Performance Metrics

TEST SET · n=525

Held-out test set. MMseqs2 30% similarity split prevents sequence-based data leakage.

max_τ 2PR/(P+R)

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Fmax (CAFA)

Primary CAFA metric. Threshold-independent. Macro-averaged over all test proteins.

∫₀¹ TPR d(FPR)

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AUROC

Area Under Receiver Operating Characteristic. Measures discriminative ability across all thresholds.

∫₀¹ P d(R)

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AUPRC

Area Under Precision-Recall Curve. Preferred for class-imbalanced GO annotation.

Per-Namespace F1

Metric Interpretation

Metric	Value	Context
Fmax=0.3212	Competitive	CAFA3 median for pathogen proteins is ~0.30–0.35. Multilabel GO prediction is inherently challenging.
AUROC=0.857	Strong	AUROC > 0.85 indicates the model discriminates positive/negative GO associations well at all thresholds.
AUPRC=0.218	Expected	AUPRC lower than AUROC is expected with class imbalance — most proteins do not have most GO terms.