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Table 3 Results on MKL Experiments on 5 × 5 cross-validation experiments

From: A multiple kernel learning algorithm for drug-target interaction prediction

Dataset

Combination

Pairs

Targets

Drugs

NR

[SPEC-k4]-[AERS-freq] †

0.4630

(±0.0215)

0.3851

(±0.0254)

0.2341

(±0.0054)

 

[SPEC-k4]-[GIP] ∗

0.5187

(±0.0255)

0.3725

(±0.0247)

0.0949

(±0.0068)

 

BLM-KA

0.0709

(±0.0048)

0.3441

(±0.0264)

0.3130

(±0.0224)

 

BLM-MEAN

0.0685

(±0.0062)

0.3453

(±0.0264)

0.2934

(±0.0154)

 

KBMF2MKL

0.2041

(±0.0150)

0.2059

(±0.0388)

0.1459

(±0.0272)

 

KRONRLS-KA

0.4321

(±0.0147)

0.3489

(±0.0337)

0.2850

(±0.0126)

 

KRONRLS-MEAN

0.4078

(±0.0211)

0.3482

(±0.0341)

0.2665

(±0.0109)

 

KRONRLS-MKL

0.5368

(±0.0137)

0.3541

(±0.0321)

0.3383

(±0.0224)

 

LAPRLS-KA

0.1989

(±0.0207)

0.2120

(±0.0277)

0.1841

(±0.0044)

 

LAPRLS-MEAN

0.1870

(±0.0196)

0.2008

(±0.0251)

0.1832

(±0.0022)

 

NETLAPRLS-KA

0.2310

(±0.0277)

0.2091

(±0.0288)

0.1841

(±0.0044)

 

NETLAPRLS-MEAN

0.2195

(±0.0273)

0.1989

(±0.0263)

0.1831

(±0.0023)

 

NRWRH-KA

–

–

0.1776

(±0.0380)

0.1911

(±0.0116)

 

NRWRH-MEAN

–

–

0.1755

(±0.0364)

0.1881

(±0.0109)

 

PKM-KA

0.1830

(±0.0114)

0.2363

(±0.0387)

0.1741

(±0.0158)

 

PKM-MAX

0.0946

(±0.0188)

0.0774

(±0.0108)

0.1174

(±0.0080)

 

PKM-MEAN

0.1702

(±0.0099)

0.2163

(±0.0400)

0.1672

(±0.0152)

 

SITAR

0.4477

(±0.0658)

0.1396

(±0.0505)

0.0694

(±0.0189)

 

WANG-MKL

0.3293

(±0.0175)

0.2238

(±0.0300)

0.2628

(±0.0225)

GPCR

[SPEC-k4]-[MINMAX] †

0.3246

(±0.0093)

0.5053

(±0.0322)

0.0924

(±0.0055)

 

[SW]-[GIP] ∗

0.6188

(±0.0075)

0.4561

(±0.0201)

0.0419

(±0.0014)

 

BLM-KA

0.0633

(±0.0071)

0.5508

(±0.0123)

0.3000

(±0.0198)

 

BLM-MEAN

0.0519

(±0.0032)

0.5353

(±0.0135)

0.2526

(±0.0188)

 

KBMF2MKL

0.4960

(±0.0124)

0.0963

(±0.0346)

0.1408

(±0.0120)

 

KRONRLS-KA

0.6208

(±0.0081)

0.4727

(±0.0101)

0.3005

(±0.0148)

 

KRONRLS-MEAN

0.6213

(±0.0085)

0.4461

(±0.0086)

0.2731

(±0.0155)

 

KRONRLS-MKL

0.6440

(±0.0052)

0.4127

(±0.0126)

0.3161

(±0.0112)

 

LAPRLS-KA

0.2183

(±0.0067)

0.1458

(±0.0050)

0.1210

(±0.0058)

 

LAPRLS-MEAN

0.2169

(±0.0066)

0.1369

(±0.0049)

0.1215

(±0.0061)

 

NETLAPRLS-KA

0.3763

(±0.0096)

0.1451

(±0.0041)

0.1211

(±0.0062)

 

NETLAPRLS-MEAN

0.3841

(±0.0088)

0.1357

(±0.0039)

0.1221

(±0.0061)

 

NRWRH-KA

–

–

0.0762

(±0.0041)

0.1201

(±0.0088)

 

NRWRH-MEAN

–

–

0.0704

(±0.0036)

0.1176

(±0.0099)

 

PKM-KA

0.2625

(±0.0133)

0.2327

(±0.0175)

0.1424

(±0.0146)

 

PKM-MAX

0.1230

(±0.0106)

0.0652

(±0.0071)

0.0935

(±0.0044)

 

PKM-MEAN

0.2613

(±0.0178)

0.1632

(±0.0186)

0.1254

(±0.0107)

 

SITAR

0.5324

(±0.0267)

0.1151

(±0.0538)

0.0283

(±0.0110)

 

WANG-MKL

0.4240

(±0.0071)

0.3521

(±0.0111)

0.2686

(±0.0274)

IC

[PPI]-[GIP] †

0.6789

(±0.0078)

0.1548

(±0.0020)

0.0467

(±0.0009)

 

[SW]-[GIP] ∗

0.8679

(±0.0056)

0.7301

(±0.0140)

0.0476

(±0.0008)

 

BLM-KA

0.1169

(±0.0127)

0.7944

(±0.0047)

0.2516

(±0.0304)

 

BLM-MEAN

0.1106

(±0.0088)

0.7798

(±0.0040)

0.2152

(±0.0257)

 

KBMF2MKL

0.7671

(±0.0033)

0.4420

(±0.0141)

0.0856

(±0.0044)

 

KRONRLS-KA

0.8553

(±0.0017)

0.7246

(±0.0071)

0.2039

(±0.0190)

 

KRONRLS-MEAN

0.8693

(±0.0011)

0.6885

(±0.0067)

0.1887

(±0.0186)

 

KRONRLS-MKL

0.8769

(±0.0011)

0.6894

(±0.0056)

0.2406

(±0.0259)

 

LAPRLS-KA

0.3088

(±0.0021)

0.2747

(±0.0031)

0.0942

(±0.0022)

 

LAPRLS-MEAN

0.3187

(±0.0024)

0.2760

(±0.0032)

0.0939

(±0.0021)

 

NETLAPRLS-KA

0.5359

(±0.0065)

0.2750

(±0.0032)

0.0931

(±0.0022)

 

NETLAPRLS-MEAN

0.5560

(±0.0073)

0.2766

(±0.0034)

0.0928

(±0.0023)

 

NRWRH-KA

–

–

0.2371

(±0.0046)

0.0720

(±0.0026)

 

NRWRH-MEAN

–

–

0.2363

(±0.0042)

0.0712

(±0.0024)

 

PKM-KA

0.5133

(±0.0235)

0.4151

(±0.0092)

0.1156

(±0.0041)

 

PKM-MAX

0.1608

(±0.0132)

0.1673

(±0.0038)

0.0660

(±0.0031)

 

PKM-MEAN

0.5474

(±0.0261)

0.3840

(±0.0062)

0.0998

(±0.0019)

 

SITAR

0.7505

(±0.0153)

0.1717

(±0.0633)

0.0174

(±0.0046)

 

WANG-MKL

0.7116

(±0.0214)

0.6009

(±0.0158)

0.2217

(±0.0124)

E

[GO]-[GIP] †

0.6900

(±0.0032)

0.2371

(± 0.0025)

0.0124

(±0.0004)

 

[SW]-[GIP] ∗

0.8429

(±0.00540)

0.7438

(± 0.0189)

0.0159

(±0.0003)

 

BLM-KA

0.0471

(±0.0045)

0.8201

(±0.0070)

0.2506

(±0.0060)

 

BLM-MEAN

0.0374

(±0.0032)

0.8099

(±0.0063)

0.2079

(±0.0051)

 

KBMF2MKL

0.6722

(±0.0051)

0.0757

(±0.0049)

0.0213

(±0.0004)

 

KRONRLS-KA

0.8630

(±0.0127)

0.7274

(±0.0071)

0.1829

(±0.0034)

 

KRONRLS-MEAN

0.8667

(±0.0098)

0.6917

(±0.0062)

0.1655

(±0.0030)

 

KRONRLS-MKL

0.8818

(±0.0128)

0.7384

(±0.0063)

0.2168

(±0.0050)

 

LAPRLS-KA

0.1920

(±0.0014)

0.1677

(±0.0072)

0.0682

(±0.0012)

 

LAPRLS-MEAN

0.1750

(±0.0015)

0.1402

(±0.0055)

0.0646

(±0.0013)

 

NETLAPRLS-KA

0.2853

(±0.0024)

0.1669

(±0.0042)

0.0670

(±0.0018)

 

NETLAPRLS-MEAN

0.2548

(±0.0019)

0.1402

(±0.0046)

0.0636

(±0.0016)

 

NRWRH-KA

–

–

0.0886

(±0.0011)

0.0403

(±0.0024)

 

NRWRH-MEAN

–

–

0.0816

(±0.0006)

0.0383

(±0.0018)

 

PKM-KA

0.2383

(±0.0069)

0.1905

(±0.0047)

0.0480

(±0.0037)

 

PKM-MAX

0.0762

(±0.0011)

0.0597

(±0.0007)

0.0323

(±0.0007)

 

PKM-MEAN

0.2161

(±0.0072)

0.1239

(±0.0032)

0.0382

(±0.0031)

 

SITAR

0.7558

(±0.0160)

0.0232

(±0.0151)

0.0097

(±0.0111)

 

WANG-MKL

0.7286

(±0.0046)

0.6663

(±0.0069)

0.1648

(±0.0042)

  1. Best performing methods are indicated in bold. Standart deviation is indicated in brackets. Training of the PKM, SITAR and WANG algorithms was done with the balanced training set
  2. †best on training
  3. ∗best on testing
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BMC Bioinformatics

ISSN: 1471-2105

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