Loading dataset
Points: 120; Features 241; Classes 2
Building the HD model
Selecting features.. This may take a while

Feature                                   Importance
--------------------------------------  ------------
s__Bifidobacterium_pseudocatenulatum               0
s__Eubacterium_sp_CAG_38                           1
s__Bacteroides_caccae                              2
s__Bacteroides_xylanisolvens                       3
s__Acidaminococcus_intestini                       4
s__Bacteroides_eggerthii                           5
s__Parabacteroides_merdae                          6
s__Eubacterium_hallii                              7
s__Bacteroides_faecis                              8
s__Bifidobacterium_bifidum                         9
s__Gordonibacter_pamelaeae                        10
s__Lawsonibacter_asaccharolyticus                 10
s__Oscillibacter_sp_CAG_241                       10
s__Firmicutes_bacterium_CAG_110                   11
s__Klebsiella_pneumoniae                          12
s__Streptococcus_oralis                           13
s__Megamonas_funiformis                           14
s__Lactobacillus_rogosae                          15
s__Bacteroides_intestinalis                       16
s__Intestinimonas_butyriciproducens               16
s__Ruminococcaceae_bacterium_D5                   16
s__Streptococcus_parasanguinis                    16
s__Alloprevotella_tannerae                        17
s__Holdemania_filiformis                          17
s__Ruminococcus_callidus                          18
s__Phascolarctobacterium_sp_CAG_266               19
s__Blautia_hansenii                               20
s__Eikenella_corrodens                            20
s__Morganella_morganii                            20
s__Peptostreptococcus_stomatis                    20
s__Porphyromonas_asaccharolytica                  20
s__Veillonella_dispar                             21
s__Blautia_producta                               22
s__Clostridium_symbiosum                          22
s__Sellimonas_intestinalis                        23
s__Firmicutes_bacterium_CAG_170                   24
s__Coprobacter_fastidiosus                        25
s__Bifidobacterium_dentium                        26
s__Parvimonas_micra                               26
s__Lactobacillus_paragasseri                      27
s__Fusobacterium_nucleatum                        28
s__Firmicutes_bacterium_CAG_238                   29
s__Olsenella_scatoligenes                         29
s__Collinsella_stercoris                          30
s__Streptococcus_pasteurianus                     30
s__Akkermansia_muciniphila                        31
s__Clostridium_bolteae                            32
s__Erysipelatoclostridium_ramosum                 32
s__Megasphaera_elsdenii                           32
s__Turicimonas_muris                              32
s__Blautia_sp_CAG_257                             33
s__Butyricimonas_virosa                           33
s__Butyricimonas_synergistica                     34
s__Actinomyces_odontolyticus                      35
s__Coprococcus_catus                              36
s__Firmicutes_bacterium_CAG_95                    36
s__Catenibacterium_mitsuokai                      37
s__Enterobacter_cloacae_complex                   37
s__Flavonifractor_plautii                         38
s__Streptococcus_australis                        38
s__Blautia_obeum                                  39
s__Actinomyces_sp_HMSC035G02                      40
s__Butyrivibrio_sp_CAG_318                        40
s__Alistipes_inops                                41
s__Bacteroides_nordii                             42
s__Rothia_mucilaginosa                            43
s__Bifidobacterium_catenulatum                    44
s__Bacteroides_massiliensis                       45
s__Paraprevotella_clara                           46
s__Bacteroides_clarus                             47
s__Eubacterium_ventriosum                         48
s__Parabacteroides_sp_CAG_409                     49
s__Holdemanella_biformis                          50
s__Actinomyces_graevenitzii                       51
s__Anaeromassilibacillus_sp_An250                 52
s__Allisonella_histaminiformans                   53
s__Sanguibacteroides_justesenii                   53
s__Clostridium_disporicum                         54
s__Alloscardovia_omnicolens                       55
s__Bacteroides_coprophilus                        55
s__Bacteroides_plebeius                           56
s__Clostridium_sp_CAG_58                          57
s__Clostridium_paraputrificum                     58
s__Mitsuokella_jalaludinii                        58
s__Bacteroides_fragilis                           59
s__Roseburia_hominis                              60
s__Eubacterium_rectale                            61
s__Lachnospira_pectinoschiza                      61
s__Asaccharobacter_celatus                        62
s__Coprococcus_eutactus                           62
s__Enterococcus_faecalis                          62
s__Klebsiella_oxytoca                             62
s__Veillonella_infantium                          63
s__Clostridium_innocuum                           64
s__Firmicutes_bacterium_CAG_94                    64
s__Lactobacillus_fermentum                        65
s__Bacteroides_galacturonicus                     66
s__Clostridium_sp_CAG_253                         66
s__Bifidobacterium_breve                          67
s__Dorea_formicigenerans                          67
s__Desulfovibrionaceae_bacterium                  68
s__Dialister_pneumosintes                         68
s__Absiella_dolichum                              69
s__Cloacibacillus_porcorum                        69
s__Desulfovibrio_piger                            70
s__Gemmiger_formicilis                            71
s__Prevotella_sp_CAG_520                          71
s__Pseudoflavonifractor_sp_An184                  71
s__Megamonas_hypermegale                          72
s__Bacteroides_sp_CAG_144                         73
s__Alistipes_onderdonkii                          74
s__Bacteroides_thetaiotaomicron                   74
s__Escherichia_coli                               74
s__Gemella_sanguinis                              75
s__Monoglobus_pectinilyticus                      75
s__Streptococcus_mitis                            75
s__Parabacteroides_johnsonii                      76
s__Solobacterium_moorei                           76
s__Adlercreutzia_equolifaciens                    77
s__Clostridium_bolteae_CAG_59                     78
s__Alistipes_finegoldii                           79
s__Bifidobacterium_animalis                       79
s__Fretibacterium_fastidiosum                     79
s__Enterococcus_faecium                           80
s__Streptococcus_sanguinis                        81
s__Faecalicoccus_pleomorphus                      82
s__Mogibacterium_diversum                         82
s__Prevotella_sp_CAG_279                          82
s__Eggerthella_lenta                              83
s__Phascolarctobacterium_succinatutens            84
s__Clostridium_clostridioforme                    85
s__Mitsuokella_multacida                          86
s__Turicibacter_sanguinis                         87
s__Paraprevotella_xylaniphila                     88
s__Anaerostipes_hadrus                            89
s__Firmicutes_bacterium_CAG_83                    90
s__Eubacterium_ramulus                            91
s__Roseburia_inulinivorans                        91
s__Roseburia_faecis                               92
s__Eubacterium_sp_CAG_274                         93
s__Proteobacteria_bacterium_CAG_139               93
s__Streptococcus_anginosus_group                  93
s__Streptococcus_mutans                           93
s__Bilophila_wadsworthia                          94
s__Odoribacter_splanchnicus                       95
s__Streptococcus_gordonii                         95
s__Dialister_sp_CAG_357                           96
s__Tyzzerella_nexilis                             96
s__Anaerotignum_lactatifermentans                 97
s__Bacteroides_dorei                              97
s__Citrobacter_youngae                            97
s__Bacteroides_stercoris                          98
s__Clostridium_citroniae                          98
s__Eisenbergiella_massiliensis                    98
s__Victivallis_vadensis                           99
s__Bacteroides_salyersiae                        100
s__Bacteroides_vulgatus                          101
s__Prevotella_copri                              102
s__Ruminococcus_gnavus                           103
s__Bifidobacterium_adolescentis                  104
s__Streptococcus_thermophilus                    104
s__Bacteroides_uniformis                         105
s__Faecalibacterium_prausnitzii                  105
s__Streptococcus_salivarius                      106
s__Bacteroides_cellulosilyticus                  107
s__Eisenbergiella_tayi                           107
s__Eubacterium_eligens                           107
s__Eubacterium_sp_CAG_251                        107
s__Ruminococcus_bromii                           107
s__Streptococcus_infantis                        107
s__Sutterella_parvirubra                         107
s__Clostridium_sp_CAG_242                        108
s__Collinsella_aerofaciens                       108
s__Firmicutes_bacterium_CAG_145                  108
s__Parabacteroides_goldsteinii                   109
s__Coprococcus_comes                             110
s__Intestinibacter_bartlettii                    110
s__Bacteroides_faecis_CAG_32                     111
s__Bacteroides_coprocola                         112
s__Slackia_isoflavoniconvertens                  112
s__Butyricicoccus_pullicaecorum                  113
s__Coprobacillus_cateniformis                    113
s__Eubacterium_dolichum_CAG_375                  113
s__Klebsiella_michiganensis                      113
s__Ruminococcus_torques                          113
s__Blautia_wexlerae                              114
s__Lactobacillus_delbrueckii                     115
s__Lactobacillus_gasseri                         115
s__Raoultella_ornithinolytica                    115
s__Bacteroides_finegoldii                        116
s__Prevotella_stercorea                          116
s__Actinomyces_turicensis                        117
s__Haemophilus_parainfluenzae                    117
s__Bifidobacterium_longum                        118
s__Agathobaculum_butyriciproducens               119
s__Actinomyces_sp_ICM47                          120
s__Clostridium_asparagiforme                     120
s__Clostridium_lavalense                         120
s__Bacteroides_ovatus                            121
s__Clostridium_sp_CAG_299                        122
s__Eubacterium_sp_CAG_180                        122
s__Anaerotruncus_colihominis                     123
s__Collinsella_intestinalis                      123
s__Roseburia_sp_CAG_471                          123
s__Ruminococcus_lactaris                         123
s__Veillonella_parvula                           123
s__Parasutterella_excrementihominis              124
s__Fusicatenibacter_saccharivorans               125
s__Actinomyces_sp_oral_taxon_181                 126
s__Clostridium_spiroforme                        126
s__Gemella_morbillorum                           126
s__Klebsiella_quasipneumoniae                    126
s__Ruthenibacterium_lactatiformans               127
s__Clostridium_saccharolyticum                   128
s__Clostridium_sp_CAG_167                        128
s__Alistipes_shahii                              129
s__Klebsiella_variicola                          129
s__Oscillibacter_sp_57_20                        129
s__Ruminococcus_bicirculans                      130
s__Veillonella_atypica                           130
s__Dialister_invisus                             131
s__Haemophilus_sp_HMSC71H05                      131
s__Eubacterium_siraeum                           132
s__Parabacteroides_distasonis                    132
s__Dorea_longicatena                             133
s__Enorma_massiliensis                           134
s__Phascolarctobacterium_faecium                 134
s__Clostridium_leptum                            135
s__Roseburia_intestinalis                        135
s__Hungatella_hathewayi                          136
s__Pyramidobacter_piscolens                      136
s__Alistipes_indistinctus                        137
s__Blautia_hydrogenotrophica                     137
s__Coprobacter_secundus                          137
s__Slackia_exigua                                137
s__[Collinsella]_massiliensis                    137
s__Barnesiella_intestinihominis                  138
s__Streptococcus_vestibularis                    138
s__Ruminococcaceae_bacterium_D16                 139
s__Prevotella_sp_CAG_1185                        140
s__Alistipes_putredinis                          141

  Importance    Score (accuracy)
------------  ------------------
           0              0
           1              0.65
           2              0.675
           3              0.7167
           4              0.7167
           5              0.7083
           6              0.7
           7              0.6833
           8              0.7167
           9              0.7083
          10              0.7167
          11              0.7167
          12              0.725
          13              0.7083
          14              0.7167
          15              0.7333
          16              0.7333
          17              0.7583
          18              0.775
          19              0.7667
          20              0.7583
          21              0.7667
          22              0.75
          23              0.7667
          24              0.775
          25              0.7833
          26              0.7917
          27              0.775
          28              0.7833
          29              0.775
          30              0.7917
          31              0.7917
          32              0.7917
          33              0.8083
          34              0.8167
          35              0.8
          36              0.7917
          37              0.7917
          38              0.7917
          39              0.775
          40              0.775
          41              0.7917
          42              0.7833
          43              0.8
          44              0.7833
          45              0.7917
          46              0.7917
          47              0.7833
          48              0.775
          49              0.7917
          50              0.775
          51              0.775
          52              0.775
          53              0.775
          54              0.7833
          55              0.775
          56              0.7833
          57              0.7583
          58              0.7667
          59              0.7833
          60              0.7667
          61              0.7417
          62              0.75
          63              0.75
          64              0.7667
          65              0.7583
          66              0.75
          67              0.7583
          68              0.7667
          69              0.7583
          70              0.7583
          71              0.7667
          72              0.7833
          73              0.7667
          74              0.775
          75              0.775
          76              0.775
          77              0.8083
          78              0.7917
          79              0.7917
          80              0.8167
          81              0.8
          82              0.7917
          83              0.8
          84              0.8
          85              0.8
          86              0.8167
          87              0.8083
          88              0.8
          89              0.8083
          90              0.8167
          91              0.775
          92              0.775
          93              0.7667
          94              0.7917
          95              0.7833
          96              0.7833
          97              0.775
          98              0.75
          99              0.7583
         100              0.7667
         101              0.7333
         102              0.725
         103              0.7083
         104              0.7083
         105              0.7
         106              0.7
         107              0.6833
         108              0.6833
         109              0.6833
         110              0.6833
         111              0.6917
         112              0.6833
         113              0.6833
         114              0.6833
         115              0.6833
         116              0.6833
         117              0.6833
         118              0.7
         119              0.7
         120              0.6833
         121              0.7083
         122              0.6917
         123              0.6917
         124              0.7083
         125              0.7083
         126              0.7
         127              0.7
         128              0.7
         129              0.7
         130              0.6917
         131              0.7
         132              0.6917
         133              0.6917
         134              0.6917
         135              0.6917
         136              0.6917
         137              0.6833
         138              0.6917
         139              0.7
         140              0.6917
         141              0.6833

Best importance: 86
Selected features: 132

Features
--------------------------------------
s__Absiella_dolichum
s__Acidaminococcus_intestini
s__Actinomyces_graevenitzii
s__Actinomyces_odontolyticus
s__Actinomyces_sp_HMSC035G02
s__Adlercreutzia_equolifaciens
s__Akkermansia_muciniphila
s__Alistipes_finegoldii
s__Alistipes_inops
s__Alistipes_onderdonkii
s__Allisonella_histaminiformans
s__Alloprevotella_tannerae
s__Alloscardovia_omnicolens
s__Anaeromassilibacillus_sp_An250
s__Asaccharobacter_celatus
s__Bacteroides_caccae
s__Bacteroides_clarus
s__Bacteroides_coprophilus
s__Bacteroides_eggerthii
s__Bacteroides_faecis
s__Bacteroides_fragilis
s__Bacteroides_galacturonicus
s__Bacteroides_intestinalis
s__Bacteroides_massiliensis
s__Bacteroides_nordii
s__Bacteroides_plebeius
s__Bacteroides_sp_CAG_144
s__Bacteroides_thetaiotaomicron
s__Bacteroides_xylanisolvens
s__Bifidobacterium_animalis
s__Bifidobacterium_bifidum
s__Bifidobacterium_breve
s__Bifidobacterium_catenulatum
s__Bifidobacterium_dentium
s__Bifidobacterium_pseudocatenulatum
s__Blautia_hansenii
s__Blautia_obeum
s__Blautia_producta
s__Blautia_sp_CAG_257
s__Butyricimonas_synergistica
s__Butyricimonas_virosa
s__Butyrivibrio_sp_CAG_318
s__Catenibacterium_mitsuokai
s__Cloacibacillus_porcorum
s__Clostridium_bolteae
s__Clostridium_bolteae_CAG_59
s__Clostridium_clostridioforme
s__Clostridium_disporicum
s__Clostridium_innocuum
s__Clostridium_paraputrificum
s__Clostridium_sp_CAG_253
s__Clostridium_sp_CAG_58
s__Clostridium_symbiosum
s__Collinsella_stercoris
s__Coprobacter_fastidiosus
s__Coprococcus_catus
s__Coprococcus_eutactus
s__Desulfovibrio_piger
s__Desulfovibrionaceae_bacterium
s__Dialister_pneumosintes
s__Dorea_formicigenerans
s__Eggerthella_lenta
s__Eikenella_corrodens
s__Enterobacter_cloacae_complex
s__Enterococcus_faecalis
s__Enterococcus_faecium
s__Erysipelatoclostridium_ramosum
s__Escherichia_coli
s__Eubacterium_hallii
s__Eubacterium_rectale
s__Eubacterium_sp_CAG_38
s__Eubacterium_ventriosum
s__Faecalicoccus_pleomorphus
s__Firmicutes_bacterium_CAG_110
s__Firmicutes_bacterium_CAG_170
s__Firmicutes_bacterium_CAG_238
s__Firmicutes_bacterium_CAG_94
s__Firmicutes_bacterium_CAG_95
s__Flavonifractor_plautii
s__Fretibacterium_fastidiosum
s__Fusobacterium_nucleatum
s__Gemella_sanguinis
s__Gemmiger_formicilis
s__Gordonibacter_pamelaeae
s__Holdemanella_biformis
s__Holdemania_filiformis
s__Intestinimonas_butyriciproducens
s__Klebsiella_oxytoca
s__Klebsiella_pneumoniae
s__Lachnospira_pectinoschiza
s__Lactobacillus_fermentum
s__Lactobacillus_paragasseri
s__Lactobacillus_rogosae
s__Lawsonibacter_asaccharolyticus
s__Megamonas_funiformis
s__Megamonas_hypermegale
s__Megasphaera_elsdenii
s__Mitsuokella_jalaludinii
s__Mitsuokella_multacida
s__Mogibacterium_diversum
s__Monoglobus_pectinilyticus
s__Morganella_morganii
s__Olsenella_scatoligenes
s__Oscillibacter_sp_CAG_241
s__Parabacteroides_johnsonii
s__Parabacteroides_merdae
s__Parabacteroides_sp_CAG_409
s__Paraprevotella_clara
s__Parvimonas_micra
s__Peptostreptococcus_stomatis
s__Phascolarctobacterium_sp_CAG_266
s__Phascolarctobacterium_succinatutens
s__Porphyromonas_asaccharolytica
s__Prevotella_sp_CAG_279
s__Prevotella_sp_CAG_520
s__Pseudoflavonifractor_sp_An184
s__Roseburia_hominis
s__Rothia_mucilaginosa
s__Ruminococcaceae_bacterium_D5
s__Ruminococcus_callidus
s__Sanguibacteroides_justesenii
s__Sellimonas_intestinalis
s__Solobacterium_moorei
s__Streptococcus_australis
s__Streptococcus_mitis
s__Streptococcus_oralis
s__Streptococcus_parasanguinis
s__Streptococcus_pasteurianus
s__Streptococcus_sanguinis
s__Turicimonas_muris
s__Veillonella_dispar
s__Veillonella_infantium

Total ML models: 15816

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

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

Fold 1 (1 retrainings)
	Error rate: 0.08333333333333333
	Accuracy: 0.7917
	F1: 0.7928
	Precision: 0.8188
	Recall: 0.7917
	Matthews Corr. Coeff.: 0.6078
	Confusion Matrix:
		TN: 10
		FP: 4
		FN: 1
		TP: 9

Fold 2 (2 retrainings)
	Error rate: 0.010416666666666666
	Accuracy: 0.7500
	F1: 0.7517
	Precision: 0.7639
	Recall: 0.7500
	Matthews Corr. Coeff.: 0.5071
	Confusion Matrix:
		TN: 10
		FP: 4
		FN: 2
		TP: 8

Fold 3 (0 retrainings)
	Error rate: 0.0625
	Accuracy: 0.7500
	F1: 0.7389
	Precision: 0.7752
	Recall: 0.7500
	Matthews Corr. Coeff.: 0.5136
	Confusion Matrix:
		TN: 12
		FP: 1
		FN: 5
		TP: 6

Fold 4 (0 retrainings)
	Error rate: 0.08333333333333333
	Accuracy: 0.7917
	F1: 0.7906
	Precision: 0.8149
	Recall: 0.7917
	Matthews Corr. Coeff.: 0.6078
	Confusion Matrix:
		TN: 9
		FP: 4
		FN: 1
		TP: 10

Fold 5 (1 retrainings)
	Error rate: 0.0625
	Accuracy: 0.6250
	F1: 0.6148
	Precision: 0.6250
	Recall: 0.6250
	Matthews Corr. Coeff.: 0.2365
	Confusion Matrix:
		TN: 10
		FP: 3
		FN: 6
		TP: 5

Retrainings: 0.8000 (0.8367 stdev)
Error Rate: 0.0604 (0.0298 stdev)
Accuracy: 0.7417 (0.0685 stdev)
F1: 0.7378 (0.0727 stdev)
Precision: 0.7595 (0.0790 stdev)
Recall: 0.7417 (0.0685 stdev)
Matthews Corr. Coeff.: 0.4946 (0.1523 stdev)
Total elapsed time: 1361s
