The Accuracy Paradox: Empirical Diagnostic of Default Decision Thresholds in Multi-Label Enzyme Commission Prediction [With Code]

תקציר מקורי באנגליתarXiv:2609.07897v1 Announce Type: cross Abstract: Automated prediction of Enzyme Commission (EC) numbers plays a central role in functional annotation and computational drug discovery. However, standard multi-label machine learning pipelines frequently rely on default decision thresholds (t=0.50), assuming balanced prior distributions across target heads. In this study, we present a systematic empirical diagnostic of uncalibrated fixed decision boundaries operating under severe class imbalance across N = 14,096 annotated compounds categorized into six primary EC classes (EC1-EC6). Our results highlight a pronounced Accuracy Paradox: while the multi-label system achieves a deceivingly high mean accuracy of 77.16%, the macro F1-score (0.3976) and macro recall (0.3872) reveal severe predictiv