WOMBAT is a benchmark comprising 14 whitebox graph neural networks (GNNs) whose message‑passing weights are manually set to detect specific SMARTS motifs. Each model’s decision rule is explicitly known, providing a ground truth for attribution that allows researchers to identify and study errors in post‑hoc explainers such as GNNExplainer, PGExplainer, and Integrated Gradients. The authors validate the models on millions of PubChem molecules, demonstrate how Integrated Gradients can be misled to spread attribution, and release the dataset, models, and evaluation code for future XAI tool development.
By Dominik Matuszek, Bartosz Zieli\'nski, Tomasz Danel, Dawid Rymarczyk
arXiv:2609.37555v1 Announce Type: new
Abstract: Drug discovery is a costly and high-risk process, where toxicity-related failures remain a major cause of attrition in both preclinical and clinical st...
By Noel Suarez-Barro, Manuel Lama, Juan C. Vidal
The paper introduces a fragment‑level graph encoding for molecular property prediction, using BRICS decomposition to represent molecules as graphs of synthetically meaningful fragments. This change of input representation allows any message‑passing GNN and post‑hoc attribution method to produce explanations at the functional‑group level, matching atom‑level accuracy on smaller graphs. Experiments across multiple architectures, tasks, and explainers show that fragment‑level encoding recovers known pharmacophores more reliably than post‑hoc aggregation of atom‑level explanations.
By Rafael Lopes Almeida (School of Pharmacy, University of Eastern Finland, Kuopio, Finland), Ina P\"ohner (School of Pharmacy, University of Eastern Finland, Kuopio, Finland)
arXiv:2506. 13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery.
By Han Liu, Keyan Ding, Peilin Chen, Yinwei Wei, Liqiang Nie, Dapeng Wu, Shiqi Wang
arXiv:2608.30636v1 Announce Type: new
Abstract: Optimizing absorption, distribution, metabolism, and excretion (ADME) is an important part of small molecule drug discovery. Many machine learning mode...
By Christina X. Ji
arXiv:2607. 02212v1 Announce Type: cross Abstract: Aqueous solubility is a key property in early-stage drug discovery, but most predictive models merge physicochemical descriptors and molecular graph information into a single representation, obscuring whether a prediction is driven by global chemistry, molecular structure, or both.
By Sampreeti Bhattacharya, Arkaprava Roy