Loading dataset
Points: 84; Features 241; Classes 2
Building the HD model
Selecting features.. This may take a while

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

  Importance    Score (accuracy)
------------  ------------------
           0              0
           1              0.6904
           2              0.6904
           3              0.7507
           4              0.786
           5              0.7743
           6              0.8221
           7              0.8331
           8              0.8449
           9              0.8349
          10              0.8353
          11              0.8471
          12              0.8353
          13              0.8341
          14              0.8221
          15              0.8346
          16              0.8228
          17              0.8463
          18              0.8463
          19              0.8463
          20              0.8463
          21              0.8581
          22              0.8338
          23              0.8221
          24              0.8221
          25              0.8338
          26              0.8221
          27              0.8331
          28              0.8221
          29              0.8221
          30              0.8338
          31              0.8099
          32              0.7985
          33              0.8098
          34              0.8338
          35              0.8221
          36              0.8096
          37              0.8103
          38              0.7978
          39              0.7743
          40              0.7971
          41              0.8096
          42              0.8213
          43              0.8096
          44              0.7974
          45              0.8088
          46              0.8213
          47              0.8096
          48              0.7971
          49              0.7971
          50              0.7971
          51              0.7971
          52              0.7971
          53              0.7971
          54              0.7853
          55              0.7734
          56              0.7853
          57              0.7735
          58              0.7735
          59              0.7978
          60              0.7978
          61              0.7976
          62              0.7978
          63              0.8096
          64              0.8096
          65              0.7975
          66              0.7978
          67              0.7735
          68              0.7735
          69              0.7735
          70              0.7732
          71              0.7735
          72              0.7846
          73              0.7853
          74              0.7853
          75              0.786
          76              0.786
          77              0.786
          78              0.786
          79              0.786
          80              0.786
          81              0.786
          82              0.7743
          83              0.7743
          84              0.774
          85              0.786
          86              0.7615
          87              0.7853
          88              0.7615
          89              0.75
          90              0.7618
          91              0.75
          92              0.7382
          93              0.7265

Best importance: 21
Selected features: 33

Features
------------------------------------
s__Actinomyces_sp_HMSC035G02
s__Alistipes_indistinctus
s__Bacteroides_dorei
s__Bacteroides_fragilis
s__Bacteroides_ovatus
s__Bacteroides_salyersiae
s__Bifidobacterium_adolescentis
s__Bifidobacterium_catenulatum
s__Bifidobacterium_pseudocatenulatum
s__Clostridium_clostridioforme
s__Clostridium_sp_CAG_242
s__Collinsella_aerofaciens
s__Coprococcus_comes
s__Dorea_longicatena
s__Eisenbergiella_tayi
s__Eubacterium_dolichum_CAG_375
s__Firmicutes_bacterium_CAG_238
s__Haemophilus_parainfluenzae
s__Haemophilus_sp_HMSC71H05
s__Lachnospira_pectinoschiza
s__Morganella_morganii
s__Parabacteroides_merdae
s__Paraprevotella_xylaniphila
s__Parvimonas_micra
s__Prevotella_stercorea
s__Roseburia_faecis
s__Roseburia_sp_CAG_471
s__Rothia_mucilaginosa
s__Slackia_isoflavoniconvertens
s__Streptococcus_pasteurianus
s__Streptococcus_salivarius
s__Streptococcus_vestibularis
s__[Collinsella]_massiliensis

Total ML models: 9295

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

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

Fold 1 (2 retrainings)
	Error rate: 0.08955223880597014
	Accuracy: 0.7647
	F1: 0.7469
	Precision: 0.8371
	Recall: 0.7647
	Matthews Corr. Coeff.: 0.5883
	Confusion Matrix:
		TN: 4
		FP: 4
		FN: 0
		TP: 9

Fold 2 (0 retrainings)
	Error rate: 0.16417910447761194
	Accuracy: 0.9412
	F1: 0.9412
	Precision: 0.9477
	Recall: 0.9412
	Matthews Corr. Coeff.: 0.8889
	Confusion Matrix:
		TN: 8
		FP: 0
		FN: 1
		TP: 8

Fold 3 (1 retrainings)
	Error rate: 0.13432835820895522
	Accuracy: 0.7059
	F1: 0.7059
	Precision: 0.7108
	Recall: 0.7059
	Matthews Corr. Coeff.: 0.4167
	Confusion Matrix:
		TN: 6
		FP: 3
		FN: 2
		TP: 6

Fold 4 (1 retrainings)
	Error rate: 0.16417910447761194
	Accuracy: 0.7647
	F1: 0.7597
	Precision: 0.7772
	Recall: 0.7647
	Matthews Corr. Coeff.: 0.5367
	Confusion Matrix:
		TN: 8
		FP: 1
		FN: 3
		TP: 5

Fold 5 (0 retrainings)
	Error rate: 0.19117647058823528
	Accuracy: 0.9375
	F1: 0.9373
	Precision: 0.9444
	Recall: 0.9375
	Matthews Corr. Coeff.: 0.8819
	Confusion Matrix:
		TN: 7
		FP: 1
		FN: 0
		TP: 8

Retrainings: 0.8000 (0.8367 stdev)
Error Rate: 0.1487 (0.0387 stdev)
Accuracy: 0.8228 (0.1091 stdev)
F1: 0.8182 (0.1123 stdev)
Precision: 0.8434 (0.1038 stdev)
Recall: 0.8228 (0.1091 stdev)
Matthews Corr. Coeff.: 0.6625 (0.2128 stdev)
Total elapsed time: 326s
