the practicability of our approach. Y1 - 2021 U6 - https://doi.org/10.1140/epjs/s11734-021-00191-0 VL - 230 SP - 3249 EP - 3271 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Ribera Borrell, Enric A1 - Schütte, Christof A1 - Koltai, Peter T1 - Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics JF - Journal of Nonlinear Science Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/s00332-020-09652-7 VL - 30 SP - 3321 EP - 3366 ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Fischer, Alexander A1 - Schütte, Christof T1 - Automated Model Reduction for Complex Systems exhibiting Metastability JF - Mult. Mod. Sim. Y1 - 2006 UR - http://publications.imp.fu-berlin.de/44/ U6 - https://doi.org/10.1137/050623310 VL - 5 IS - 3 SP - 802 EP - 827 ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Lankas, F. A1 - Maddocks, J. A1 - Metzner, Ph. A1 - Schütte, Christof T1 - Macroscopic Dynamics of Complex Metastable Systems JF - J. Appl. Dyn. Syst. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/56/ U6 - https://doi.org/10.1137/050630064 VL - 7 IS - 2 SP - 532 EP - 560 ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Schütte, Christof T1 - Reduced Stochastic Models for Complex Molecular Systems JF - Comp. Vis. Sci. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/59/ U6 - https://doi.org/10.1007/s00791-006-0021-1 VL - 9 IS - 2 SP - 89 EP - 102 ER - TY - JOUR A1 - Horenko, Illia A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Noé, Frank T1 - Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes JF - Phys. Rev. E Y1 - 2007 UR - http://publications.imp.fu-berlin.de/31/ U6 - https://doi.org/10.1103/PhysRevE.76.016706 VL - 76 IS - 01 SP - 016706 ER - TY - JOUR A1 - Horenko, Illia A1 - Klein, Rupert A1 - Dolaptchiev, S. A1 - Schütte, Christof T1 - Automated Generation of Reduced Stochastic Weather Models I JF - Mult. Mod. Sim. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/15/ U6 - https://doi.org/10.1137/060670535 VL - 6 IS - 4 SP - 1125 EP - 1145 ER - TY - JOUR A1 - Horenko, Illia A1 - Lorenz, S. A1 - Schütte, Christof A1 - Huisinga, Wilhelm T1 - Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics JF - J. Comp. Chem. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/49/ U6 - https://doi.org/10.1002/jcc.20234 VL - 26 IS - 9 SP - 941 EP - 948 ER - TY - JOUR A1 - Horenko, Illia A1 - Salzmann, Ch. A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Quantum-Classical Liouville Approach to Molecular Dynamics JF - J. Chem. Phys. Y1 - 2002 UR - http://publications.imp.fu-berlin.de/75/ U6 - https://doi.org/10.1063/1.1522712 VL - 117 IS - 24 SP - 11075 EP - 11088 ER - TY - JOUR A1 - Horenko, Illia A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions JF - J. Chem. Phys. Y1 - 2002 UR - http://publications.imp.fu-berlin.de/73/ U6 - https://doi.org/10.1063/1.1498467 VL - 117 IS - 10 SP - 4643 EP - 4650 ER - TY - JOUR A1 - Horenko, Illia A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - A Theoretical Model for Molecules Interacting with Intense Laser Pulses JF - J. Chem. Phys. Y1 - 2001 UR - http://publications.imp.fu-berlin.de/79/ U6 - https://doi.org/10.1063/1.1398577 VL - 115 IS - 13 SP - 5733 EP - 5743 ER - TY - GEN A1 - Horenko, Illia A1 - Schmidt-Ehrenberg, Johannes A1 - Schütte, Christof T1 - Set-oriented dimension reduction: Localizing principal component analysis via hidden Markov models T2 - Computational Life Sciences II Y1 - 2006 VL - 4216 SP - 98 EP - 115 PB - Springer ER - TY - CHAP A1 - Horenko, Illia A1 - Schmidt-Ehrenberg, Johannes A1 - Schütte, Christof ED - Berthold, Michael R. ED - Glen, Robert C. ED - Fischer, Ingrid T1 - Set-oriented dimension reduction: Localizing principal component analysis via hidden Markov models T2 - Computational Life Sciences II: Second International Symposium CompLife 2006, Cambridge (UK), Sept. 2006 Y1 - 2006 UR - http://publications.imp.fu-berlin.de/121/ U6 - https://doi.org/10.1007/11875741_8 VL - 4216 SP - 74 EP - 85 PB - Springer ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - On metastable conformational analysis of non-equilibrium biomolecular time series JF - Multiscale Modeling & Simulation Y1 - 2010 UR - http://publications.imp.fu-berlin.de/146/ U6 - https://doi.org/10.1137/080744347 VL - 8 IS - 2 SP - 701 EP - 716 ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics JF - Mult. Mod. Sim. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/39/ U6 - https://doi.org/10.1137/070687451 VL - 7 IS - 2 SP - 731 EP - 773 ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications JF - Adv. Data Anal. Class., submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/32/ ER - TY - JOUR A1 - Horenko, Illia A1 - Weiser, Martin A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Fully Adaptive Propagation of the Quantum-Classical Liouville Equation JF - J. Chem. Phys. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/65/ U6 - https://doi.org/10.1063/1.1691015 VL - 120 IS - 19 SP - 8913 EP - 8923 ER - TY - GEN A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Cordes, Frank A1 - Roitzsch, Rainer A1 - Schütte, Christof T1 - From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods N2 - Statistical methods for analyzing large data sets of molecular configurations within the chemical concept of molecular conformations are described. The strategies are based on dependencies between configurations of a molecular ensemble; the article concentrates on dependencies induces by a) correlations between the molecular degrees of freedom, b) geometrical similarities of configurations, and c) dynamical relations between subsets of configurations. The statistical technique realizing aspect a) is based on an approach suggested by {\sc Amadei et al.} (Proteins, 17 (1993)). It allows to identify essential degrees of freedom of a molecular system and is extended in order to determine single configurations as representatives for the crucial features related to these essential degrees of freedom. Aspects b) and c) are based on statistical cluster methods. They lead to a decomposition of the available simulation data into {\em conformational ensembles} or {\em subsets} with the property that all configurations in one of these subsets share a common chemical property. In contrast to the restriction to single representative conformations, conformational ensembles include information about, e.g., structural flexibility or dynamical connectivity. The conceptual similarities and differences of the three approaches are discussed in detail and are illustrated by application to simulation data originating from a hybrid Monte Carlo sampling of a triribonucleotide. T3 - ZIB-Report - SC-98-36 KW - conformational ensemble KW - cluster method KW - structural and dynamical similarity KW - representative KW - conformation KW - essential degrees of freedom KW - transi Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3797 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Cordes, Frank A1 - Roitzsch, Rainer A1 - Schütte, Christof T1 - Identification of Molecular Conformations via Statistical Analysis of Simulation Data JF - Comp. Chem. Y1 - 1999 VL - 20 SP - 1760 EP - 1774 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Roitzsch, Rainer A1 - Schütte, Christof A1 - Cordes, Frank T1 - From Simulation Data to Conformational Ensembles JF - J. Comp. Chem. Y1 - 1999 VL - 20 IS - 16 SP - 1760 EP - 1774 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Roitzsch, Rainer A1 - Schütte, Christof A1 - Cordes, Frank T1 - From Simulation Data to Conformational Ensembles JF - J. Comp. Chem. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/92/ U6 - https://doi.org/10.1002/(SICI)1096-987X(199912)20:16<1760::AID-JCC8>3.0.CO;2-2 VL - 20 IS - 16 SP - 1760 EP - 1774 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Meyn, S. A1 - Schütte, Christof T1 - Phase Transitions and Metastability in Markovian and Molecular Systems JF - Ann. Appl. Prob. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/67/ U6 - https://doi.org/10.1214/aoap/1075828057 VL - 14 IS - 1 SP - 419 EP - 458 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Schütte, Christof A1 - Stuart, Andrew T1 - Extracting Macroscopic Stochastic Dynamics JF - Comm. Pure Appl. Math. Y1 - 2003 UR - http://publications.imp.fu-berlin.de/72/ U6 - https://doi.org/10.1002/cpa.10057 VL - 56 IS - 2 SP - 234 EP - 269 ER - TY - JOUR A1 - Huttary, Rudolf A1 - Goubergrits, Leonid A1 - Schütte, Christof A1 - Bernhard, Stefan T1 - Simulation, Identification and Statistical Variation in Cardiovascular Analysis (SISCA) - a Software Framework for Multi-compartment Lumped Modeling JF - Computers in Biology and Medicine Y1 - 2017 U6 - https://doi.org/10.1016/j.compbiomed.2017.05.021 VL - 87 SP - 104 EP - 123 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Objective priors in the empirical Bayes framework JF - Scandinavian Journal of Statistics N2 - When dealing with Bayesian inference the choice of the prior often remains a debatable question. Empirical Bayes methods offer a data-driven solution to this problem by estimating the prior itself from an ensemble of data. In the nonparametric case, the maximum likelihood estimate is known to overfit the data, an issue that is commonly tackled by regularization. However, the majority of regularizations are ad hoc choices which lack invariance under reparametrization of the model and result in inconsistent estimates for equivalent models. We introduce a nonparametric, transformation-invariant estimator for the prior distribution. Being defined in terms of the missing information similar to the reference prior, it can be seen as an extension of the latter to the data-driven setting. This implies a natural interpretation as a trade-off between choosing the least informative prior and incorporating the information provided by the data, a symbiosis between the objective and empirical Bayes methodologies. Y1 - 2021 U6 - https://doi.org/10.1111/sjos.12485 VL - 48 IS - 4 SP - 1212 EP - 1233 PB - Wiley Online Library ER - TY - GEN A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Prior estimation and Bayesian inference from large cohort data sets N2 - One of the main goals of mathematical modelling in systems biology related to medical applications is to obtain patient-specific parameterisations and model predictions. In clinical practice, however, the number of available measurements for single patients is usually limited due to time and cost restrictions. This hampers the process of making patient-specific predictions about the outcome of a treatment. On the other hand, data are often available for many patients, in particular if extensive clinical studies have been performed. Using these population data, we propose an iterative algorithm for contructing an informative prior distribution, which then serves as the basis for computing patient-specific posteriors and obtaining individual predictions. We demonsrate the performance of our method by applying it to a low-dimensional parameter estimation problem in a toy model as well as to a high-dimensional ODE model of the human menstrual cycle, which represents a typical example from systems biology modelling. T3 - ZIB-Report - 16-09 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57475 SN - 1438-0064 ER -