arXiv AI
ReLaG: A Scalable Framework Generalizing Random Splits to Data with Latent Relations
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arXiv Machine Learning
Jul 23
Refnd: Preventing Data Leakage in Relational Datasets
arXiv:2607. 19376v1 Announce Type: cross Abstract: 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.
arXiv AI
Jun 16
Spokes: Optimizing for Diverse Pretraining Data Selection
arXiv:2606. 15216v1 Announce Type: cross Abstract: Diversity plays a critical role in data selection, improving performance under fixed data budgets by reducing redundancy and repetition.
arXiv AI
Jun 3
TadA-Bench: A Million-Variant Benchmark for Future-Round Discovery Toward Agentic Protein Engineering
arXiv:2606. 02624v1 Announce Type: cross Abstract: AI for scientific discovery is entering an agentic era, where protein-engineering systems are expected to prioritize future wet-lab experiments rather than merely fit static measurements.
arXiv AI
Jul 3
MKGR: Multimodal Knowledge-Graph Representation Learning for Cold-Start Protein-Protein Interaction Prediction
arXiv:2607. 01627v1 Announce Type: cross Abstract: Accurate protein-protein interaction (PPI) prediction is central to functional genomics, disease mechanism discovery, and drug development.
arXiv AI
Jul 13
TheBioCollection: Unified Pre-Training Scale LLM Corpus for Biology
arXiv:2607. 08803v1 Announce Type: cross Abstract: The push toward large language models for biology (BioLM) has created a need for training corpora that can endow models with a genuine understanding of biology.
arXiv Machine Learning
Aug 20
Monroe: A Molecular Foundation Model for In-Context Probabilistic Inference
Monroe is a new molecular foundation model that improves upon existing models by pre‑training on over 81 million molecules from the PM6 quantum chemistry dataset, enhancing stereochemistry representation, and introducing novel training losses such as conformer denoising and embedding decorrelation. It also incorporates a prior‑data‑fitted model (TabPFN) for downstream in‑context prediction and demonstrates superior performance on Polaris benchmarks and activity cliff tests. Ablation studies show that the PFN‑based downstream approach can upgrade other models, producing state‑of‑the‑art variants MiniMol_PFN and CheMeleon_PFN.