Loading dataset
Points: 193; Features 241; Classes 2
Building the HD model
Selecting features.. This may take a while

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

  Importance    Score (accuracy)
------------  ------------------
           0              0
           1              0.5703
           2              0.596
           3              0.6349
           4              0.6454
           5              0.6479
           6              0.6532
           7              0.6451
           8              0.6442
           9              0.6681
          10              0.675
          11              0.6784
          12              0.6602
          13              0.6807
          14              0.675
          15              0.6972
          16              0.704
          17              0.7065
          18              0.7178
          19              0.7126
          20              0.7204
          21              0.7165
          22              0.6965
          23              0.6954
          24              0.7127
          25              0.7154
          26              0.7075
          27              0.6982
          28              0.6997
          29              0.6974
          30              0.6857
          31              0.6867
          32              0.6916
          33              0.7024
          34              0.6992
          35              0.705
          36              0.6912
          37              0.705
          38              0.6968
          39              0.6997
          40              0.6976
          41              0.6904
          42              0.6961
          43              0.7023
          44              0.7103
          45              0.6756
          46              0.676
          47              0.6862
          48              0.6756
          49              0.6908
          50              0.686
          51              0.6831
          52              0.676
          53              0.6752
          54              0.6922
          55              0.6751
          56              0.6816
          57              0.6817
          58              0.6823
          59              0.6604
          60              0.6686
          61              0.649
          62              0.6554
          63              0.6582
          64              0.6487

Best importance: 20
Selected features: 71

Features
------------------------------------
s__Actinomyces_graevenitzii
s__Actinomyces_odontolyticus
s__Actinomyces_sp_oral_taxon_181
s__Adlercreutzia_equolifaciens
s__Agathobaculum_butyriciproducens
s__Alistipes_indistinctus
s__Alistipes_inops
s__Alloscardovia_omnicolens
s__Anaeromassilibacillus_sp_An250
s__Bacteroides_caccae
s__Bacteroides_clarus
s__Bacteroides_dorei
s__Bacteroides_galacturonicus
s__Bacteroides_plebeius
s__Bacteroides_sp_CAG_144
s__Bacteroides_uniformis
s__Bacteroides_xylanisolvens
s__Barnesiella_intestinihominis
s__Bifidobacterium_adolescentis
s__Bifidobacterium_bifidum
s__Bifidobacterium_longum
s__Bifidobacterium_pseudocatenulatum
s__Blautia_hydrogenotrophica
s__Blautia_sp_CAG_257
s__Butyricicoccus_pullicaecorum
s__Butyricimonas_virosa
s__Clostridium_citroniae
s__Collinsella_aerofaciens
s__Collinsella_stercoris
s__Dialister_pneumosintes
s__Escherichia_coli
s__Eubacterium_dolichum_CAG_375
s__Eubacterium_eligens
s__Eubacterium_rectale
s__Eubacterium_sp_CAG_38
s__Faecalicoccus_pleomorphus
s__Firmicutes_bacterium_CAG_110
s__Firmicutes_bacterium_CAG_145
s__Flavonifractor_plautii
s__Fretibacterium_fastidiosum
s__Gemella_sanguinis
s__Haemophilus_sp_HMSC71H05
s__Holdemania_filiformis
s__Hungatella_hathewayi
s__Klebsiella_oxytoca
s__Klebsiella_pneumoniae
s__Klebsiella_quasipneumoniae
s__Klebsiella_variicola
s__Lactobacillus_delbrueckii
s__Megamonas_hypermegale
s__Megasphaera_elsdenii
s__Odoribacter_splanchnicus
s__Parabacteroides_goldsteinii
s__Paraprevotella_xylaniphila
s__Peptostreptococcus_stomatis
s__Prevotella_copri
s__Prevotella_sp_CAG_1185
s__Prevotella_sp_CAG_279
s__Prevotella_sp_CAG_520
s__Proteobacteria_bacterium_CAG_139
s__Raoultella_ornithinolytica
s__Roseburia_faecis
s__Ruminococcus_gnavus
s__Ruminococcus_lactaris
s__Sanguibacteroides_justesenii
s__Sellimonas_intestinalis
s__Solobacterium_moorei
s__Streptococcus_australis
s__Streptococcus_mitis
s__Streptococcus_oralis
s__Streptococcus_vestibularis

Total ML models: 7594

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

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

Fold 1 (0 retrainings)
	Error rate: 0.22077922077922077
	Accuracy: 0.6667
	F1: 0.6599
	Precision: 0.6762
	Recall: 0.6667
	Matthews Corr. Coeff.: 0.3400
	Confusion Matrix:
		TN: 16
		FP: 4
		FN: 9
		TP: 10

Fold 2 (0 retrainings)
	Error rate: 0.2597402597402597
	Accuracy: 0.6923
	F1: 0.6919
	Precision: 0.6952
	Recall: 0.6923
	Matthews Corr. Coeff.: 0.3879
	Confusion Matrix:
		TN: 13
		FP: 7
		FN: 5
		TP: 14

Fold 3 (1 retrainings)
	Error rate: 0.22727272727272727
	Accuracy: 0.6923
	F1: 0.6927
	Precision: 0.6968
	Recall: 0.6923
	Matthews Corr. Coeff.: 0.3879
	Confusion Matrix:
		TN: 14
		FP: 7
		FN: 5
		TP: 13

Fold 4 (0 retrainings)
	Error rate: 0.27741935483870966
	Accuracy: 0.6842
	F1: 0.6842
	Precision: 0.6880
	Recall: 0.6842
	Matthews Corr. Coeff.: 0.3722
	Confusion Matrix:
		TN: 13
		FP: 7
		FN: 5
		TP: 13

Fold 5 (0 retrainings)
	Error rate: 0.23870967741935484
	Accuracy: 0.7895
	F1: 0.7895
	Precision: 0.7895
	Recall: 0.7895
	Matthews Corr. Coeff.: 0.5778
	Confusion Matrix:
		TN: 16
		FP: 4
		FN: 4
		TP: 14

Retrainings: 0.2000 (0.4472 stdev)
Error Rate: 0.2448 (0.0235 stdev)
Accuracy: 0.7050 (0.0484 stdev)
F1: 0.7036 (0.0498 stdev)
Precision: 0.7091 (0.0456 stdev)
Recall: 0.7050 (0.0484 stdev)
Matthews Corr. Coeff.: 0.4131 (0.0941 stdev)
Total elapsed time: 877s
