In this review paper, we will present different data-driven dimension reduction techniques for dynamical systems that are based on transfer operator theory as well as methods to approximate transfer operators and their eigenvalues, eigenfunctions, and eigenmodes. The goal is to point out similarities and differences between methods developed independently by the dynamical systems, fluid dynamics, and molecular dynamics communities such as time-lagged independent component analysis (TICA), dynamic mode decomposition (DMD), and their respective generalizations. As a result, extensions and best practices developed for one particular method can be carried over to other related methods.

Dynamical systems often exhibit the emergence of long-lived coherent sets, which are regions in state space that keep their geometric integrity to a high extent and thus play an important role in transport. In this article, we provide a method for extracting coherent sets from possibly sparse Lagrangian trajectory data. Our method can be seen as an extension of diffusion maps to trajectory space, and it allows us to construct "dynamical coordinates" which reveal the intrinsic low-dimensional organization of the data with respect to transport. The only a priori knowledge about the dynamics that we require is a locally valid notion of distance, which renders our method highly suitable for automated data analysis. We show convergence of our method to the analytic transfer operator framework of coherence in the infinite data limit, and illustrate its potential on several two-and three-dimensional examples as well as real world data.

Markov state models (MSMs) and master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, a powerful generalization of MSMs has been introduced, the variational approach conformation dynamics/molecular kinetics (VAC) and its special case the time-lagged independent component analysis (TICA), which allow us to approximate slow collective variables and molecular kinetics by linear combinations of smooth basis functions or order parameters. While it is known how to estimate MSMs from trajectories whose starting points are not sampled from an equilibrium ensemble, this has not yet been the case for TICA and the VAC. Previous estimates from short trajectories have been strongly biased and thus not variationally optimal. Here, we employ the Koopman operator theory and the ideas from dynamic mode decomposition to extend the VAC and TICA to non-equilibrium data. The main insight is that the VAC and TICA provide a coefficient matrix that we call Koopman model, as it approximates the underlying dynamical (Koopman) operator in conjunction with the basis set used. This Koopman model can be used to compute a stationary vector to reweight the data to equilibrium. From such a Koopman-reweighted sample, equilibrium expectation values and variationally optimal reversible Koopman models can be constructed even with short simulations. The Koopman model can be used to propagate densities, and its eigenvalue decomposition provides estimates of relaxation time scales and slow collective variables for dimension reduction. Koopman models are generalizations of Markov state models, TICA, and the linear VAC and allow molecular kinetics to be described without a cluster discretization.

The long-term distributions of trajectories of a flow are described by invariant densities, i.e. fixed points of an associated transfer operator. In addition, global slowly mixing structures, such as almost-invariant sets, which partition phase space into regions that are almost dynamically disconnected, can also be identified by certain eigenfunctions of this operator. Indeed, these structures are often hard to obtain by brute-force trajectory-based analyses. In a wide variety of applications, transfer operators have proven to be very efficient tools for an analysis of the global behavior of a dynamical system.The computationally most expensive step in the construction of an approximate transfer operator is the numerical integration of many short term trajectories. In this paper, we propose to directly work with the infinitesimal generator instead of the operator, completely avoiding trajectory integration. We propose two different discretization schemes; a cell based discretization and a spectral collocation approach. Convergence can be shown in certain circumstances. We demonstrate numerically that our approach is much more efficient than the operator approach, sometimes by several orders of magnitude.

Periodically driven flows are fundamental models of chaotic behavior and the study of their transport properties is an active area of research. A well-known analytic construction is the augmentation of phase space with an additional time dimension; in this augmented space, the flow becomes autonomous or time-independent. We prove several results concerning the connections between the original time-periodic representation and the time-extended representation, focusing on transport properties. In the deterministic setting, these include single-period outflows and time-asymptotic escape rates from time-parameterized families of sets. We also consider stochastic differential equations with time-periodic advection term. In this stochastic setting one has a time-periodic generator (the differential operator given by the right-hand-side of the corresponding time-periodic Fokker-Planck equation). We define in a natural way an autonomous generator corresponding to the flow on time-extended phase space. We prove relationships between these two generator representations and use these to quantify decay rates of observables and to determine time-periodic families of sets with slow escape rate. Finally, we use the generator on the time-extended phase space to create efficient numerical schemes to implement the various theoretical constructions. These ideas build on the work of [FJK13], and no expensive time integration is required. We introduce an efficient new hybrid approach, which treats the space and time dimensions separately.