Fundamental Dynamical Units for Physics-Informed Structural Inference from Perturbation Time-Series in Networked Systems

We investigate a structure-first approach to dynamical learning in which the organization of stateful interactions is prescribed explicitly rather than left entirely to a generic recurrent parameterization. We introduce causal recurrent units built from an ordered sequence of local, state-modulated transformations. The construction is motivated by wave-based interaction models, but the units studied here do not impose scattering, passivity, or energy-balance constraints. Because fixed recurrent dynamics, designed reservoir topologies, readout-only learning, and recurrent depth are already well established, the empirical question is deliberately narrower: does the proposed interaction organization provide a useful inductive bias under controlled computational conditions? We compare a one-layer structured model, a two-layer structured model, and a generic echo-state network (ESN), all with 12 recurrent states and the same strictly linear ridge readout. Each model family receives the same random-search budget on calibration data that are disjoint from the final test data, after which the selected hyperparameters are frozen. On a custom nonlinear identification task, the one-layer structured model attains a mean validation NMSE of 2.76 x 10^{-4}, compared with 3.19 x 10^{-4} for the two-layer model and 3.94 x 10^{-4} for the ESN. On NARMA10 the ordering reverses: the ESN attains 0.312, compared with 0.348 and 0.357 for the one- and two-layer structured models. Thus, the proposed organization can be competitive and advantageous on one task, but it is not universally superior; moreover, recurrent depth does not provide a systematic benefit under matched state dimension. The results support a task-dependent interpretation of structural inductive bias and position the present architecture as a controlled precursor to stronger wave- and system-theoretic constructions.

Many multivariate dynamical systems are observed only through trajectories, leaving the mechanisms governing their joint dynamics hidden. Existing approaches can impose interpretable dynamics or learn flexible state transitions, yet the resulting interaction structure is typically either specified in advance or left implicit within the learned dynamics. We introduce MF-Net, a recurrent dynamical model that represents all variables in a shared field state and updates this state through a learned relation law. Each variable carries a field component, and these components evolve jointly through a learnable mechanical transition. Here, mechanical refers to the relation-to-motion organization of the transition, where learned relations shape state-dependent flows, field responses, and motion tendencies that move the field state forward. The resulting structure is part of the rollout itself: learned relations influence how the field moves, and the same internal quantities support both forecasting and structural readout. Across known-law interaction systems, chaotic benchmarks, real neural recordings, and ecological time series, MF-Net achieves competitive short- and medium-horizon forecasting while retaining inspectable structural readout. On the 40-dimensional Lorenz--96 testbed, MF-Net achieves an eight-step $R^2$ of $0.798\pm0.018$; across five seeds, its learned relation matrix recovers the local coupling support with a local/nonlocal strength ratio of $19.80\pm1.00$ and Precision@$K$ of $1.000\pm0.000$. MF-Net provides a structure-readable dynamical modeling framework in which learned relations are trained through forward evolution and, on real data, interpreted as functional predictive couplings under appropriate observational limits.

Modeling dynamical systems and unraveling their underlying structural dependencies is central to many domains in the natural sciences. Various physical systems, such as those arising in cell biology, are inherently high-dimensional and stochastic in nature, and admit only partial, noisy state measurements. Our primary motivating setting is single-cell biology, where destructive measurements yield unpaired population snapshots rather than longitudinal trajectories of the same cells. This poses a significant challenge for addressing the problems of modeling the underlying dynamics and inferring the network structure of these systems. Existing methods are typically tailored either for structure learning or modeling dynamics at the population level, but are limited in their ability to address both problems together. In this work, we address both problems simultaneously: we present StructureFlow, a novel and principled simulation-free training approach for jointly learning the structure and stochastic population dynamics of physical systems. We showcase the utility of StructureFlow for the tasks of structure learning from interventions and dynamical (trajectory) inference of conditional population dynamics. We empirically evaluate our approach on high-dimensional synthetic systems, a set of biologically plausible simulated systems, and an experimental single-cell dataset. We show that StructureFlow can learn the structure of underlying systems while simultaneously modeling their conditional population dynamics --- a key step toward model-based mechanistic understanding of systems behavior.