arXiv:2608. 04257v1 Announce Type: new Abstract: Blood-brain barrier permeability (BBBP) prediction is a critical screening task in central nervous system drug discovery, where candidate molecules must be assessed for whether they can cross, or should be prevented from crossing, the blood-brain barrier.
By Marco Vieto Vega, Long D. Nguyen, Binh P. Nguyen
The paper introduces a new algorithm that uses decision trees and random forests to estimate individual treatment effects while providing interpretability. It modifies the standard random forest splitting criterion by combining a heterogeneity-focused criterion with a bias-correction criterion, enabling the model to handle observational studies with varying treatment propensities without separately estimating propensity scores. The resulting tree structure directly reveals which features drive treatment effect differences, and simulation studies show the method matches or surpasses existing approaches in prediction accuracy while improving interpretability.
By Nicolas Alexander Ihlo, Merle Behr
arXiv:2608. 11444v1 Announce Type: cross Abstract: Drug response prediction (DRP) models are an active area of research in pharmacogenomics, with growing potential to accelerate the identification of effective anticancer drugs.
By Vincent Lavelle, Yitan Zhu, Kaitlyn Marlor, Thomas Brettin, Rick Stevens
arXiv:2606. 08973v1 Announce Type: cross Abstract: Fundamental investigations into how different molecular encoding methods affect molecular property prediction remain relatively limited.
By Sheng-Ya Chen, Shan-Ju Yeh
arXiv:2603. 02221v2 Announce Type: replace-cross Abstract: In clinical tabular prediction, classical machine learning models with feature engineering often outperform neural methods.
By Zizheng Zhang, Yiming Li, Justin Xu, Jinyu Wang, Rui Wang, Lei Song, Jiang Bian, David W Eyre, Jingjing Fu
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.
By Blazej Banaszewski, Andrew W. Fitzgibbon