Atom-Wise Allocation of Message-Passing Scale for Molecular Property Prediction

Regina Qianru Zhang, Honggang Wen, Zongru Li, Jinsong Ouyang, Zhiqin Chu +3

Molecular properties depend on chemical structure at different ranges, from local polar groups governing solvation to extended substructures shaping bioactivity, yet graph neural networks usually fix one propagation scale for every atom. We present PRISM (Per-atom Routing over Intermediate States of Message Passing), in which each atom's encoded features produce a bounded scalar that positions a unimodal distribution over retained message-passing states and matching circular-fingerprint radii. Because one coordinate translates the whole profile, allocated depth responds to the routing scalar in closed form: at fixed temperature it is nondecreasing, its sensitivity scales with the profile variance, and it saturates in the clipped regions. Beyond providing closed-form analyzability, this constrained one-parameter profile matches or significantly outperforms parameter-matched, unconstrained node-wise gates and Jumping Knowledge attention. Under scaffold partitions with equal tuning budgets against eight graph, fingerprint, and geometric baselines, PRISM trained from scratch without three-dimensional coordinates achieves the lowest mean error on aqueous solubility and hydration free…