Interpretable Machine Learning of Nanoparticle Stability through Topological Layer Embeddings

The stability of chemically complex nanoparticles is governed by an immense configurational space arising from heterogeneous local atomic environments across surface and interior regions. Efficiently identifying low-energy configurations within this space remains a central challenge for first-principles-based materials discovery, particularly when the available reference data are limited. Here, we introduce a data-efficient and physically interpretable machine-learning framework based on a fragmented, layer-resolved descriptor that explicitly decomposes nanoparticles into surface, intermediate, and core environments using a topology-driven definition. This representation preserves a compact and fixed feature dimensionality while retaining spatial resolution, enabling controlled emphasis on different regions of the nanoparticle through physically motivated weighting schemes. Coupled with gradient-boosted decision-tree models and a ranking-based learning strategy, the proposed framework enables accurate identification of the most stable nanoparticle configurations using only a few hundred density functional theory reference calculations. Ranking performance metrics demonstrate near-saturation of correlation, high top-k recall, and rapidly vanishing regret at moderate training set sizes, highlighting the strong data efficiency of the approach. Beyond predictive performance, layer-weighting and SHAP-based interpretability analyses reveal how surface segregation, coordination topology, and local chemical disorder contribute differently to stability across spatial regions of the nanoparticle. The framework is system and code-agnostic, requiring only atomic coordinates, chemical species, and a scalar target energy, and is therefore directly transferable to other multicomponent nanostructures and to alternative first-principles or machine-learning energy methods.