RDKit-Guided Topological State Machine (TSM) for constrained SMILES generation with OLMo-7B. Solves BPE-tokenizer mismatch via RDKit-in-the-loop decoding. Achieved 100% validity on allenai/OLMo-7B-hf.
Empirical analysis quantifying the 0.009 ROC-AUC gap between PyTorch GNNs (2D graphs) and OLMo-7B (1D SMILES) on Tox21. Exposes the Random Split illusion and provides the baseline justification for Topological State Machine (TSM) integration.
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