accuracy of markov state models msms and hidden markov
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Accuracy of Markov State Models (MSMs) and Hidden Markov Models - PowerPoint PPT Presentation

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Accuracy of Markov State Models (MSMs) and Hidden Markov Models (HMMs) Frank No (FU Berlin) frank.noe@fu-berlin.de Discretization Backward propagator Spectral decomposition Processes: Eigenvalues / timescales i-1 Prinz et al, JCP 134 ,

  1. Accuracy of Markov State Models (MSMs) and Hidden Markov Models (HMMs) Frank Noé (FU Berlin) frank.noe@fu-berlin.de

  2. Discretization Backward propagator Spectral decomposition Processes: Eigenvalues / timescales κ i-1 Prinz et al, JCP 134 , 174105 (2011)

  3. Discretization Prinz et al, JCP 134 , 174105 (2011)

  4. Two flavors of discretization errors Projection error

  6. Hidden Markov Model

  7. Hidden Markov Model

  8. Hidden Markov Model

  9. Hidden Markov Model

  10. Case 1: coarse discretization

  11. Case 1: coarse discretization MSM: Implied timescales

  12. Case 1: coarse discretization MSM: Chapman-Kolmogorov Test

  13. Case 1: coarse discretization HMM: Implied timescales

  14. Case 1: coarse discretization HMM: Chapman-Kolmogorov Test

  15. Case 1: coarse discretization Why does the HMM work better than the MSM? MSM at lag 40: HMM at lag 40:

  16. Case 2: bad projection Probability density Energy surface Brownian dynamics simulation

  18. Acknowledgements Funding Positions available Collaborations frank.noe@fu-berlin.de Funding Cecilia Clementi (Rice) Christof Schütte (FU Berlin) Vijay Pande (Stanford) Eric Vanden-Eijnden (Courant Institut NY) Katja, Faelber, Oliver Daumke (MDC) Thomas Weikl (MPI Potsdam) John Chodera (MSKCC NY) Marcus Sauer, Sören Doose (Uni Würzburg) Gianni de Fabritiis (Barcelona)

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