Misspecification uncertainties in near-deterministic regression

The expected loss is an upper bound to the model generalization error which admits robust PAC-Bayes bounds for learning. However, loss minimization is known to ignore misspecification, where models cannot exactly reproduce observations. This leads to significant underestimates of parameter uncertainties in the large data, or underparameterized, limit. We analyze the generalization error of near-deterministic, misspecified and underparametrized surrogate models, a regime of broad relevance in science and engineering. We show posterior distributions must cover every training point to avoid a divergent generalization error and derive an ensemble {ansatz} that respects this constraint, which for linear models incurs minimal overhead. The efficient approach is demonstrated on model problems before application to high dimensional datasets in atomistic machine learning. Parameter uncertainties from misspecification survive in the underparametrized limit, giving accurate prediction and bounding of test errors.

Improving Estimation of the Koopman Operator with Kolmogorov-Smirnov Indicator Functions

It has become common to perform kinetic analysis using approximate Koopman operators that transforms high-dimensional time series of observables into ranked dynamical modes. Key to a practical success of the approach is the identification of a set of observables which form a good basis in which to expand the slow relaxation modes. Good observables are, however, difficult to identify {\em a priori} and sub-optimal choices can lead to significant underestimations of characteristic timescales. Leveraging the representation of slow dynamics in terms of Hidden Markov Model (HMM), we propose a simple and computationally efficient clustering procedure to infer surrogate observables that form a good basis for slow modes. We apply the approach to an analytically solvable model system, as well as on three protein systems of different complexities. We consistently demonstrate that the inferred indicator functions can significantly improve the estimation of the leading eigenvalues of the Koopman operators and correctly identify key states and transition timescales of stochastic systems, even when good observables are not known {\em a priori}.