Data-based detection and quantification of causation in complex, nonlinear dynamical systems is of paramount importance to science, engineering, and beyond. Inspired by the widely used methodology in recent years, the cross-map-based techniques, we develop a general framework to advance towards a comprehensive understanding of dynamical causal mechanisms, which is consistent with the natural interpretation of causality. In particular, instead of measuring the smoothness of the cross-map as conventionally implemented, we define causation through measuring the scaling law for the continuity of the investigated dynamical system directly. The uncovered scaling law enables accurate, reliable, and efficient detection of causation and assessment of its strength in general complex dynamical systems, outperforming those existing representative methods. The continuity scaling-based framework is rigorously established and demonstrated using datasets from model complex systems and the real world.

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Persistent homology is constrained to purely topological persistence, while multiscale graphs account only for geometric information. This work introduces persistent spectral theory to create a unified low-dimensional multiscale paradigm for revealing topological persistence and extracting geometric shapes from high-dimensional datasets. For a point-cloud dataset, a filtration procedure is used to generate a sequence of chain complexes and associated families of simplicial complexes and chains, from which we construct persistent combinatorial Laplacian matrices. We show that a full set of topological persistence can be completely recovered from the harmonic persistent spectra, that is, the spectra that have zero eigenvalues, of the persistent combinatorial Laplacian matrices. However, non-harmonic spectra of the Laplacian matrices induced by the filtration offer another powerful tool for data analysis, modeling, and prediction. In this work, fullerene stability is predicted by using both harmonic spectra and non-harmonic persistent spectra, while the latter spectra are successfully devised to analyze the structure of fullerenes and model protein flexibility, which cannot be straightforwardly extracted from the current persistent homology. The proposed method is found to provide excellent predictions of the protein B-factors for which current popular biophysical models break down.