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Table 9 Comparison of the Se, Sp, ACC and MCC between seven traditional models and the evolutionary information model on Dataset 2

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

TPSSM

Our model

 

Se

0.8571

0.7633

0.7265

0.7959

0.7633

0.7673

0.8653

0.8082

Type I

Sp

0.9586

0.9574

0.9512

0.9705

0.9556

0.9550

0.9759

0.9845

 

ACC

0.9517

0.9442

0.9359

0.9587

0.9426

0.9423

0.9684

0.9725

 

MCC

0.6943

0.6290

0.5821

0.7048

0.6224

0.6229

0.7748

0.7853

 

Se

0.4304

0.4051

0.3038

0.4810

0.2785

0.4304

0.4557

0.4684

Type II

Sp

0.9887

0.9881

0.9904

0.9889

0.9952

0.0.9858

0.9906

0.9901

 

ACC

0.9764

0.9753

0.9753

0.9778

0.9795

0.9736

0.9789

0.9786

 

MCC

0.4327

0.4059

0.3423

0.4759

0.3873

0.4039

0.4769

0.4797

 

Se

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.1111

Type III

Sp

1.0

1.0

1.0

1.0

1.0

1.0

1.0

0.9958

 

ACC

0.9975

0.9975

0.9975

0.9975

0.9975

0.9975

0.9975

0.9936

 

MCC

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0803

 

Se

0.1765

0.1176

0.0588

0.3529

0.1176

0.2353

0.3529

0.3529

Type IV

Sp

0.9994

0.9997

1.0

1.0

1.0

1.0

1.0

0.9980

 

ACC

0.9956

0.9956

0.9956

0.9969

0.9958

0.9964

0.9969

0.9950

 

MCC

0.3238

0.2788

0.2420

0.5932

0.3423

0.4842

0.5932

0.4011

 

Se

0.9044

0.8971

0.8882

0.9350

0.9023

0.8910

0.9435

0.9443

Mutipass

Sp

0.9494

0.9050

0.7655

0.9263

0.8712

0.9334

0.9316

0.9574

 

ACC

0.9184

0.8996

0.8499

0.9323

0.8926

0.9043

0.9398

0.9484

 

MCC

0.8232

0.7776

0.6517

0.8464

0.7572

0.7930

0.8627

0.8839

 

Se

0.1111

0.0278

0.0833

0.0833

0.0278

0.0833

0.0833

0.6111

Lipid-chain-anchored

Sp

0.9986

0.9997

0.9997

0.9986

0.9994

0.9992

0.9983

0.9927

 

ACC

0.9897

0.9900

0.9906

0.9895

0.9897

0.9900

0.9892

0.9889

 

MCC

0.2186

0.1161

0.2480

0.1731

0.0939

0.2012

0.1627

0.5238

 

Se

0.4146

0.2927

0.2439

0.4146

0.2927

0.3902

0.4146

0.7073

GPI-anchored

Sp

0.9961

0.9986

0.9983

0.9949

0.9992

0.9983

0.9992

0.9966

 

ACC

0.9895

0.9906

0.9897

0.9914

0.9911

0.9881

0.9925

0.9933

 

MCC

0.4717

0.4508

0.3864

0.5381

0.4807

0.4226

0.5907

0.7039

 

Se

0.8884

0.8183

0.6581

0.8512

0.7883

0.8326

0.8741

0.8627

Peripheral

Sp

0.9253

0.9050

0.9112

0.9312

0.9046

0.9064

0.9377

0.9404

 

ACC

0.9181

0.8882

0.8621

0.9156

0.8821

0.8921

0.9254

0.9254

 

MCC

0.7616

0.6742

0.5635

0.7460

0.6513

0.6872

0.7752

0.7725

  1. Note: Best performing method in bold.