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Table 8 Comparison of the Se, Sp, ACC and MCC between seven traditional models and the evolutionary information model on Dataset 1

From: Accurate classification of membrane protein types based on sequence and evolutionary information using deep learning

Membrane protein types

Index

PsePSSM

RPSSM

EDPSSM

KPSSM

CPSSM

CoPSSM

TriPSSM

Our model

 

Se

0.9122

0.8761

0.8491

0.9054

0.8739

0.8806

0.9122

0.9144

Type I

Sp

0.9776

0.9733

0.9622

0.9859

0.9666

0.9781

0.9884

0.9920

 

ACC

0.9709

0.9633

0.9506

0.9776

0.9571

0.9682

0.9806

0.9841

 

MCC

0.8505

0.8112

0.7546

0.8800

0.7856

0.8328

0.8953

0.9129

 

Se

0.7308

0.6410

0.5256

0.6923

0.4231

0.6923

0.8205

0.8462

Type II

Sp

0.9927

0.9918

0.9960

0.9913

0.9979

0.9922

0.9929

0.9944

 

ACC

0.9880

0.9855

0.9875

0.9859

0.9875

0.9868

0.9898

0.9912

 

MCC

0.6819

0.6067

0.6035

0.6339

0.5713

0.6489

0.7424

0.7748

 

Se

0.1667

0.0

0.0

0.1667

0.0

0.0

0.1667

0.1667

Type III

Sp

1.0

0.9998

1.0

1.0

1.0

1.0

1.0

0.9993

 

ACC

0.9988

0.9984

0.9986

0.9988

0.9986

0.9986

0.9988

0.9984

 

MCC

0.4080

-0.0006

0.0

0.4080

0.0

0.0

0.4080

0.2032

 

Se

0.4167

0.5000

0.4167

0.6667

0.0833

0.3333

0.6667

0.75

Type IV

Sp

0.9995

0.9993

1.0

0.9995

1.0

0.9998

0.9995

0.9995

 

ACC

0.9979

0.9979

0.9984

0.9986

0.9975

0.9979

0.9986

0.9982

 

MCC

0.5446

0.5763

0.6450

0.7296

0.2883

0.5156

0.7296

0.7828

 

Se

0.9275

0.9394

0.9219

0.9495

0.9305

0.9326

0.9553

0.9593

Mutipass

Sp

0.9654

0.9438

0.8305

0.9625

0.9026

0.9682

0.9691

0.9785

 

ACC

0.9444

0.9405

0.8994

0.9527

0.9236

0.9414

0.9587

0.9640

 

MCC

0.8619

0.8493

0.7360

0.8799

0.8042

0.8560

0.8947

0.9083

 

Se

0.3158

0.2368

0.2105

0.3684

0.2105

0.3684

0.3158

0.6053

Lipid-chain-anchored

Sp

0.9986

0.9979

0.9977

0.9984

0.9991

0.9972

0.9970

0.9960

 

ACC

0.9926

0.9912

0.9908

0.9928

0.9922

0.9917

0.9910

0.9926

 

MCC

0.4557

0.3403

0.3018

0.4924

0.3719

0.4414

0.3850

0.5862

 

Se

0.6522

0.5217

0.3913

0.6957

0.3913

0.7174

0.6957

0.8043

GPI-anchored

Sp

0.9963

0.9986

0.9967

0.9986

0.9988

0.9951

0.9984

0.9963

 

ACC

0.9926

0.9935

0.9903

0.9954

0.9924

0.9922

0.9952

0.9942

 

MCC

0.6484

0.6431

0.4645

0.7631

0.5503

0.6582

0.7531

0.7465

 

Se

0.9077

0.8536

0.6824

0.8784

0.8176

0.8851

0.8964

0.9009

Peripheral

Sp

0.9537

0.9509

0.9481

0.9524

0.9403

0.9452

0.9578

0.9637

 

ACC

0.9490

0.9409

0.9208

0.9448

0.9278

0.9391

0.9515

0.9573

 

MCC

0.7655

0.7218

0.5959

0.7427

0.6678

0.7260

0.7711

0.7933

  1. Note: Best performing method in bold.