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.
Cell-type deconvolution, the task of estimating the proportions of constituent cell types in a heterogeneous biological sample, is a core problem in computational biology. Methods that rely on epigenetic marks such as DNA methylation typically operate on aggregated methylation es…
Classifying heterogeneous omics data remains a fundamental challenge in computational biology, particularly in high-dimensional, small-sample settings where nonlinear interactions dominate and class imbalance further complicates reliable prediction of minority phenotypes. While t…
Breast cancer is one of the most widespread types of cancer, affecting approximately 8 million women worldwide. Electronic health records of patients diagnosed with this disease can serve as valuable datasets for computational analyses, enabling the discovery of new insights abou…
Current computational approaches for drug design typically focus on generating molecules conditioned on specific targets or general molecular properties, often neglecting the influence of disease context on target behavior and therapeutic outcomes. To address this gap, we introdu…
Antibody expression ranking is a critical task in antibody design, yet its modelling is severely hindered by the scarcity of labeled experimental data. To address this, we propose a unified preference-based learning framework that integrates scarce quantitative expression data wi…
Accurate forecasting of blood glucose concentration is key in the management of Type 1 Diabetes, facilitating early detection of adverse glycemic events and supporting timely therapeutic interventions. Despite recent advances in glucose prediction, most existing approaches rely o…