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

Feature                                   Importance
--------------------------------------  ------------
s__Parvimonas_micra                                0
s__Oscillibacter_sp_CAG_241                        1
s__Anaerotruncus_colihominis                       2
s__Gemella_morbillorum                             3
s__Sanguibacteroides_justesenii                    3
s__Clostridium_innocuum                            4
s__Slackia_isoflavoniconvertens                    5
s__Streptococcus_infantis                          5
s__Clostridium_symbiosum                           6
s__Coprobacter_fastidiosus                         7
s__Clostridium_sp_CAG_253                          8
s__Lactobacillus_paragasseri                       9
s__Megasphaera_elsdenii                            9
s__Turicibacter_sanguinis                          9
s__Desulfovibrio_piger                            10
s__Actinomyces_sp_oral_taxon_181                  11
s__Bacteroides_intestinalis                       11
s__Bacteroides_clarus                             12
s__Anaeromassilibacillus_sp_An250                 13
s__Holdemanella_biformis                          13
s__Bacteroides_galacturonicus                     14
s__Clostridium_leptum                             14
s__Phascolarctobacterium_faecium                  14
s__Absiella_dolichum                              15
s__Eubacterium_siraeum                            15
s__Firmicutes_bacterium_CAG_145                   15
s__Blautia_wexlerae                               16
s__Dialister_pneumosintes                         16
s__Eisenbergiella_tayi                            16
s__Firmicutes_bacterium_CAG_170                   16
s__Escherichia_coli                               17
s__Eubacterium_eligens                            18
s__Ruminococcaceae_bacterium_D16                  18
s__Eubacterium_rectale                            19
s__Firmicutes_bacterium_CAG_94                    19
s__Bacteroides_salyersiae                         20
s__Pyramidobacter_piscolens                       20
s__Veillonella_dispar                             20
s__Ruminococcus_bicirculans                       21
s__Bacteroides_ovatus                             22
s__Clostridium_spiroforme                         22
s__Enorma_massiliensis                            22
s__Prevotella_sp_CAG_1185                         23
s__Peptostreptococcus_stomatis                    24
s__Collinsella_stercoris                          25
s__Parasutterella_excrementihominis               25
s__Veillonella_infantium                          25
s__Gemella_sanguinis                              26
s__Lactobacillus_delbrueckii                      26
s__Catenibacterium_mitsuokai                      27
s__Roseburia_intestinalis                         28
s__Victivallis_vadensis                           28
s__Firmicutes_bacterium_CAG_83                    29
s__Actinomyces_graevenitzii                       30
s__Eubacterium_sp_CAG_251                         31
s__Coprobacillus_cateniformis                     32
s__Alloscardovia_omnicolens                       33
s__Eubacterium_sp_CAG_38                          33
s__Parabacteroides_sp_CAG_409                     33
s__Clostridium_asparagiforme                      34
s__Eubacterium_hallii                             35
s__Phascolarctobacterium_succinatutens            35
s__Bacteroides_cellulosilyticus                   36
s__Klebsiella_pneumoniae                          36
s__Morganella_morganii                            36
s__Parabacteroides_johnsonii                      37
s__Bacteroides_stercoris                          38
s__[Collinsella]_massiliensis                     38
s__Bacteroides_coprocola                          39
s__Eubacterium_dolichum_CAG_375                   39
s__Lawsonibacter_asaccharolyticus                 39
s__Alistipes_inops                                40
s__Ruminococcus_bromii                            40
s__Bifidobacterium_breve                          41
s__Clostridium_bolteae                            41
s__Prevotella_stercorea                           41
s__Eisenbergiella_massiliensis                    42
s__Enterococcus_faecium                           42
s__Bacteroides_sp_CAG_144                         43
s__Butyrivibrio_sp_CAG_318                        43
s__Parabacteroides_goldsteinii                    44
s__Bacteroides_faecis                             45
s__Bifidobacterium_animalis                       45
s__Bifidobacterium_dentium                        45
s__Cloacibacillus_porcorum                        45
s__Erysipelatoclostridium_ramosum                 45
s__Eubacterium_sp_CAG_180                         45
s__Firmicutes_bacterium_CAG_238                   45
s__Ruminococcus_torques                           45
s__Adlercreutzia_equolifaciens                    46
s__Faecalibacterium_prausnitzii                   47
s__Streptococcus_vestibularis                     47
s__Clostridium_sp_CAG_299                         48
s__Ruthenibacterium_lactatiformans                49
s__Bacteroides_caccae                             50
s__Blautia_sp_CAG_257                             50
s__Butyricimonas_synergistica                     50
s__Citrobacter_youngae                            50
s__Clostridium_citroniae                          51
s__Clostridium_sp_CAG_167                         52
s__Bacteroides_nordii                             53
s__Clostridium_disporicum                         53
s__Clostridium_saccharolyticum                    54
s__Eubacterium_ramulus                            54
s__Mitsuokella_jalaludinii                        54
s__Actinomyces_sp_ICM47                           55
s__Klebsiella_variicola                           55
s__Rothia_mucilaginosa                            55
s__Sutterella_parvirubra                          56
s__Turicimonas_muris                              57
s__Bacteroides_dorei                              58
s__Bacteroides_massiliensis                       59
s__Bilophila_wadsworthia                          59
s__Roseburia_inulinivorans                        59
s__Bifidobacterium_longum                         60
s__Odoribacter_splanchnicus                       61
s__Blautia_obeum                                  62
s__Phascolarctobacterium_sp_CAG_266               62
s__Raoultella_ornithinolytica                     62
s__Alistipes_indistinctus                         63
s__Lactobacillus_fermentum                        63
s__Roseburia_sp_CAG_471                           63
s__Alistipes_onderdonkii                          64
s__Bacteroides_faecis_CAG_32                      64
s__Eubacterium_ventriosum                         64
s__Megamonas_hypermegale                          64
s__Butyricimonas_virosa                           65
s__Alloprevotella_tannerae                        66
s__Mitsuokella_multacida                          66
s__Fretibacterium_fastidiosum                     67
s__Blautia_hansenii                               68
s__Blautia_hydrogenotrophica                      68
s__Clostridium_sp_CAG_58                          68
s__Coprobacter_secundus                           68
s__Enterobacter_cloacae_complex                   68
s__Roseburia_hominis                              68
s__Akkermansia_muciniphila                        69
s__Bacteroides_thetaiotaomicron                   69
s__Clostridium_paraputrificum                     69
s__Fusobacterium_nucleatum                        69
s__Hungatella_hathewayi                           69
s__Megamonas_funiformis                           69
s__Prevotella_sp_CAG_279                          69
s__Streptococcus_thermophilus                     69
s__Anaerostipes_hadrus                            70
s__Asaccharobacter_celatus                        71
s__Clostridium_sp_CAG_242                         71
s__Coprococcus_comes                              71
s__Dorea_longicatena                              71
s__Streptococcus_gordonii                         71
s__Bifidobacterium_catenulatum                    72
s__Eikenella_corrodens                            73
s__Haemophilus_sp_HMSC71H05                       73
s__Bacteroides_fragilis                           74
s__Faecalicoccus_pleomorphus                      74
s__Streptococcus_parasanguinis                    75
s__Sellimonas_intestinalis                        76
s__Butyricicoccus_pullicaecorum                   77
s__Monoglobus_pectinilyticus                      78
s__Bacteroides_finegoldii                         79
s__Actinomyces_turicensis                         80
s__Bacteroides_eggerthii                          80
s__Blautia_producta                               80
s__Holdemania_filiformis                          81
s__Streptococcus_pasteurianus                     81
s__Roseburia_faecis                               82
s__Coprococcus_catus                              83
s__Lachnospira_pectinoschiza                      84
s__Parabacteroides_merdae                         85
s__Clostridium_clostridioforme                    86
s__Dialister_sp_CAG_357                           86
s__Collinsella_intestinalis                       87
s__Lactobacillus_rogosae                          87
s__Agathobaculum_butyriciproducens                88
s__Enterococcus_faecalis                          88
s__Dialister_invisus                              89
s__Oscillibacter_sp_57_20                         89
s__Porphyromonas_asaccharolytica                  89
s__Dorea_formicigenerans                          90
s__Paraprevotella_xylaniphila                     90
s__Streptococcus_oralis                           90
s__Tyzzerella_nexilis                             90
s__Coprococcus_eutactus                           91
s__Streptococcus_australis                        91
s__Intestinimonas_butyriciproducens               92
s__Solobacterium_moorei                           92
s__Streptococcus_anginosus_group                  92
s__Veillonella_atypica                            93
s__Veillonella_parvula                            93
s__Bacteroides_coprophilus                        94
s__Gordonibacter_pamelaeae                        95
s__Bacteroides_vulgatus                           96
s__Klebsiella_oxytoca                             96
s__Pseudoflavonifractor_sp_An184                  96
s__Streptococcus_mutans                           96
s__Bacteroides_xylanisolvens                      97
s__Bifidobacterium_adolescentis                   97
s__Gemmiger_formicilis                            97
s__Prevotella_sp_CAG_520                          97
s__Slackia_exigua                                 98
s__Lactobacillus_gasseri                          99
s__Clostridium_lavalense                         100
s__Eubacterium_sp_CAG_274                        100
s__Allisonella_histaminiformans                  101
s__Bacteroides_uniformis                         102
s__Mogibacterium_diversum                        103
s__Alistipes_finegoldii                          104
s__Desulfovibrionaceae_bacterium                 104
s__Ruminococcaceae_bacterium_D5                  104
s__Ruminococcus_lactaris                         105
s__Firmicutes_bacterium_CAG_95                   106
s__Haemophilus_parainfluenzae                    107
s__Streptococcus_salivarius                      107
s__Clostridium_bolteae_CAG_59                    108
s__Klebsiella_quasipneumoniae                    108
s__Bifidobacterium_pseudocatenulatum             109
s__Flavonifractor_plautii                        109
s__Actinomyces_sp_HMSC035G02                     110
s__Paraprevotella_clara                          111
s__Parabacteroides_distasonis                    112
s__Intestinibacter_bartlettii                    113
s__Alistipes_putredinis                          114
s__Streptococcus_mitis                           115
s__Bacteroides_plebeius                          116
s__Anaerotignum_lactatifermentans                117
s__Proteobacteria_bacterium_CAG_139              117
s__Alistipes_shahii                              118
s__Barnesiella_intestinihominis                  118
s__Klebsiella_michiganensis                      118
s__Bifidobacterium_bifidum                       119
s__Ruminococcus_gnavus                           119
s__Acidaminococcus_intestini                     120
s__Actinomyces_odontolyticus                     120
s__Olsenella_scatoligenes                        120
s__Streptococcus_sanguinis                       120
s__Collinsella_aerofaciens                       121
s__Fusicatenibacter_saccharivorans               122
s__Eggerthella_lenta                             123
s__Prevotella_copri                              124
s__Ruminococcus_callidus                         124
s__Firmicutes_bacterium_CAG_110                  125

  Importance    Score (accuracy)
------------  ------------------
           0              0
           1              0.7519
           2              0.7519
           3              0.8435
           4              0.8251
           5              0.8483
           6              0.8805
           7              0.8619
           8              0.8619
           9              0.8616
          10              0.8801
          11              0.8892
          12              0.8892
          13              0.871
          14              0.8434
          15              0.871
          16              0.88
          17              0.8892
          18              0.871
          19              0.8712
          20              0.8683
          21              0.8801
          22              0.8805
          23              0.89
          24              0.8805
          25              0.8747
          26              0.8714
          27              0.8896
          28              0.8807
          29              0.881
          30              0.8991
          31              0.8719
          32              0.8805
          33              0.853
          34              0.8719
          35              0.8442
          36              0.844
          37              0.8623
          38              0.8439
          39              0.8348
          40              0.8437
          41              0.8437
          42              0.8433
          43              0.8528
          44              0.8528
          45              0.8347
          46              0.8437
          47              0.8392
          48              0.8437
          49              0.8346
          50              0.8256
          51              0.8346
          52              0.8532
          53              0.8348
          54              0.8345
          55              0.8348
          56              0.8255
          57              0.8255
          58              0.8255
          59              0.8072
          60              0.816
          61              0.8165
          62              0.8074
          63              0.8074
          64              0.8258
          65              0.826
          66              0.8258
          67              0.8355
          68              0.8351
          69              0.8078
          70              0.8264
          71              0.8074
          72              0.8169
          73              0.8165
          74              0.8074
          75              0.8078
          76              0.8074
          77              0.8078
          78              0.8078
          79              0.8169
          80              0.7986
          81              0.7985
          82              0.8078
          83              0.8078
          84              0.8074
          85              0.8169
          86              0.8078
          87              0.7983
          88              0.8076
          89              0.7983
          90              0.7891
          91              0.7885
          92              0.7886
          93              0.7887
          94              0.8074
          95              0.7983
          96              0.7701
          97              0.789
          98              0.7978
          99              0.8069
         100              0.7974
         101              0.8074
         102              0.8074
         103              0.7978
         104              0.7983
         105              0.8165
         106              0.8165
         107              0.7981
         108              0.7981
         109              0.7983
         110              0.8074
         111              0.8065
         112              0.8074
         113              0.8074
         114              0.8074
         115              0.7978
         116              0.8165
         117              0.8071
         118              0.798
         119              0.7983
         120              0.7795
         121              0.816
         122              0.7883
         123              0.7797
         124              0.7885
         125              0.8065

Best importance: 30
Selected features: 54

Features
-----------------------------------
s__Absiella_dolichum
s__Actinomyces_graevenitzii
s__Actinomyces_sp_oral_taxon_181
s__Anaeromassilibacillus_sp_An250
s__Anaerotruncus_colihominis
s__Bacteroides_clarus
s__Bacteroides_galacturonicus
s__Bacteroides_intestinalis
s__Bacteroides_ovatus
s__Bacteroides_salyersiae
s__Blautia_wexlerae
s__Catenibacterium_mitsuokai
s__Clostridium_innocuum
s__Clostridium_leptum
s__Clostridium_sp_CAG_253
s__Clostridium_spiroforme
s__Clostridium_symbiosum
s__Collinsella_stercoris
s__Coprobacter_fastidiosus
s__Desulfovibrio_piger
s__Dialister_pneumosintes
s__Eisenbergiella_tayi
s__Enorma_massiliensis
s__Escherichia_coli
s__Eubacterium_eligens
s__Eubacterium_rectale
s__Eubacterium_siraeum
s__Firmicutes_bacterium_CAG_145
s__Firmicutes_bacterium_CAG_170
s__Firmicutes_bacterium_CAG_83
s__Firmicutes_bacterium_CAG_94
s__Gemella_morbillorum
s__Gemella_sanguinis
s__Holdemanella_biformis
s__Lactobacillus_delbrueckii
s__Lactobacillus_paragasseri
s__Megasphaera_elsdenii
s__Oscillibacter_sp_CAG_241
s__Parasutterella_excrementihominis
s__Parvimonas_micra
s__Peptostreptococcus_stomatis
s__Phascolarctobacterium_faecium
s__Prevotella_sp_CAG_1185
s__Pyramidobacter_piscolens
s__Roseburia_intestinalis
s__Ruminococcaceae_bacterium_D16
s__Ruminococcus_bicirculans
s__Sanguibacteroides_justesenii
s__Slackia_isoflavoniconvertens
s__Streptococcus_infantis
s__Turicibacter_sanguinis
s__Veillonella_dispar
s__Veillonella_infantium
s__Victivallis_vadensis

Total ML models: 15465

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

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

Fold 1 (1 retrainings)
	Error rate: 0.034482758620689655
	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 (3 retrainings)
	Error rate: 0.05747126436781609
	Accuracy: 0.8182
	F1: 0.8152
	Precision: 0.8701
	Recall: 0.8182
	Matthews Corr. Coeff.: 0.6901
	Confusion Matrix:
		TN: 8
		FP: 4
		FN: 0
		TP: 10

Fold 3 (7 retrainings)
	Error rate: 0.011494252873563218
	Accuracy: 0.8182
	F1: 0.8182
	Precision: 0.8182
	Recall: 0.8182
	Matthews Corr. Coeff.: 0.6333
	Confusion Matrix:
		TN: 10
		FP: 2
		FN: 2
		TP: 8

Fold 4 (2 retrainings)
	Error rate: 0.08045977011494253
	Accuracy: 0.9545
	F1: 0.9546
	Precision: 0.9587
	Recall: 0.9545
	Matthews Corr. Coeff.: 0.9129
	Confusion Matrix:
		TN: 11
		FP: 1
		FN: 0
		TP: 10

Fold 5 (2 retrainings)
	Error rate: 0.09090909090909091
	Accuracy: 0.7619
	F1: 0.7608
	Precision: 0.7632
	Recall: 0.7619
	Matthews Corr. Coeff.: 0.5230
	Confusion Matrix:
		TN: 9
		FP: 2
		FN: 3
		TP: 7

Retrainings: 3.0000 (2.3452 stdev)
Error Rate: 0.0550 (0.0326 stdev)
Accuracy: 0.8433 (0.0719 stdev)
F1: 0.8423 (0.0725 stdev)
Precision: 0.8552 (0.0722 stdev)
Recall: 0.8433 (0.0719 stdev)
Matthews Corr. Coeff.: 0.6970 (0.1430 stdev)
Total elapsed time: 847s
