Learning the Geometry of Materials Space with Trained Neural Tangent Kernels

Existing molecular and materials learning approaches often rely on a limited set of structural representations, which may capture only selected aspects of complex three-dimensional structure. Here, we introduce mathematical invariant-enabled topological neural networks (MITNNs), a framework that represents complex structures through multiple complementary mathematical views and integrates them with topological neural architectures. MITNNs combine multiscale invariants from topology, spectral theory, commutative algebra, differential geometry, and discrete curvature, capturing complementary structural information from the same system. Systematic invariant-subset, architecture-subset, and ensemble analyses show that predictive performance depends on how mathematical representations and neural architectures are paired, with selected combinations outperforming individual models and the aggregation of all available components. Across protein-ligand binding, metal-organic framework properties, mutation-induced protein solubility, and molecular toxicity prediction, MITNN consistently outperforms existing methods. These results establish MITNN as a mathematically multimodal framework for scientific machine learning.

A persistent empirical observation is that trained neural networks outperform their neural tangent kernel (NTK) limit on tasks with compositional structure, yet a quantitative account of $\textbf{when}$ and $\textbf{by how much}$ has been lacking. Working on the unit circle, we give such an account through a dichotomy between two complexity measures of the target: its $\textbf{Fourier complexity}$, which controls NTK kernel regression, and its $\textbf{architectural complexity}$, which controls learning over depth-$L$, width-$w$ ReLU networks with the variation norm of the weights bounded by $R$. We first characterize the minimax rate of the architecture class $\mathcal{C}_{L,w,R}$, pinning it down up to a single factor of $L$: between $Ω(Lw^2R^2/n)$ and $\tilde{O}(L^2w^2R^2/n)$. We then show the NTK estimator sits $\textbf{exponentially}$ above this floor whenever the two complexities decouple: for the depth-$L$ iterated sawtooth, NTK regression needs $Ω(4^L)$ samples while the minimax floor is polynomial in $L$. Numerical experiments confirm the theoretical claims: on bandlimited smooth targets, the NTK is competitive or better, while on the hypercube sparse-parity model, a standard two-layer network beats the NTK by four to six orders of magnitude in test error. The gap is thus a function-space property, a mismatch between the kernel's smoothness bias and the target's compositional structure, rather than a generic kernel-versus-network phenomenon.

Final predictive accuracy is the standard basis for comparing graph neural networks (GNNs) in materials-property prediction, but it does not show how strongly performance depends on access to trainable parameter-space directions. Here, we introduce trainable-degree dependence as a complementary characterization of materials GNN learning. Using random-subspace intrinsic-dimension analysis, we train CGCNN, ALIGNN, and DimeNet++ in randomly oriented parameter subspaces across six prediction tasks and measure how performance recovers as independent trainable degrees of freedom are restored. The resulting recovery curves separate endpoint accuracy from the trainable-dimensional demand required to recover it. They reveal distinctions that final errors alone miss: metallic classification and log-bulk-modulus regression recover near-reference performance from small fractional subspaces, formation-energy and band-gap prediction show stronger architecture dependence, and phonon prediction is most sensitive to dimensional restriction. Dataset-size sweeps show that band-gap models require larger fractional subspaces as training data grows, whereas formation-energy and bulk-modulus responses are more stable. A width sweep shows that fractional thresholds can remain stable while absolute threshold dimensions increase with model size. Random-subspace analysis therefore provides a targeted stress test for how materials GNNs use their optimization space.