Loading dataset
Points: 109; Features 241; Classes 2
Building the HD model
Selecting features.. This may take a while

Feature                                   Importance
--------------------------------------  ------------
s__Phascolarctobacterium_succinatutens             0
s__Prevotella_copri                                1
s__Bacteroides_caccae                              2
s__Fusicatenibacter_saccharivorans                 2
s__Gemella_morbillorum                             3
s__Solobacterium_moorei                            4
s__Coprobacter_fastidiosus                         5
s__Catenibacterium_mitsuokai                       6
s__Ruminococcus_bromii                             7
s__Coprococcus_catus                               8
s__Prevotella_sp_CAG_279                           8
s__Roseburia_faecis                                8
s__Klebsiella_quasipneumoniae                      9
s__Parabacteroides_johnsonii                       9
s__Lawsonibacter_asaccharolyticus                 10
s__Alistipes_indistinctus                         11
s__Alistipes_onderdonkii                          12
s__Clostridium_sp_CAG_167                         12
s__Lactobacillus_paragasseri                      12
s__Ruthenibacterium_lactatiformans                12
s__Streptococcus_oralis                           12
s__Anaeromassilibacillus_sp_An250                 13
s__Fusobacterium_nucleatum                        13
s__Mitsuokella_multacida                          13
s__Streptococcus_mitis                            13
s__Veillonella_atypica                            13
s__Bacteroides_sp_CAG_144                         14
s__Hungatella_hathewayi                           14
s__Lachnospira_pectinoschiza                      14
s__Megamonas_hypermegale                          14
s__Peptostreptococcus_stomatis                    14
s__Bacteroides_thetaiotaomicron                   15
s__Bacteroides_galacturonicus                     16
s__Eubacterium_siraeum                            16
s__Actinomyces_graevenitzii                       17
s__Akkermansia_muciniphila                        17
s__Barnesiella_intestinihominis                   17
s__Mogibacterium_diversum                         17
s__Roseburia_inulinivorans                        17
s__Streptococcus_sanguinis                        17
s__Bacteroides_cellulosilyticus                   18
s__Butyrivibrio_sp_CAG_318                        18
s__Streptococcus_vestibularis                     18
s__Parabacteroides_merdae                         19
s__Acidaminococcus_intestini                      20
s__Clostridium_symbiosum                          20
s__Collinsella_stercoris                          20
s__Eisenbergiella_tayi                            20
s__Firmicutes_bacterium_CAG_83                    20
s__Lactobacillus_rogosae                          20
s__Odoribacter_splanchnicus                       20
s__Ruminococcus_bicirculans                       20
s__Tyzzerella_nexilis                             20
s__Collinsella_aerofaciens                        21
s__Desulfovibrionaceae_bacterium                  21
s__Parabacteroides_distasonis                     21
s__Streptococcus_parasanguinis                    21
s__Bacteroides_clarus                             22
s__Bacteroides_vulgatus                           22
s__Victivallis_vadensis                           22
s__Actinomyces_sp_HMSC035G02                      23
s__Clostridium_sp_CAG_299                         23
s__Clostridium_asparagiforme                      24
s__Alloscardovia_omnicolens                       25
s__Morganella_morganii                            26
s__Prevotella_stercorea                           27
s__Firmicutes_bacterium_CAG_238                   28
s__Clostridium_lavalense                          29
s__Eggerthella_lenta                              29
s__Prevotella_sp_CAG_520                          30
s__Actinomyces_odontolyticus                      31
s__Blautia_obeum                                  31
s__Cloacibacillus_porcorum                        31
s__Eikenella_corrodens                            31
s__Firmicutes_bacterium_CAG_170                   31
s__Parasutterella_excrementihominis               31
s__Sellimonas_intestinalis                        31
s__Slackia_exigua                                 31
s__Paraprevotella_xylaniphila                     32
s__Allisonella_histaminiformans                   33
s__Bacteroides_intestinalis                       33
s__Clostridium_paraputrificum                     33
s__Lactobacillus_gasseri                          33
s__Bacteroides_faecis_CAG_32                      34
s__Enorma_massiliensis                            34
s__Eubacterium_sp_CAG_38                          34
s__Firmicutes_bacterium_CAG_145                   34
s__Pyramidobacter_piscolens                       34
s__Blautia_wexlerae                               35
s__Dorea_longicatena                              35
s__Parabacteroides_sp_CAG_409                     35
s__Porphyromonas_asaccharolytica                  35
s__Coprobacillus_cateniformis                     36
s__Eubacterium_sp_CAG_251                         36
s__Firmicutes_bacterium_CAG_95                    36
s__Raoultella_ornithinolytica                     36
s__Actinomyces_sp_oral_taxon_181                  37
s__Eubacterium_rectale                            37
s__Actinomyces_turicensis                         38
s__Alloprevotella_tannerae                        38
s__Bifidobacterium_dentium                        38
s__Blautia_producta                               38
s__Clostridium_citroniae                          38
s__Clostridium_sp_CAG_242                         38
s__Dialister_pneumosintes                         38
s__Eubacterium_ventriosum                         38
s__Parvimonas_micra                               38
s__Roseburia_sp_CAG_471                           38
s__Ruminococcaceae_bacterium_D16                  38
s__Ruminococcus_torques                           38
s__Streptococcus_mutans                           38
s__Turicimonas_muris                              38
s__Veillonella_dispar                             38
s__Bifidobacterium_pseudocatenulatum              39
s__Clostridium_clostridioforme                    39
s__Intestinibacter_bartlettii                     39
s__Phascolarctobacterium_faecium                  39
s__Ruminococcus_callidus                          39
s__Ruminococcus_lactaris                          39
s__Butyricimonas_virosa                           40
s__Veillonella_parvula                            41
s__Klebsiella_oxytoca                             42
s__Ruminococcaceae_bacterium_D5                   42
s__Anaerotruncus_colihominis                      43
s__Sutterella_parvirubra                          44
s__Alistipes_finegoldii                           45
s__Anaerostipes_hadrus                            45
s__Bifidobacterium_bifidum                        45
s__Enterococcus_faecalis                          46
s__Mitsuokella_jalaludinii                        46
s__Bacteroides_faecis                             47
s__Holdemanella_biformis                          47
s__Rothia_mucilaginosa                            48
s__Alistipes_inops                                49
s__Bifidobacterium_animalis                       49
s__Clostridium_saccharolyticum                    49
s__Veillonella_infantium                          49
s__Bacteroides_coprophilus                        50
s__Blautia_hydrogenotrophica                      50
s__Clostridium_sp_CAG_253                         50
s__Eubacterium_sp_CAG_274                         50
s__Bifidobacterium_breve                          51
s__Coprococcus_comes                              51
s__Gemmiger_formicilis                            51
s__Haemophilus_parainfluenzae                     51
s__Haemophilus_sp_HMSC71H05                       51
s__Paraprevotella_clara                           51
s__Streptococcus_pasteurianus                     51
s__Streptococcus_salivarius                       51
s__Turicibacter_sanguinis                         51
s__Firmicutes_bacterium_CAG_110                   52
s__Megamonas_funiformis                           52
s__Roseburia_intestinalis                         52
s__Bacteroides_fragilis                           53
s__Bilophila_wadsworthia                          54
s__Bifidobacterium_longum                         55
s__Clostridium_bolteae                            55
s__Enterobacter_cloacae_complex                   56
s__Fretibacterium_fastidiosum                     56
s__Megasphaera_elsdenii                           56
s__Dialister_invisus                              57
s__Bacteroides_coprocola                          58
s__Faecalibacterium_prausnitzii                   58
s__Alistipes_putredinis                           59
s__Bacteroides_ovatus                             59
s__Coprococcus_eutactus                           60
s__Clostridium_bolteae_CAG_59                     61
s__Oscillibacter_sp_CAG_241                       62
s__Anaerotignum_lactatifermentans                 63
s__Dorea_formicigenerans                          63
s__Flavonifractor_plautii                         63
s__Roseburia_hominis                              64
s__Bacteroides_finegoldii                         65
s__Eubacterium_ramulus                            65
s__Streptococcus_thermophilus                     65
s__Bacteroides_massiliensis                       66
s__Parabacteroides_goldsteinii                    66
s__Absiella_dolichum                              67
s__Bacteroides_nordii                             68
s__Coprobacter_secundus                           68
s__Holdemania_filiformis                          69
s__Olsenella_scatoligenes                         69
s__Klebsiella_variicola                           70
s__Eubacterium_dolichum_CAG_375                   71
s__Phascolarctobacterium_sp_CAG_266               71
s__Gemella_sanguinis                              72
s__Eisenbergiella_massiliensis                    73
s__Sanguibacteroides_justesenii                   73
s__Streptococcus_australis                        73
s__Bacteroides_dorei                              74
s__Collinsella_intestinalis                       74
s__Adlercreutzia_equolifaciens                    75
s__Bacteroides_stercoris                          76
s__Clostridium_leptum                             76
s__Pseudoflavonifractor_sp_An184                  76
s__[Collinsella]_massiliensis                     77
s__Lactobacillus_fermentum                        78
s__Proteobacteria_bacterium_CAG_139               78
s__Slackia_isoflavoniconvertens                   79
s__Prevotella_sp_CAG_1185                         80
s__Bacteroides_eggerthii                          81
s__Klebsiella_michiganensis                       82
s__Erysipelatoclostridium_ramosum                 83
s__Agathobaculum_butyriciproducens                84
s__Firmicutes_bacterium_CAG_94                    84
s__Clostridium_spiroforme                         85
s__Bacteroides_salyersiae                         86
s__Actinomyces_sp_ICM47                           87
s__Bacteroides_plebeius                           88
s__Asaccharobacter_celatus                        89
s__Escherichia_coli                               89
s__Eubacterium_eligens                            89
s__Oscillibacter_sp_57_20                         90
s__Bifidobacterium_adolescentis                   91
s__Clostridium_innocuum                           91
s__Alistipes_shahii                               92
s__Bifidobacterium_catenulatum                    92
s__Desulfovibrio_piger                            92
s__Lactobacillus_delbrueckii                      92
s__Streptococcus_gordonii                         93
s__Citrobacter_youngae                            94
s__Butyricimonas_synergistica                     95
s__Butyricicoccus_pullicaecorum                   96
s__Streptococcus_infantis                         97
s__Streptococcus_anginosus_group                  98
s__Faecalicoccus_pleomorphus                      99
s__Intestinimonas_butyriciproducens              100
s__Monoglobus_pectinilyticus                     100
s__Bacteroides_xylanisolvens                     101
s__Clostridium_sp_CAG_58                         102
s__Blautia_hansenii                              103
s__Clostridium_disporicum                        103
s__Bacteroides_uniformis                         104
s__Blautia_sp_CAG_257                            104
s__Dialister_sp_CAG_357                          105
s__Enterococcus_faecium                          105
s__Eubacterium_hallii                            105
s__Eubacterium_sp_CAG_180                        105
s__Gordonibacter_pamelaeae                       105
s__Klebsiella_pneumoniae                         105
s__Ruminococcus_gnavus                           106

  Importance    Score (accuracy)
------------  ------------------
           0              0
           1              0.587
           2              0.6149
           3              0.6524
           4              0.6887
           5              0.6887
           6              0.7069
           7              0.6706
           8              0.7166
           9              0.7165
          10              0.7351
          11              0.726
          12              0.7444
          13              0.7537
          14              0.7536
          15              0.7537
          16              0.7532
          17              0.7536
          18              0.7625
          19              0.7719
          20              0.7442
          21              0.7067
          22              0.688
          23              0.6881
          24              0.697
          25              0.6974
          26              0.6974
          27              0.6974
          28              0.6974
          29              0.6972
          30              0.7156
          31              0.7061
          32              0.7156
          33              0.7061
          34              0.7154
          35              0.7245
          36              0.7242
          37              0.7152
          38              0.7061
          39              0.7061
          40              0.7251
          41              0.7242
          42              0.7154
          43              0.7242
          44              0.7152
          45              0.7245
          46              0.7247
          47              0.7247
          48              0.7242
          49              0.7241
          50              0.7242
          51              0.715
          52              0.7242
          53              0.7242
          54              0.7429
          55              0.7338
          56              0.7339
          57              0.7433
          58              0.7249
          59              0.7063
          60              0.7147
          61              0.7152
          62              0.7333
          63              0.6967
          64              0.7152
          65              0.6974
          66              0.697
          67              0.7065
          68              0.7154
          69              0.6972
          70              0.7061
          71              0.6881
          72              0.697
          73              0.697
          74              0.6879
          75              0.7065
          76              0.6971
          77              0.6974
          78              0.7154
          79              0.7061
          80              0.7338
          81              0.7338
          82              0.7247
          83              0.7152
          84              0.7152
          85              0.697
          86              0.7065
          87              0.7156
          88              0.697
          89              0.7066
          90              0.7065
          91              0.6701
          92              0.6699
          93              0.7156
          94              0.7156
          95              0.6788
          96              0.7065
          97              0.6883
          98              0.6792
          99              0.6883
         100              0.679
         101              0.6792
         102              0.6788
         103              0.6699
         104              0.6608
         105              0.6609
         106              0.661

Best importance: 19
Selected features: 44

Features
--------------------------------------
s__Actinomyces_graevenitzii
s__Akkermansia_muciniphila
s__Alistipes_indistinctus
s__Alistipes_onderdonkii
s__Anaeromassilibacillus_sp_An250
s__Bacteroides_caccae
s__Bacteroides_cellulosilyticus
s__Bacteroides_galacturonicus
s__Bacteroides_sp_CAG_144
s__Bacteroides_thetaiotaomicron
s__Barnesiella_intestinihominis
s__Butyrivibrio_sp_CAG_318
s__Catenibacterium_mitsuokai
s__Clostridium_sp_CAG_167
s__Coprobacter_fastidiosus
s__Coprococcus_catus
s__Eubacterium_siraeum
s__Fusicatenibacter_saccharivorans
s__Fusobacterium_nucleatum
s__Gemella_morbillorum
s__Hungatella_hathewayi
s__Klebsiella_quasipneumoniae
s__Lachnospira_pectinoschiza
s__Lactobacillus_paragasseri
s__Lawsonibacter_asaccharolyticus
s__Megamonas_hypermegale
s__Mitsuokella_multacida
s__Mogibacterium_diversum
s__Parabacteroides_johnsonii
s__Parabacteroides_merdae
s__Peptostreptococcus_stomatis
s__Phascolarctobacterium_succinatutens
s__Prevotella_copri
s__Prevotella_sp_CAG_279
s__Roseburia_faecis
s__Roseburia_inulinivorans
s__Ruminococcus_bromii
s__Ruthenibacterium_lactatiformans
s__Solobacterium_moorei
s__Streptococcus_mitis
s__Streptococcus_oralis
s__Streptococcus_sanguinis
s__Streptococcus_vestibularis
s__Veillonella_atypica

Total ML models: 14288

Building a model with the selected features only
Cross-validating model with 5 folds

Class labels: ['CRC', 'control']

Fold 1 (0 retrainings)
	Error rate: 0.1839080459770115
	Accuracy: 0.8636
	F1: 0.8628
	Precision: 0.8656
	Recall: 0.8636
	Matthews Corr. Coeff.: 0.7258
	Confusion Matrix:
		TN: 11
		FP: 1
		FN: 2
		TP: 8

Fold 2 (0 retrainings)
	Error rate: 0.14942528735632185
	Accuracy: 0.6818
	F1: 0.6825
	Precision: 0.6860
	Recall: 0.6818
	Matthews Corr. Coeff.: 0.3651
	Confusion Matrix:
		TN: 8
		FP: 4
		FN: 3
		TP: 7

Fold 3 (0 retrainings)
	Error rate: 0.13793103448275862
	Accuracy: 0.7273
	F1: 0.7226
	Precision: 0.7305
	Recall: 0.7273
	Matthews Corr. Coeff.: 0.4485
	Confusion Matrix:
		TN: 10
		FP: 2
		FN: 4
		TP: 6

Fold 4 (0 retrainings)
	Error rate: 0.11494252873563218
	Accuracy: 0.5455
	F1: 0.5455
	Precision: 0.5545
	Recall: 0.5455
	Matthews Corr. Coeff.: 0.1000
	Confusion Matrix:
		TN: 6
		FP: 6
		FN: 4
		TP: 6

Fold 5 (0 retrainings)
	Error rate: 0.13636363636363635
	Accuracy: 0.8571
	F1: 0.8565
	Precision: 0.8598
	Recall: 0.8571
	Matthews Corr. Coeff.: 0.7156
	Confusion Matrix:
		TN: 10
		FP: 1
		FN: 2
		TP: 8

Retrainings: 0.0000 (0.0000 stdev)
Error Rate: 0.1445 (0.0253 stdev)
Accuracy: 0.7351 (0.1326 stdev)
F1: 0.7340 (0.1322 stdev)
Precision: 0.7393 (0.1299 stdev)
Recall: 0.7351 (0.1326 stdev)
Matthews Corr. Coeff.: 0.4710 (0.2618 stdev)
Total elapsed time: 1146s
