Machine learning models trained on biochemical data are routinely evaluated using splits that fail to account for relational structure, causing information leakage and over-optimistic performance estimates. Existing splitting methods lack theoretical grounding and scale at best quadratically. We introduce the Relational Generative Process (RGP), a mathematical formalization explaining why relational structure arises in biochemical datasets, and Refnd, a splitting algorithm that leverages a proximity graph computed in loglinear time using Hierarchical Navigable Small World (HNSW). We validate on an antimicrobial peptide dataset, showing that Refnd splits yield lower but more realistic evaluation performance than traditional splits. Refnd is applicable to any dataset arising from an RGP such as protein sequences and structures, small molecules, and nucleotide sequences, and is openly available as a Rust accelerated Python package: pip install refnd.
Relational Prior-Data Fitted Networks (PFNs) such as RDB-PFN approximate Bayesian inference over multi-table relational databases by pretraining on millions of synthetic tasks. We investigate three intertwined questions about this paradigm. First, can a structurally different syn…
Synthetic face datasets are increasingly used to reduce privacy exposure and data access constraints in biometric recognition. Yet the generators that produce these datasets are trained on real faces, so synthetic data may still reveal their real source data. We study this risk t…
Multiclass classification is a fundamental problem across a wide range of domains. It is still challenging due to possession of high inter-class similarity, class imbalance datasets, and variability in data distributions. Rule-based classifiers such as XGBoost often achieve stron…
Relational Foundation Models (RFMs) require large-scale synthetic relational databases for pretraining, but existing approaches tightly couple data generation with the model training pipeline. We study whether PluRel, a general-purpose synthetic relational database generator, can…
Bayesian optimization (BO) is an optimization method that sequentially proposes the next candidate explainable variables for optimizing target variables by balancing exploration and exploitation. BO is often used under a limited evaluation budget, such as hyperparameter tuning of…
Near 1310 nm photonic-crystal surface-emitting lasers (PCSELs) are attractive narrow-beam sources for optical communication and sensing, but their final design refinement is costly. Small geometry changes simultaneously shift the band-edge resonance, cavity leakage, far-field div…