AILDRvN

mean_test_score [0.91880158 0.91880158 0.91879668 0.91882867 0.91852982 0.91852982

0.91852982 0.91852982 0.91832732 0.91832732 0.91832732 0.91832732

0.91766838 0.91766838 0.91766838 0.91766838 0.92154691 0.92154691

0.92169895 0.92177604 0.92156682 0.92156682 0.92156682 0.92156682

0.92063025 0.92063025 0.92063025 0.92063025 0.92063238 0.92063238

0.92063238 0.92063238 0.92374512 0.92374512 0.92388471 0.92359933

0.92293282 0.92293282 0.92293282 0.92293282 0.92214013 0.92214013

0.92214013 0.92214013 0.92044339 0.92044339 0.92044339 0.92044339

0.92526689 0.92526689 0.92489439 0.92457887 0.92387256 0.92387256

0.92387256 0.92387256 0.92169011 0.92169011 0.92169011 0.92169011

0.91999839 0.91999839 0.91999839 0.91999839 0.92636605 0.92636605

0.92581518 0.92629364 0.92462329 0.92462329 0.92462329 0.92462329

0.92147023 0.92147023 0.92147023 0.92147023 0.91838064 0.91838064

0.91838064 0.91838064]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 3, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.93 0.59 0.94 0.95 0.92 0.7

STD 0.003 0.005 0.002 0.001 0.003 0.008

Number of act mutations in the train set: 896

Number of deact mutations in the train set: 145

########################

Feature Importance

9 bpsh_0 0.073051

6 specParalogs_0 0.061039

4 allHomologs_0 0.058078

8 bpso_0 0.057870

7 orthologs_0 0.050552

10 D_A_0_pfam 0.045917

1 hmmScoreMUT 0.025796

3 p_0_pfam 0.025291

0 hmmScoreWT 0.023734

5 exclParalogs_0 0.022801

2 p_0 0.021951

11 D_D_0_pfam 0.020846

12 D_E_0_pfam 0.018336

########################

activatingresistance results ( 14 )

REC: 0.857

########################

########################

########################

P46734/MAP2K3/A84T 0.298 A

P11309/PIM1/S97N 0.356 A

########################

Q00535/CDK5/F82I 0.849 TBD

Q02750/MAP2K1/V211D 0.85 TBD

########################

O96017/CHEK2/K373E 0.82 Inconclusive

P06493/CDK1/V124G 0.825 Inconclusive

P46734/MAP2K3/R94L 0.694 Inconclusive

P46734/MAP2K3/R96W 0.779 Inconclusive

P46734/MAP2K3/L215W 0.861 Inconclusive

P46734/MAP2K3/T222M 0.926 Inconclusive

P11309/PIM1/Q127E 0.376 Inconclusive

Q06418/TYRO3/V669L 0.53 Inconclusive

Q13470/TNK1/A299D 0.219 Inconclusive

########################

P00533/EGFR/T790M 0.676 TBDincreaseresistance

########################

REC: neutral 0.979

########################

REC: loss 0.0

########################

REC: decrease 0.0

ALRvN

mean_test_score [0.94706829 0.94706829 0.94684167 0.94660926 0.94623975 0.94623975

0.94623975 0.94623975 0.94575606 0.94575606 0.94575606 0.94575606

0.94499978 0.94499978 0.94499978 0.94499978 0.95036313 0.95036313

0.95013522 0.95035335 0.94959712 0.94959712 0.94959712 0.94959712

0.9490823 0.9490823 0.9490823 0.9490823 0.94793646 0.94793646

0.94793646 0.94793646 0.95272472 0.95272472 0.95261328 0.95258335

0.95108612 0.95108612 0.95108612 0.95108612 0.94955595 0.94955595

0.94955595 0.94955595 0.94801951 0.94801951 0.94801951 0.94801951

0.955616 0.955616 0.95504417 0.95490247 0.95262011 0.95262011

0.95262011 0.95262011 0.95035199 0.95035199 0.95035199 0.95035199

0.94834955 0.94834955 0.94834955 0.94834955 0.95651064 0.95651064

0.95564583 0.95587704 0.95301435 0.95301435 0.95301435 0.95301435

0.94992446 0.94992446 0.94992446 0.94992446 0.94767938 0.94767938

0.94767938 0.94767938]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 3, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.96 0.71 0.94 0.95 0.93 0.79

STD 0.002 0.016 0.004 0.003 0.007 0.012

Number of act mutations in the train set: 557

Number of deact mutations in the train set: 145

########################

Feature Importance

6 specParalogs_0 0.070185

4 allHomologs_0 0.069944

10 D_A_0_pfam 0.059026

9 bpsh_0 0.055669

8 bpso_0 0.053669

0 hmmScoreWT 0.042969

7 orthologs_0 0.039746

5 exclParalogs_0 0.029403

1 hmmScoreMUT 0.027659

11 D_D_0_pfam 0.021788

2 ATPcount 0.019826

12 D_E_0_pfam 0.018728

3 p_0_pfam 0.015323

########################

activatingresistance results ( 14 )

REC: 0.857

########################

########################

########################

P46734/MAP2K3/A84T 0.219 A

P11309/PIM1/S97N 0.109 A

########################

Q00535/CDK5/F82I 0.816 TBD

Q02750/MAP2K1/V211D 0.772 TBD

########################

O96017/CHEK2/K373E 0.729 Inconclusive

P06493/CDK1/V124G 0.761 Inconclusive

P46734/MAP2K3/R94L 0.522 Inconclusive

P46734/MAP2K3/R96W 0.776 Inconclusive

P46734/MAP2K3/L215W 0.779 Inconclusive

P46734/MAP2K3/T222M 0.916 Inconclusive

P11309/PIM1/Q127E 0.41 Inconclusive

Q06418/TYRO3/V669L 0.438 Inconclusive

Q13470/TNK1/A299D 0.073 Inconclusive

########################

P00533/EGFR/T790M 0.675 TBDincreaseresistance

########################

REC: neutral 0.986

########################

REC: loss 0.0

########################

REC: decrease 0.773

AILDvN

mean_test_score [0.92921207 0.92921207 0.92924724 0.92919571 0.9293013 0.9293013

0.9293013 0.9293013 0.92882112 0.92882112 0.92882112 0.92882112

0.92827731 0.92827731 0.92827731 0.92827731 0.93077941 0.93077941

0.93081336 0.93105554 0.93087926 0.93087926 0.93087926 0.93087926

0.93067921 0.93067921 0.93067921 0.93067921 0.92979489 0.92979489

0.92979489 0.92979489 0.93243251 0.93243251 0.93217181 0.93191782

0.93115742 0.93115742 0.93115742 0.93115742 0.93042817 0.93042817

0.93042817 0.93042817 0.92969339 0.92969339 0.92969339 0.92969339

0.93276013 0.93276013 0.93297364 0.93273903 0.93259434 0.93259434

0.93259434 0.93259434 0.93168088 0.93168088 0.93168088 0.93168088

0.92967555 0.92967555 0.92967555 0.92967555 0.93357151 0.93357151

0.93475886 0.93343121 0.93157596 0.93157596 0.93157596 0.93157596

0.93033683 0.93033683 0.93033683 0.93033683 0.92853768 0.92853768

0.92853768 0.92853768]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 7, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.93 0.58 0.93 0.95 0.92 0.7

STD 0.002 0.008 0.002 0.001 0.003 0.006

Number of act mutations in the train set: 824

Number of deact mutations in the train set: 145

########################

Feature Importance

9 bpsh_0 0.063832

4 allHomologs_0 0.061637

7 orthologs_0 0.054151

6 specParalogs_0 0.051531

8 bpso_0 0.047415

10 D_A_0_pfam 0.042249

0 hmmScoreWT 0.033198

2 p_0 0.028926

5 exclParalogs_0 0.028362

12 D_E_0_pfam 0.026032

3 p_0_pfam 0.026014

1 hmmScoreMUT 0.024687

11 D_D_0_pfam 0.024546

########################

activatingresistance results ( 14 )

REC: 0.786

########################

########################

########################

P46734/MAP2K3/A84T 0.221 A

P11309/PIM1/S97N 0.319 A

########################

Q00535/CDK5/F82I 0.793 TBD

Q02750/MAP2K1/V211D 0.864 TBD

########################

O96017/CHEK2/K373E 0.807 Inconclusive

P06493/CDK1/V124G 0.799 Inconclusive

P46734/MAP2K3/R94L 0.621 Inconclusive

P46734/MAP2K3/R96W 0.745 Inconclusive

P46734/MAP2K3/L215W 0.826 Inconclusive

P46734/MAP2K3/T222M 0.902 Inconclusive

P11309/PIM1/Q127E 0.468 Inconclusive

Q06418/TYRO3/V669L 0.546 Inconclusive

Q13470/TNK1/A299D 0.171 Inconclusive

########################

P00533/EGFR/T790M 0.404 TBDincreaseresistance

########################

REC: neutral 0.986

########################

REC: loss 0.0

########################

REC: decrease 0.0

ALvN

mean_test_score [0.96348457 0.96348457 0.9633714 0.9631742 0.96309374 0.96309374

0.96309374 0.96309374 0.96288966 0.96288966 0.96288966 0.96288966

0.96242238 0.96242238 0.96242238 0.96242238 0.96602425 0.96602425

0.96624085 0.96558188 0.9648731 0.9648731 0.9648731 0.9648731

0.96445242 0.96445242 0.96445242 0.96445242 0.96337565 0.96337565

0.96337565 0.96337565 0.96595319 0.96595319 0.96595663 0.96558119

0.9650036 0.9650036 0.9650036 0.9650036 0.96420736 0.96420736

0.96420736 0.96420736 0.96315756 0.96315756 0.96315756 0.96315756

0.96721214 0.96721214 0.96722947 0.9673392 0.96586735 0.96586735

0.96586735 0.96586735 0.96454952 0.96454952 0.96454952 0.96454952

0.96334718 0.96334718 0.96334718 0.96334718 0.96753916 0.96753916

0.96705523 0.96673303 0.9652155 0.9652155 0.9652155 0.9652155

0.96380183 0.96380183 0.96380183 0.96380183 0.96332835 0.96332835

0.96332835 0.96332835]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 3, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.97 0.74 0.94 0.95 0.93 0.83

STD 0.002 0.013 0.003 0.005 0.005 0.016

Number of act mutations in the train set: 485

Number of deact mutations in the train set: 145

########################

Feature Importance

3 allHomologs_0 0.072219

8 bpsh_0 0.066740

9 D_A_0_pfam 0.062580

7 bpso_0 0.056850

5 specParalogs_0 0.051096

0 hmmScoreWT 0.043058

6 orthologs_0 0.042748

10 D_D_0_pfam 0.031090

4 exclParalogs_0 0.027716

11 D_E_0_pfam 0.022500

2 p_0_pfam 0.020712

1 hmmScoreMUT 0.019523

12 D_N_0_pfam 0.017297

########################

activatingresistance results ( 14 )

REC: 0.786

########################

########################

########################

P46734/MAP2K3/A84T 0.164 A

P11309/PIM1/S97N 0.117 A

########################

Q00535/CDK5/F82I 0.692 TBD

Q02750/MAP2K1/V211D 0.731 TBD

########################

O96017/CHEK2/K373E 0.672 Inconclusive

P06493/CDK1/V124G 0.696 Inconclusive

P46734/MAP2K3/R94L 0.514 Inconclusive

P46734/MAP2K3/R96W 0.664 Inconclusive

P46734/MAP2K3/L215W 0.707 Inconclusive

P46734/MAP2K3/T222M 0.917 Inconclusive

P11309/PIM1/Q127E 0.236 Inconclusive

Q06418/TYRO3/V669L 0.441 Inconclusive

Q13470/TNK1/A299D 0.062 Inconclusive

########################

P00533/EGFR/T790M 0.39 TBDincreaseresistance

########################

REC: neutral 0.993

########################

REC: loss 0.0

########################

REC: decrease 0.76

AIvNLD

mean_test_score [0.83470568 0.83470568 0.8350182 0.83558327 0.834419 0.834419

0.834419 0.834419 0.83477848 0.83477848 0.83477848 0.83477848

0.83266174 0.83266174 0.83266174 0.83266174 0.84498904 0.84498904

0.84513361 0.84502192 0.84358236 0.84358236 0.84358236 0.84358236

0.84321047 0.84321047 0.84321047 0.84321047 0.84184765 0.84184765

0.84184765 0.84184765 0.85107367 0.85107367 0.85114027 0.852609

0.85050281 0.85050281 0.85050281 0.85050281 0.84876851 0.84876851

0.84876851 0.84876851 0.8473457 0.8473457 0.8473457 0.8473457

0.85832341 0.85832341 0.85712977 0.8601059 0.85712915 0.85712915

0.85712915 0.85712915 0.85624224 0.85624224 0.85624224 0.85624224

0.85168838 0.85168838 0.85168838 0.85168838 0.86541387 0.86541387

0.86612187 0.86607719 0.86327004 0.86327004 0.86327004 0.86327004

0.85685654 0.85685654 0.85685654 0.85685654 0.8527271 0.8527271

0.8527271 0.8527271 ]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 7, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.86 0.49 0.56 0.66 0.51 0.94

STD 0.003 0.009 0.009 0.016 0.012 0.004

Number of act mutations in the train set: 179

Number of deact mutations in the train set: 790

########################

Feature Importance

1 hmmScoreMUT 0.034270

0 hmmScoreWT 0.031732

2 Phosphomimic 0.027003

6 exclParalogs_1 0.019809

12 D_A_0_pfam 0.019140

13 D_D_0_pfam 0.019077

8 allHomologs_2 0.016757

5 allHomologs_1 0.016644

10 specParalogs_2 0.016470

7 bpso_1 0.016447

4 bpso_0 0.016252

9 exclParalogs_2 0.015874

3 specParalogs_0 0.015692

11 orthologs_2 0.015188

########################

activatingresistance results ( 14 )

REC: 0.929

########################

########################

########################

P46734/MAP2K3/A84T 0.383 A

P11309/PIM1/S97N 0.299 A

########################

Q00535/CDK5/F82I 0.394 TBD

Q02750/MAP2K1/V211D 0.391 TBD

########################

O96017/CHEK2/K373E 0.584 Inconclusive

P06493/CDK1/V124G 0.385 Inconclusive

P46734/MAP2K3/R94L 0.522 Inconclusive

P46734/MAP2K3/R96W 0.31 Inconclusive

P46734/MAP2K3/L215W 0.323 Inconclusive

P46734/MAP2K3/T222M 0.31 Inconclusive

P11309/PIM1/Q127E 0.477 Inconclusive

Q06418/TYRO3/V669L 0.508 Inconclusive

Q13470/TNK1/A299D 0.497 Inconclusive

########################

P00533/EGFR/T790M 0.359 TBDincreaseresistance

########################

REC: neutral 0.993

########################

REC: loss 0.993

########################

REC: decrease 0.971

AIvLD

mean_test_score [0.8809525 0.8809525 0.88108657 0.88131707 0.88067023 0.88067023

0.88067023 0.88067023 0.87885842 0.87885842 0.87885842 0.87885842

0.87703328 0.87703328 0.87703328 0.87703328 0.88842227 0.88842227

0.88842945 0.88792106 0.88647245 0.88647245 0.88647245 0.88647245

0.88506252 0.88506252 0.88506252 0.88506252 0.88292283 0.88292283

0.88292283 0.88292283 0.89180079 0.89180079 0.89166966 0.89133847

0.88932795 0.88932795 0.88932795 0.88932795 0.88772936 0.88772936

0.88772936 0.88772936 0.88502671 0.88502671 0.88502671 0.88502671

0.89586749 0.89586749 0.89557154 0.89481448 0.89329383 0.89329383

0.89329383 0.89329383 0.89147255 0.89147255 0.89147255 0.89147255

0.88704746 0.88704746 0.88704746 0.88704746 0.8983604 0.8983604

0.89777877 0.89801062 0.89503088 0.89503088 0.89503088 0.89503088

0.89326021 0.89326021 0.89326021 0.89326021 0.88804198 0.88804198

0.88804198 0.88804198]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 3, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.89 0.55 0.65 0.62 0.69 0.88

STD 0.004 0.019 0.015 0.014 0.021 0.005

Number of act mutations in the train set: 179

Number of deact mutations in the train set: 645

########################

Feature Importance

1 hmmScoreMUT 0.041080

11 D_A_0_pfam 0.033575

0 hmmScoreWT 0.029653

12 D_D_0_pfam 0.024773

4 allHomologs_0 0.023197

7 bpsh_0 0.018998

3 A_MUT 0.018743

9 exclParalogs_2 0.018424

8 bpso_1 0.018358

6 bpso_0 0.018035

5 orthologs_0 0.017763

2 Phosphomimic 0.017499

15 D_S_0_pfam 0.017411

13 D_K_0_pfam 0.017018

10 orthologs_2 0.015234

14 D_N_0_pfam 0.015223

########################

activatingresistance results ( 14 )

REC: 0.929

########################

########################

########################

P46734/MAP2K3/A84T 0.575 A

P11309/PIM1/S97N 0.527 A

########################

Q00535/CDK5/F82I 0.555 TBD

Q02750/MAP2K1/V211D 0.475 TBD

########################

O96017/CHEK2/K373E 0.574 Inconclusive

P06493/CDK1/V124G 0.35 Inconclusive

P46734/MAP2K3/R94L 0.451 Inconclusive

P46734/MAP2K3/R96W 0.416 Inconclusive

P46734/MAP2K3/L215W 0.386 Inconclusive

P46734/MAP2K3/T222M 0.249 Inconclusive

P11309/PIM1/Q127E 0.607 Inconclusive

Q06418/TYRO3/V669L 0.678 Inconclusive

Q13470/TNK1/A299D 0.653 Inconclusive

########################

P00533/EGFR/T790M 0.467 TBDincreaseresistance

########################

REC: neutral 0.848

########################

REC: loss 0.988

########################

REC: decrease 0.913

AvNL

mean_test_score [0.88690844 0.88690844 0.88713047 0.8875896 0.88699626 0.88699626

0.88699626 0.88699626 0.88560195 0.88560195 0.88560195 0.88560195

0.88433474 0.88433474 0.88433474 0.88433474 0.89983399 0.89983399

0.9002225 0.90037145 0.89735919 0.89735919 0.89735919 0.89735919

0.89563716 0.89563716 0.89563716 0.89563716 0.89341699 0.89341699

0.89341699 0.89341699 0.90743528 0.90743528 0.90803938 0.90828012

0.90469262 0.90469262 0.90469262 0.90469262 0.89903638 0.89903638

0.89903638 0.89903638 0.89686565 0.89686565 0.89686565 0.89686565

0.91524051 0.91524051 0.91577768 0.91691886 0.91121871 0.91121871

0.91121871 0.91121871 0.90462757 0.90462757 0.90462757 0.90462757

0.90090311 0.90090311 0.90090311 0.90090311 0.91883675 0.91883675

0.91880411 0.91933656 0.90951328 0.90951328 0.90951328 0.90951328

0.90438 0.90438 0.90438 0.90438 0.90085826 0.90085826

0.90085826 0.90085826]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 10, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.92 0.59 0.6 0.82 0.49 0.98

STD 0.003 0.019 0.015 0.027 0.02 0.003

Number of act mutations in the train set: 82

Number of deact mutations in the train set: 548

########################

Feature Importance

2 Phosphomimic 0.031320

0 hmmScoreWT 0.030809

1 hmmScoreMUT 0.030472

9 bpso_0 0.024058

12 D_D_0_pfam 0.023588

3 ChargesMUT 0.021941

14 D_H_2_pfam 0.020835

13 D_N_0_pfam 0.019350

5 A_MUT 0.019328

4 ChargesDiff 0.018220

10 specParalogs_1 0.017601

11 A_Q_0_pfam 0.016831

8 orthologs_0 0.016208

6 allHomologs_0 0.015115

7 specParalogs_0 0.015082

########################

activatingresistance results ( 14 )

REC: 0.714

########################

########################

########################

P46734/MAP2K3/A84T 0.276 A

P11309/PIM1/S97N 0.224 A

########################

Q00535/CDK5/F82I 0.502 TBD

Q02750/MAP2K1/V211D 0.45 TBD

########################

O96017/CHEK2/K373E 0.579 Inconclusive

P06493/CDK1/V124G 0.298 Inconclusive

P46734/MAP2K3/R94L 0.481 Inconclusive

P46734/MAP2K3/R96W 0.285 Inconclusive

P46734/MAP2K3/L215W 0.283 Inconclusive

P46734/MAP2K3/T222M 0.352 Inconclusive

P11309/PIM1/Q127E 0.278 Inconclusive

Q06418/TYRO3/V669L 0.365 Inconclusive

Q13470/TNK1/A299D 0.359 Inconclusive

########################

P00533/EGFR/T790M 0.264 TBDincreaseresistance

########################

REC: neutral 1.0

########################

REC: loss 0.988

########################

REC: decrease 0.058

AvL

mean_test_score [0.94569618 0.94569618 0.94591078 0.9456596 0.9454762 0.9454762

0.9454762 0.9454762 0.94427862 0.94427862 0.94427862 0.94427862

0.94198162 0.94198162 0.94198162 0.94198162 0.95084155 0.95084155

0.95044381 0.95100826 0.94956724 0.94956724 0.94956724 0.94956724

0.94888508 0.94888508 0.94888508 0.94888508 0.94603946 0.94603946

0.94603946 0.94603946 0.95190883 0.95190883 0.95202253 0.95104196

0.94966789 0.94966789 0.94966789 0.94966789 0.95135078 0.95135078

0.95135078 0.95135078 0.9485061 0.9485061 0.9485061 0.9485061

0.95390502 0.95390502 0.9541601 0.95369013 0.95123518 0.95123518

0.95125042 0.95123518 0.95116518 0.95116518 0.95116518 0.95116518

0.94828184 0.94828184 0.94828184 0.94828184 0.95386488 0.95386488

0.95565354 0.95479141 0.95357224 0.95357224 0.95357224 0.95357224

0.95139998 0.95139998 0.95139998 0.95139998 0.94879328 0.94879328

0.94879328 0.94879328]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 7, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.96 0.71 0.75 0.73 0.79 0.94

STD 0.004 0.022 0.018 0.028 0.013 0.006

Number of act mutations in the train set: 82

Number of deact mutations in the train set: 403

########################

Feature Importance

8 D_D_0_pfam 0.043791

7 D_A_0_pfam 0.041800

0 hmmScoreWT 0.041508

1 hmmScoreMUT 0.038357

4 A_MUT 0.036042

10 D_N_0_pfam 0.035465

6 bpsh_0 0.020083

5 allHomologs_0 0.018402

12 D_Y_0_pfam 0.018103

2 Phosphomimic 0.016955

11 D_R_0_pfam 0.016057

3 ATPcount 0.015690

9 D_E_0_pfam 0.015022

########################

activatingresistance results ( 14 )

REC: 0.929

########################

########################

########################

P46734/MAP2K3/A84T 0.652 A

P11309/PIM1/S97N 0.677 A

########################

Q00535/CDK5/F82I 0.467 TBD

Q02750/MAP2K1/V211D 0.421 TBD

########################

O96017/CHEK2/K373E 0.637 Inconclusive

P06493/CDK1/V124G 0.314 Inconclusive

P46734/MAP2K3/R94L 0.571 Inconclusive

P46734/MAP2K3/R96W 0.385 Inconclusive

P46734/MAP2K3/L215W 0.392 Inconclusive

P46734/MAP2K3/T222M 0.373 Inconclusive

P11309/PIM1/Q127E 0.637 Inconclusive

Q06418/TYRO3/V669L 0.615 Inconclusive

Q13470/TNK1/A299D 0.791 Inconclusive

########################

P00533/EGFR/T790M 0.459 TBDincreaseresistance

########################

REC: neutral 0.841

########################

REC: loss 0.97

########################

REC: decrease 0.293

LDvNAI

mean_test_score [0.89367246 0.89367246 0.89371241 0.89385735 0.89336543 0.89336543

0.89336543 0.89336543 0.89327859 0.89327859 0.89327859 0.89327859

0.89302508 0.89302508 0.89302508 0.89302508 0.90230286 0.90230286

0.90268381 0.9025137 0.90198764 0.90198764 0.90198764 0.90198764

0.90182549 0.90182549 0.90182549 0.90182549 0.90100862 0.90100862

0.90100862 0.90100862 0.90841573 0.90841573 0.9081294 0.90746252

0.90595732 0.90595732 0.90595732 0.90595732 0.90600309 0.90600309

0.90600309 0.90600309 0.9048265 0.9048265 0.9048265 0.9048265

0.91367897 0.91367897 0.91411366 0.91317451 0.91101568 0.91101568

0.91101568 0.91101568 0.9093259 0.9093259 0.9093259 0.9093259

0.90771772 0.90771772 0.90771772 0.90771772 0.91688576 0.91688576

0.91642839 0.91521596 0.91374511 0.91374511 0.91374511 0.91374511

0.91128339 0.91128339 0.91128339 0.91128339 0.90826464 0.90826464

0.90826464 0.90826464]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 3, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.92 0.65 0.87 0.9 0.85 0.82

STD 0.002 0.009 0.003 0.004 0.004 0.008

Number of act mutations in the train set: 645

Number of deact mutations in the train set: 324

########################

Feature Importance

4 allHomologs_0 0.051996

11 D_A_0_pfam 0.050708

1 hmmScoreMUT 0.043642

9 bpsh_0 0.039446

0 hmmScoreWT 0.032748

7 orthologs_0 0.026616

5 exclParalogs_0 0.025990

8 bpso_0 0.025587

12 D_D_0_pfam 0.024603

3 A_MUT 0.023629

13 D_E_0_pfam 0.023012

6 specParalogs_0 0.021311

10 bpsh_2 0.018619

2 ATPcount 0.018099

14 D_G_0_pfam 0.015904

########################

activatingresistance results ( 14 )

REC: 0.071

########################

########################

########################

P46734/MAP2K3/A84T 0.197 A

P11309/PIM1/S97N 0.373 A

########################

Q00535/CDK5/F82I 0.513 TBD

Q02750/MAP2K1/V211D 0.576 TBD

########################

O96017/CHEK2/K373E 0.386 Inconclusive

P06493/CDK1/V124G 0.611 Inconclusive

P46734/MAP2K3/R94L 0.423 Inconclusive

P46734/MAP2K3/R96W 0.52 Inconclusive

P46734/MAP2K3/L215W 0.61 Inconclusive

P46734/MAP2K3/T222M 0.681 Inconclusive

P11309/PIM1/Q127E 0.248 Inconclusive

Q06418/TYRO3/V669L 0.27 Inconclusive

Q13470/TNK1/A299D 0.089 Inconclusive

########################

P00533/EGFR/T790M 0.335 TBDincreaseresistance

########################

REC: neutral 0.986

########################

REC: loss 0.0

########################

REC: decrease 0.0

LvNA

mean_test_score [0.95599359 0.95599359 0.95591815 0.9557312 0.95548164 0.95548164

0.95548164 0.95548164 0.95522816 0.95522816 0.95522816 0.95522816

0.95447426 0.95447426 0.95447426 0.95447426 0.96152092 0.96152092

0.96150701 0.96099159 0.96081071 0.96081071 0.96081071 0.96081071

0.9604644 0.9604644 0.9604644 0.9604644 0.95896898 0.95896898

0.95896898 0.95896898 0.96517872 0.96517872 0.96481437 0.96530654

0.96467502 0.96467502 0.96467502 0.96467502 0.96365328 0.96365328

0.96365328 0.96365328 0.96138395 0.96138395 0.96138395 0.96138395

0.96748345 0.96748345 0.9677429 0.96684172 0.96564021 0.96564021

0.96564021 0.96564021 0.96442196 0.96442196 0.96442196 0.96442196

0.96293676 0.96293676 0.96293676 0.96293676 0.96839886 0.96839886

0.96849898 0.96802191 0.96650923 0.96650923 0.96650923 0.96650923

0.96471066 0.96471066 0.96471066 0.96471066 0.96332893 0.96332893

0.96332893 0.96332893]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 10, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 7, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.97 0.8 0.92 0.95 0.89 0.92

STD 0.002 0.012 0.004 0.006 0.006 0.01

Number of act mutations in the train set: 403

Number of deact mutations in the train set: 227

########################

Feature Importance

9 D_A_0_pfam 0.071594

8 bpsh_0 0.060635

4 allHomologs_0 0.047376

0 hmmScoreWT 0.044559

7 bpso_0 0.032577

1 hmmScoreMUT 0.030192

3 A_MUT 0.027890

14 D_H_2_pfam 0.027616

10 D_D_0_pfam 0.026751

6 orthologs_0 0.026410

5 specParalogs_0 0.022771

11 D_E_0_pfam 0.021821

13 D_N_0_pfam 0.020553

2 ATPcount 0.019402

12 D_K_0_pfam 0.017103

########################

activatingresistance results ( 14 )

REC: 0.071

########################

########################

########################

P46734/MAP2K3/A84T 0.111 A

P11309/PIM1/S97N 0.095 A

########################

Q00535/CDK5/F82I 0.433 TBD

Q02750/MAP2K1/V211D 0.537 TBD

########################

O96017/CHEK2/K373E 0.301 Inconclusive

P06493/CDK1/V124G 0.567 Inconclusive

P46734/MAP2K3/R94L 0.319 Inconclusive

P46734/MAP2K3/R96W 0.532 Inconclusive

P46734/MAP2K3/L215W 0.566 Inconclusive

P46734/MAP2K3/T222M 0.589 Inconclusive

P11309/PIM1/Q127E 0.137 Inconclusive

Q06418/TYRO3/V669L 0.235 Inconclusive

Q13470/TNK1/A299D 0.044 Inconclusive

########################

P00533/EGFR/T790M 0.317 TBDincreaseresistance

########################

REC: neutral 0.993

########################

REC: loss 0.0

########################

REC: decrease 0.496

LvN

mean_test_score [0.98107401 0.98107401 0.98116037 0.98093322 0.98072706 0.98072706

0.98072706 0.98072706 0.98054405 0.98054405 0.98054405 0.98054405

0.97992535 0.97992535 0.97992535 0.97992535 0.98170418 0.98170418

0.98168092 0.98168168 0.9816689 0.9816689 0.9816689 0.9816689

0.98127224 0.98127224 0.98127224 0.98127224 0.98027491 0.98027491

0.98027491 0.98027491 0.98171176 0.98171176 0.98183113 0.98176542

0.98107172 0.98107172 0.98107172 0.98107172 0.98067413 0.98067413

0.98067413 0.98067413 0.98014265 0.98014265 0.98014265 0.98014265

0.98234951 0.98234951 0.98236443 0.98200061 0.98212387 0.98212387

0.98212387 0.98212387 0.98083104 0.98083104 0.98083104 0.98083104

0.97993391 0.97993391 0.97993391 0.97993391 0.98218946 0.98218946

0.98209408 0.98197732 0.98191013 0.98191013 0.98191013 0.98191013

0.98094718 0.98094718 0.98094718 0.98094718 0.9799324 0.9799324

0.9799324 0.9799324 ]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 7, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 7, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.98 0.83 0.95 0.97 0.94 0.91

STD 0.002 0.008 0.003 0.004 0.003 0.011

Number of act mutations in the train set: 403

Number of deact mutations in the train set: 145

########################

Feature Importance

10 D_A_0_pfam 0.076851

4 allHomologs_0 0.063151

8 bpso_0 0.062570

9 bpsh_0 0.058846

0 hmmScoreWT 0.056847

6 specParalogs_0 0.055144

7 orthologs_0 0.042193

11 D_D_0_pfam 0.035695

12 D_E_0_pfam 0.027843

2 ATPcount 0.025384

14 D_N_0_pfam 0.019440

15 D_H_2_pfam 0.018787

3 p_0 0.018612

5 exclParalogs_0 0.017832

1 hmmScoreMUT 0.017603

13 D_K_0_pfam 0.017364

########################

activatingresistance results ( 14 )

REC: 0.357

########################

########################

########################

P46734/MAP2K3/A84T 0.083 A

P11309/PIM1/S97N 0.151 A

########################

Q00535/CDK5/F82I 0.504 TBD

Q02750/MAP2K1/V211D 0.657 TBD

########################

O96017/CHEK2/K373E 0.4 Inconclusive

P06493/CDK1/V124G 0.63 Inconclusive

P46734/MAP2K3/R94L 0.247 Inconclusive

P46734/MAP2K3/R96W 0.514 Inconclusive

P46734/MAP2K3/L215W 0.692 Inconclusive

P46734/MAP2K3/T222M 0.87 Inconclusive

P11309/PIM1/Q127E 0.216 Inconclusive

Q06418/TYRO3/V669L 0.242 Inconclusive

Q13470/TNK1/A299D 0.036 Inconclusive

########################

P00533/EGFR/T790M 0.374 TBDincreaseresistance

########################

REC: neutral 0.979

########################

REC: loss 0.0

########################

REC: decrease 0.665

RvN

mean_test_score [0.91088605 0.91088605 0.91120153 0.91203231 0.90395153 0.90395153

0.90395153 0.90395153 0.88979677 0.88979677 0.88979677 0.88979677

0.87122279 0.87122279 0.87122279 0.87122279 0.91667772 0.91667772

0.91554082 0.91626361 0.90726616 0.90726616 0.90726616 0.90726616

0.88948639 0.88948639 0.88948639 0.88948639 0.87498895 0.87498895

0.87498895 0.87498895 0.91799065 0.91799065 0.91869303 0.91783673

0.9033716 0.9033716 0.9033716 0.9033716 0.89016837 0.89016837

0.89016837 0.89016837 0.87089541 0.87089541 0.87089541 0.87089541

0.91864371 0.91864371 0.91895918 0.92050595 0.90681803 0.90681803

0.90681803 0.90681803 0.89124405 0.89124405 0.89124405 0.89124405

0.8710119 0.8710119 0.8710119 0.8710119 0.91823044 0.91823044

0.91863435 0.91959014 0.90446514 0.90446514 0.90446514 0.90446514

0.89087585 0.89087585 0.89087585 0.89087585 0.87073214 0.87073214

0.87073214 0.87073214]

-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

Best model: {'criterion': 'gini', 'max_depth': 7, 'max_features': 'sqrt', 'min_samples_leaf': 3, 'min_samples_split': 10, 'n_estimators': 100}

---------------------------------------------------------------------------------------------------

Stratified CV results

MET AUC MCC F1 PRE REC SPE

AVG 0.92 0.67 0.76 0.82 0.73 0.91

STD 0.006 0.028 0.021 0.023 0.022 0.009

Number of act mutations in the train set: 72

Number of deact mutations in the train set: 145

########################

Feature Importance

10 orthologs_0 0.056061

11 bpso_0 0.049344

7 allHomologs_0 0.040175

12 bpsh_0 0.035302

9 specParalogs_0 0.030124

18 R_V_0_pfam 0.022876

17 R_R_0_pfam 0.022829

13 allHomologs_2 0.021895

5 orthologs_-2 0.020516

8 exclParalogs_0 0.020450

15 R_H_0_pfam 0.020327

2 IUPRED 0.018889

3 exclParalogs_-2 0.018806

14 A_A_-1_pfam 0.018659

0 hmmScoreWT 0.016526

16 R_L_0_pfam 0.016506

6 exclParalogs_-1 0.016412

4 specParalogs_-2 0.016120

19 D_F_2_pfam 0.016001

1 hmmScoreMUT 0.015061

########################

activatingresistance results ( 14 )

REC: 0.786

########################

########################

########################

P46734/MAP2K3/A84T 0.301 A

P11309/PIM1/S97N 0.123 A

########################

Q00535/CDK5/F82I 0.763 TBD

Q02750/MAP2K1/V211D 0.5 TBD

########################

O96017/CHEK2/K373E 0.416 Inconclusive

P06493/CDK1/V124G 0.603 Inconclusive

P46734/MAP2K3/R94L 0.391 Inconclusive

P46734/MAP2K3/R96W 0.324 Inconclusive

P46734/MAP2K3/L215W 0.668 Inconclusive

P46734/MAP2K3/T222M 0.668 Inconclusive

P11309/PIM1/Q127E 0.265 Inconclusive

Q06418/TYRO3/V669L 0.343 Inconclusive

Q13470/TNK1/A299D 0.173 Inconclusive

########################

P00533/EGFR/T790M 0.752 TBDincreaseresistance

########################

REC: neutral 0.986

########################

REC: loss 0.623

########################

REC: decrease 0.384