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Accuracy of Markov State Models (MSMs) and Hidden Markov Models - - PowerPoint PPT Presentation
Accuracy of Markov State Models (MSMs) and Hidden Markov Models - - PowerPoint PPT Presentation
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 ,
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Discretization
Prinz et al, JCP 134, 174105 (2011)
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Two flavors of discretization errors
Projection error
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Hidden Markov Model
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Hidden Markov Model
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Hidden Markov Model
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Hidden Markov Model
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Case 1: coarse discretization
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MSM: Implied timescales
Case 1: coarse discretization
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MSM: Chapman-Kolmogorov Test
Case 1: coarse discretization
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Case 1: coarse discretization
HMM: Implied timescales
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Case 1: coarse discretization
HMM: Chapman-Kolmogorov Test
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HMM at lag 40:
Case 1: coarse discretization
Why does the HMM work better than the MSM? MSM at lag 40:
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Case 2: bad projection
Probability density Energy surface Brownian dynamics simulation
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Funding
Cecilia Clementi (Rice) Christof Schütte (FU Berlin) Eric Vanden-Eijnden (Courant Institut NY) Thomas Weikl (MPI Potsdam) Marcus Sauer, Sören Doose (Uni Würzburg)
Collaborations
Vijay Pande (Stanford) Katja, Faelber, Oliver Daumke (MDC) John Chodera (MSKCC NY) Gianni de Fabritiis (Barcelona)