Random splitting can yield non-independent train--test subsets when a dataset contains related samples, as is common in certain applications such as biochemical studies. This leads to overly optimistic generalization estimates. Here, we introduce ReLaG, a modality-agnostic framework that models sample relatedness through a hierarchical latent-variable process and infers groups of related samples using proximity graphs and community detection to produce independent train--test subsets. Across molecular and protein datasets, ReLaG matches existing relation-aware methods while scaling substantially better, enabling splits at previously impractical dataset sizes. We further introduce a label-free procedure that adapts the splitting resolution to production data, aligning evaluation with the intended deployment setting. ReLaG's inferred groups provide a cheap estimate of effective dataset size, enabling diversity-aware dataset scaling. ReLaG is open source and can be installed with pip install relag.

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