Table 5 Open in new tab Performance on...

Method	\|$\boldsymbol{F_{max}}$\|			\|$\boldsymbol{S_{min}}$\|			AUPR
HUMAN (9606)
Naive	0.475	0.309	0.623	5.244	27.744	6.934	0.330	0.235	0.612
DiamondBLAST	0.493	0.303	0.473	6.158	30.145	8.118	0.239	0.083	0.239
DiamondScore	0.547	0.349	0.500	4.492	26.173	7.118	0.364	0.130	0.309
DeepGOCNN	0.589	0.367	0.645	5.137	26.728	6.795	0.438	0.265	0.608
DeepGOPlus	0.593	0.400	0.631	4.684	26.809	6.896	0.479	0.231	0.577
LR-ESM	0.720	0.407	0.680	3.790	24.892	6.158	0.660	0.320	0.697
PredGO	0.733	0.435	0.686	3.722	24.620	5.990	0.672	0.341	0.715
MOUSE (10 090)
Naive	0.541	0.307	0.611	6.042	33.266	9.87	0.254	0.238	0.557
DiamondBLAST	0.421	0.311	0.518	5.502	33.686	10.409	0.208	0.100	0.267
DiamondScore	0.440	0.325	0.544	4.842	30.651	9.321	0.304	0.160	0.336
DeepGOCNN	0.595	0.340	0.626	5.950	32.473	9.777	0.303	0.240	0.553
DeepGOPlus	0.647	0.387	0.631	5.599	31.693	9.393	0.389	0.237	0.559
LR-ESM	0.673	0.384	0.634	4.584	30.157	9.424	0.516	0.339	0.612
PredGO	0.697	0.403	0.646	4.679	29.653	9.194	0.516	0.341	0.633
FISSION YEAST (284 812)
Naive	0.525	0.324	0.728	7.536	22.706	9.493	0.272	0.240	0.657
DiamondBLAST	0.593	0.464	0.617	6.587	24.762	11.955	0.345	0.257	0.324
DiamondScore	0.626	0.459	0.657	4.012	18.392	9.569	0.489	0.290	0.402
DeepGOCNN	0.502	0.341	0.726	7.647	23.189	9.556	0.283	0.196	0.597
DeepGOPlus	0.625	0.499	0.717	6.905	20.017	8.460	0.499	0.345	0.629
LR-ESM	0.772	0.503	0.800	5.231	18.339	8.922	0.599	0.408	0.731
PredGO	0.789	0.521	0.782	4.731	18.183	8.771	0.642	0.436	0.766

Method

|$\boldsymbol{F_{max}}$|

|$\boldsymbol{S_{min}}$|

AUPR

MFO

BPO

CCO

MFO

BPO

CCO

MFO

BPO

CCO

HUMAN (9606)

Naive

0.475

0.309

0.623

5.244

27.744

6.934

0.330

0.235

0.612

DiamondBLAST

0.493

0.303

0.473

6.158

30.145

8.118

0.239

0.083

0.239

DiamondScore

0.547

0.349

0.500

4.492

26.173

7.118

0.364

0.130

0.309

DeepGOCNN

0.589

0.367

0.645

5.137

26.728

6.795

0.438

0.265

0.608

DeepGOPlus

0.593

0.400

0.631

4.684

26.809

6.896

0.479

0.231

0.577

LR-ESM

0.720

0.407

0.680

3.790

24.892

6.158

0.660

0.320

0.697

PredGO

0.733

0.435

0.686

3.722

24.620

5.990

0.672

0.341

0.715

MOUSE (10 090)

Naive

0.541

0.307

0.611

6.042

33.266

9.87

0.254

0.238

0.557

DiamondBLAST

0.421

0.311

0.518

5.502

33.686

10.409

0.208

0.100

0.267

DiamondScore

0.440

0.325

0.544

4.842

30.651

9.321

0.304

0.160

0.336

DeepGOCNN

0.595

0.340

0.626

5.950

32.473

9.777

0.303

0.240

0.553

DeepGOPlus

0.647

0.387

0.631

5.599

31.693

9.393

0.389

0.237

0.559

LR-ESM

0.673

0.384

0.634

4.584

30.157

9.424

0.516

0.339

0.612

PredGO

0.697

0.403

0.646

4.679

29.653

9.194

0.516

0.341

0.633

FISSION YEAST (284 812)

Naive

0.525

0.324

0.728

7.536

22.706

9.493

0.272

0.240

0.657

DiamondBLAST

0.593

0.464

0.617

6.587

24.762

11.955

0.345

0.257

0.324

DiamondScore

0.626

0.459

0.657

4.012

18.392

9.569

0.489

0.290

0.402

DeepGOCNN

0.502

0.341

0.726

7.647

23.189

9.556

0.283

0.196

0.597

DeepGOPlus

0.625

0.499

0.717

6.905

20.017

8.460

0.499

0.345

0.629

LR-ESM

0.772

0.503

0.800

5.231

18.339

8.922

0.599

0.408

0.731

PredGO

0.789

0.521

0.782

4.731

18.183

8.771

0.642

0.436

0.766

Method	\|$\boldsymbol{F_{max}}$\|			\|$\boldsymbol{S_{min}}$\|			AUPR
HUMAN (9606)
Naive	0.475	0.309	0.623	5.244	27.744	6.934	0.330	0.235	0.612
DiamondBLAST	0.493	0.303	0.473	6.158	30.145	8.118	0.239	0.083	0.239
DiamondScore	0.547	0.349	0.500	4.492	26.173	7.118	0.364	0.130	0.309
DeepGOCNN	0.589	0.367	0.645	5.137	26.728	6.795	0.438	0.265	0.608
DeepGOPlus	0.593	0.400	0.631	4.684	26.809	6.896	0.479	0.231	0.577
LR-ESM	0.720	0.407	0.680	3.790	24.892	6.158	0.660	0.320	0.697
PredGO	0.733	0.435	0.686	3.722	24.620	5.990	0.672	0.341	0.715
MOUSE (10 090)
Naive	0.541	0.307	0.611	6.042	33.266	9.87	0.254	0.238	0.557
DiamondBLAST	0.421	0.311	0.518	5.502	33.686	10.409	0.208	0.100	0.267
DiamondScore	0.440	0.325	0.544	4.842	30.651	9.321	0.304	0.160	0.336
DeepGOCNN	0.595	0.340	0.626	5.950	32.473	9.777	0.303	0.240	0.553
DeepGOPlus	0.647	0.387	0.631	5.599	31.693	9.393	0.389	0.237	0.559
LR-ESM	0.673	0.384	0.634	4.584	30.157	9.424	0.516	0.339	0.612
PredGO	0.697	0.403	0.646	4.679	29.653	9.194	0.516	0.341	0.633
FISSION YEAST (284 812)
Naive	0.525	0.324	0.728	7.536	22.706	9.493	0.272	0.240	0.657
DiamondBLAST	0.593	0.464	0.617	6.587	24.762	11.955	0.345	0.257	0.324
DiamondScore	0.626	0.459	0.657	4.012	18.392	9.569	0.489	0.290	0.402
DeepGOCNN	0.502	0.341	0.726	7.647	23.189	9.556	0.283	0.196	0.597
DeepGOPlus	0.625	0.499	0.717	6.905	20.017	8.460	0.499	0.345	0.629
LR-ESM	0.772	0.503	0.800	5.231	18.339	8.922	0.599	0.408	0.731
PredGO	0.789	0.521	0.782	4.731	18.183	8.771	0.642	0.436	0.766

Table 5

Open in new tab

Performance on different species

Method	\|$\boldsymbol{F_{max}}$\|			\|$\boldsymbol{S_{min}}$\|			AUPR
	MFO	BPO	CCO	MFO	BPO	CCO	MFO	BPO	CCO
HUMAN (9606)
Naive	0.475	0.309	0.623	5.244	27.744	6.934	0.330	0.235	0.612
DiamondBLAST	0.493	0.303	0.473	6.158	30.145	8.118	0.239	0.083	0.239
DiamondScore	0.547	0.349	0.500	4.492	26.173	7.118	0.364	0.130	0.309
DeepGOCNN	0.589	0.367	0.645	5.137	26.728	6.795	0.438	0.265	0.608
DeepGOPlus	0.593	0.400	0.631	4.684	26.809	6.896	0.479	0.231	0.577
LR-ESM	0.720	0.407	0.680	3.790	24.892	6.158	0.660	0.320	0.697
PredGO	0.733	0.435	0.686	3.722	24.620	5.990	0.672	0.341	0.715
MOUSE (10 090)
Naive	0.541	0.307	0.611	6.042	33.266	9.87	0.254	0.238	0.557
DiamondBLAST	0.421	0.311	0.518	5.502	33.686	10.409	0.208	0.100	0.267
DiamondScore	0.440	0.325	0.544	4.842	30.651	9.321	0.304	0.160	0.336
DeepGOCNN	0.595	0.340	0.626	5.950	32.473	9.777	0.303	0.240	0.553
DeepGOPlus	0.647	0.387	0.631	5.599	31.693	9.393	0.389	0.237	0.559
LR-ESM	0.673	0.384	0.634	4.584	30.157	9.424	0.516	0.339	0.612
PredGO	0.697	0.403	0.646	4.679	29.653	9.194	0.516	0.341	0.633
FISSION YEAST (284 812)
Naive	0.525	0.324	0.728	7.536	22.706	9.493	0.272	0.240	0.657
DiamondBLAST	0.593	0.464	0.617	6.587	24.762	11.955	0.345	0.257	0.324
DiamondScore	0.626	0.459	0.657	4.012	18.392	9.569	0.489	0.290	0.402
DeepGOCNN	0.502	0.341	0.726	7.647	23.189	9.556	0.283	0.196	0.597
DeepGOPlus	0.625	0.499	0.717	6.905	20.017	8.460	0.499	0.345	0.629
LR-ESM	0.772	0.503	0.800	5.231	18.339	8.922	0.599	0.408	0.731
PredGO	0.789	0.521	0.782	4.731	18.183	8.771	0.642	0.436	0.766

Method	\|$\boldsymbol{F_{max}}$\|			\|$\boldsymbol{S_{min}}$\|			AUPR
	MFO	BPO	CCO	MFO	BPO	CCO	MFO	BPO	CCO
HUMAN (9606)
Naive	0.475	0.309	0.623	5.244	27.744	6.934	0.330	0.235	0.612
DiamondBLAST	0.493	0.303	0.473	6.158	30.145	8.118	0.239	0.083	0.239
DiamondScore	0.547	0.349	0.500	4.492	26.173	7.118	0.364	0.130	0.309
DeepGOCNN	0.589	0.367	0.645	5.137	26.728	6.795	0.438	0.265	0.608
DeepGOPlus	0.593	0.400	0.631	4.684	26.809	6.896	0.479	0.231	0.577
LR-ESM	0.720	0.407	0.680	3.790	24.892	6.158	0.660	0.320	0.697
PredGO	0.733	0.435	0.686	3.722	24.620	5.990	0.672	0.341	0.715
MOUSE (10 090)
Naive	0.541	0.307	0.611	6.042	33.266	9.87	0.254	0.238	0.557
DiamondBLAST	0.421	0.311	0.518	5.502	33.686	10.409	0.208	0.100	0.267
DiamondScore	0.440	0.325	0.544	4.842	30.651	9.321	0.304	0.160	0.336
DeepGOCNN	0.595	0.340	0.626	5.950	32.473	9.777	0.303	0.240	0.553
DeepGOPlus	0.647	0.387	0.631	5.599	31.693	9.393	0.389	0.237	0.559
LR-ESM	0.673	0.384	0.634	4.584	30.157	9.424	0.516	0.339	0.612
PredGO	0.697	0.403	0.646	4.679	29.653	9.194	0.516	0.341	0.633
FISSION YEAST (284 812)
Naive	0.525	0.324	0.728	7.536	22.706	9.493	0.272	0.240	0.657
DiamondBLAST	0.593	0.464	0.617	6.587	24.762	11.955	0.345	0.257	0.324
DiamondScore	0.626	0.459	0.657	4.012	18.392	9.569	0.489	0.290	0.402
DeepGOCNN	0.502	0.341	0.726	7.647	23.189	9.556	0.283	0.196	0.597
DeepGOPlus	0.625	0.499	0.717	6.905	20.017	8.460	0.499	0.345	0.629
LR-ESM	0.772	0.503	0.800	5.231	18.339	8.922	0.599	0.408	0.731
PredGO	0.789	0.521	0.782	4.731	18.183	8.771	0.642	0.436	0.766

Note: Best performance in bold.

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