Selecting an appropriate kernel is a central challenge in kernel-based spectral methods. In \emph{Kernelized Diffusion Maps} (KDM), the kernel determines the accuracy of the RKHS estimator of a diffusion-type operator and hence the quality and stability of the recovered eigenfunctions. We introduce two complementary approaches to adaptive kernel selection for KDM. First, we develop a variational outer loop that learns continuous kernel parameters, including bandwidths and mixture weights, by differentiating through the Cholesky-reduced KDM eigenproblem with an objective combining eigenvalue maximization, subspace orthonormality, and RKHS regularization. Second, we propose an unsupervised cross-validation pipeline that selects kernel families and bandwidths using an eigenvalue-sum criterion together with random Fourier features for scalability. Both methods share a common theoretical foundation: we prove Lipschitz dependence of KDM operators on kernel weights, continuity of spectral projectors under a gap condition, a residual-control theorem certifying proximity to the target eigenspace, and exponential consistency of the cross-validation selector over a finite kernel dictionary.

The ISOKANN (Invariant Subspaces of Koopman Operators Learned by Artificial Neural Networks) framework provides a data-driven route to extract collective variables (CVs) and effective dynamics from complex molecular systems. In this work, we integrate the theoretical foundation of Koopman operators with Krylov-like subspace algorithms, and reduced dynamical modeling to build a coherent picture of how to describe metastable transitions in high-dimensional systems based on CVs. Starting from the identification of CVs based on dominant invariant subspaces, we derive the corresponding effective dynamics on the latent space and connect these to transition rates and times, committor functions, and transition pathways. The combination of Koopman-based learning and reduced-dimensional effective dynamics yields a principled framework for computing transition rates and pathways from simulation data. Numerical experiments on one-, two-, and three-dimensional benchmark potentials illustrate the ability of ISOKANN to reconstruct the coarse-grained kinetics and reproduce transition times across enthalpic and entropic barriers.

This report examines numerical aspects of constructing Karhunen-Loève expansions (KLEs) for second-order stochastic processes. The KLE relies on the spectral decomposition of the covariance operator via the Fredholm integral equation of the second kind, which is then discretized on a computational grid, leading to an eigendecomposition task. We derive the algebraic equivalence between this Fredholm-based eigensolution and the singular value decomposition of the weight-scaled sample matrix, yielding consistent solutions for both model-based and data-driven KLE construction. Analytical eigensolutions for exponential and squared-exponential covariance kernels serve as reference benchmarks to assess numerical consistency and accuracy in 1D settings. The convergence of SVD-based eigenvalue estimates and of the empirical distributions of the KL coefficients to their theoretical $\mathcal{N}(0,1)$ target are characterized as a function of sample count. Higher-dimensional configurations include a two-dimensional irregular domain discretized by unstructured triangular meshes with two refinement levels, and a three-dimensional toroidal domain whose non-simply-connected topology motivates a comparison between Euclidean and shortest interior path distances between the grid points. The numerical results highlight the interplay between the discretization strategy, quadrature rule, and sample count, and their impact on the KLE results.

Finally, we provide experiments on real data comparing NTK and the Laplace kernel, along with a larger class ofγ-exponential kernels. We show that these perform almost identically.

We address data-driven learning of the infinitesimal generator of stochastic diffusion processes, essential for understanding numerical simulations of natural and physical systems.

The cortico-spinal neural pathway is fundamental for motor control and movement execution, and in humans it is typically studied using concurrent electroen-cephalography (EEG) and electromyography (EMG) recordings.

The theory of Koopman operators allows to deploy non-parametric machine learning algorithms to predict and analyze complex dynamical systems.