Rhizome OS-1: Rhizome's Semi-Autonomous Operating System for Small Molecule Drug Discovery

Abstract: We introduce a semi-autonomous discovery system in which multi-modal AI agents function as a multi-disciplinary discovery team, acting as computational chemists, medicinal chemists, and patent agents, writing and executing analysis code, visually evaluating molecular candidates, assessing patentability, and adapting generation strategy from empirical screening feedback, while r1, a 246M-parameter Graph Neural Network (GNN) trained on 800M molecules, generates novel chemical matter directly on molecular graphs. Agents executed two campaigns in oncology (BCL6, EZH2), formulating medicinal chemistry hypotheses across three strategy tiers and generating libraries of 2,355-2,876 novel molecules per target. Across both targets, 91.9% of generated Murcko scaffolds are absent from ChEMBL for their respective targets, with Tanimoto distances of 0.56-0.69 to the nearest known active, confirming that the engine produces structurally distinct chemical matter rather than recapitulating known compounds. Binding affinity predictions using Boltz-2 were calibrated against ChEMBL experimental data, achieving Spearman correlations of -0.53 to -0.64 and ROC AUC values of 0.88 to 0.93. These results demonstrate that semi-autonomous agent systems, equipped with graph-native generative tools and physics-informed scoring, provide a foundation for a modern operating system for small molecule discovery. We show that Rhizome OS-1 enables a new paradigm for early-stage drug discovery by supporting scaled, rapid, and adaptive inverse design.