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

  Importance    Score (accuracy)
------------  ------------------
           0              0
           1              0.6917
           2              0.7583
           3              0.775
           4              0.7917
           5              0.8
           6              0.8167
           7              0.825
           8              0.7917
           9              0.8167
          10              0.825
          11              0.8375
          12              0.8542
          13              0.8625
          14              0.8633
          15              0.875
          16              0.835
          17              0.8528
          18              0.8444
          19              0.844
          20              0.83
          21              0.8375
          22              0.8417
          23              0.8278
          24              0.8167
          25              0.8167
          26              0.825
          27              0.825
          28              0.825
          29              0.8167
          30              0.8
          31              0.8
          32              0.8
          33              0.8
          34              0.7917
          35              0.7917
          36              0.775
          37              0.7667
          38              0.775
          39              0.7667
          40              0.7583
          41              0.7667
          42              0.7583
          43              0.75
          44              0.75
          45              0.75
          46              0.7417
          47              0.7167
          48              0.725
          49              0.725
          50              0.725
          51              0.725
          52              0.7333
          53              0.7167

Best importance: 15
Selected features: 31

Features
------------------------------------
s__Actinomyces_odontolyticus
s__Akkermansia_muciniphila
s__Alistipes_indistinctus
s__Alistipes_shahii
s__Alloprevotella_tannerae
s__Anaerotruncus_colihominis
s__Bacteroides_dorei
s__Bacteroides_intestinalis
s__Bacteroides_uniformis
s__Bacteroides_xylanisolvens
s__Bifidobacterium_pseudocatenulatum
s__Blautia_hydrogenotrophica
s__Butyrivibrio_sp_CAG_318
s__Clostridium_leptum
s__Coprococcus_eutactus
s__Dialister_invisus
s__Enterobacter_cloacae_complex
s__Escherichia_coli
s__Eubacterium_ventriosum
s__Faecalibacterium_prausnitzii
s__Firmicutes_bacterium_CAG_145
s__Firmicutes_bacterium_CAG_94
s__Gordonibacter_pamelaeae
s__Holdemania_filiformis
s__Klebsiella_quasipneumoniae
s__Parabacteroides_johnsonii
s__Parabacteroides_merdae
s__Parvimonas_micra
s__Prevotella_stercorea
s__Sellimonas_intestinalis
s__Victivallis_vadensis

Total ML models: 5730

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

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

Fold 1 (0 retrainings)
	Error rate: 0.1875
	Accuracy: 0.8333
	F1: 0.8333
	Precision: 0.8333
	Recall: 0.8333
	Matthews Corr. Coeff.: 0.6571
	Confusion Matrix:
		TN: 12
		FP: 2
		FN: 2
		TP: 8

Fold 2 (0 retrainings)
	Error rate: 0.125
	Accuracy: 0.7083
	F1: 0.7099
	Precision: 0.7337
	Recall: 0.7083
	Matthews Corr. Coeff.: 0.4382
	Confusion Matrix:
		TN: 9
		FP: 5
		FN: 2
		TP: 8

Fold 3 (0 retrainings)
	Error rate: 0.14583333333333334
	Accuracy: 0.6667
	F1: 0.6667
	Precision: 0.6667
	Recall: 0.6667
	Matthews Corr. Coeff.: 0.3287
	Confusion Matrix:
		TN: 9
		FP: 4
		FN: 4
		TP: 7

Fold 4 (0 retrainings)
	Error rate: 0.14583333333333334
	Accuracy: 0.9167
	F1: 0.9167
	Precision: 0.9295
	Recall: 0.9167
	Matthews Corr. Coeff.: 0.8462
	Confusion Matrix:
		TN: 11
		FP: 2
		FN: 0
		TP: 11

Fold 5 (0 retrainings)
	Error rate: 0.16666666666666666
	Accuracy: 0.7917
	F1: 0.7906
	Precision: 0.7923
	Recall: 0.7917
	Matthews Corr. Coeff.: 0.5795
	Confusion Matrix:
		TN: 11
		FP: 2
		FN: 3
		TP: 8

Retrainings: 0.0000 (0.0000 stdev)
Error Rate: 0.1542 (0.0238 stdev)
Accuracy: 0.7833 (0.0995 stdev)
F1: 0.7834 (0.0992 stdev)
Precision: 0.7911 (0.0996 stdev)
Recall: 0.7833 (0.0995 stdev)
Matthews Corr. Coeff.: 0.5699 (0.1997 stdev)
Total elapsed time: 312s
