Table 2.

Results on the HPA independent test set

	Count	YLoc+	DeepLoc 1.0 β	Fuel-mLoc	LAProtT5	DeepLoc 2.0
		Animalα		Euk γ, θ		ESM1b	ProtT5
Type		Multi	Single	Multi	Single	Multi	Multi
Pred. Num. Labels (Actual: 1.22)		1.44	0.89	1.00	0.94	1.15	1.21
Accuracy	1717	0.23	0.37	0.38	0.45	0.34	0.39
Jaccard	1717	0.41	0.42	0.46	0.52	0.48	0.53
MicroF1	1717	0.51	0.46	0.52	0.56	0.57	0.60
MacroF1	1717	0.34	0.35	0.39	0.43	0.44	0.46
MCC per location (↑ is better)
Cytoplasm	562	0.14	0.23	0.23	0.33	0.29	0.36
Nucleus	893	0.20	0.28	0.41	0.45	0.41	0.44
Cell membrane	287	0.20	0.23	0.32	0.30	0.34	0.36
Mitochondrion	196	0.37	0.39	0.33	0.59	0.60	0.56
Endoplasmic reticulum	77	0.12	0.23	0.14	0.22	0.20	0.17
Golgi apparatus	86	0.08	0.10	0.24	0.26	0.17	0.31

Bold values indicate the best score

^α = GO-terms were not used

^β = Retrained on the new CV dataset

^γ = using local implementation

^θ = using reduced ProSeq database