Pretrained molecular embedding models spanning graph neural networks, text transformers, and hybrid architectures have been widely used in drug discovery, yet no large-scale, rigorous comparison of their representations existed. We evaluated 28 models across 25 classification datasets under a controlled framework using hierarchical Bayesian Bradley-Terry statistical testing. All neural models except CheMeleon failed to outperform the classical ECFP count fingerprint; CheMeleon was the only model rated as better. However, further testing on external validation datasets, based on scaffold cross-validation and a Bayesian hierarchical correlated t-test, revealed no definite advantage of either embedding method. As a practical takeaway, we recommend evaluating both ECFP fingerprints and CheMeleon embeddings in novel QSAR/QSPR studies. Overall, in the context of all neural networks evaluated, these results also challenge the perceived progress in molecular representation learning and highlight the need for rigorous evaluation standards in the field.

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