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

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

  Importance    Score (accuracy)
------------  ------------------
           0              0
           1              0.7199
           2              0.7561
           3              0.7714
           4              0.7795
           5              0.7959
           6              0.8106
           7              0.8258
           8              0.8235
           9              0.813
          10              0.8233
          11              0.8285
          12              0.8191
          13              0.8201
          14              0.8088
          15              0.8022
          16              0.7842
          17              0.7692
          18              0.7668
          19              0.7821
          20              0.7871
          21              0.7926
          22              0.7925
          23              0.7877
          24              0.7836
          25              0.7671
          26              0.7685
          27              0.7625
          28              0.757
          29              0.7406
          30              0.7356
          31              0.7207
          32              0.7153
          33              0.6993

Best importance: 11
Selected features: 23

Features
------------------------------------
s__Adlercreutzia_equolifaciens
s__Bacteroides_nordii
s__Bacteroides_salyersiae
s__Bifidobacterium_longum
s__Bifidobacterium_pseudocatenulatum
s__Clostridium_leptum
s__Clostridium_sp_CAG_242
s__Dialister_sp_CAG_357
s__Erysipelatoclostridium_ramosum
s__Eubacterium_ventriosum
s__Firmicutes_bacterium_CAG_145
s__Gemella_morbillorum
s__Holdemania_filiformis
s__Hungatella_hathewayi
s__Klebsiella_pneumoniae
s__Mitsuokella_multacida
s__Paraprevotella_xylaniphila
s__Parvimonas_micra
s__Prevotella_sp_CAG_279
s__Roseburia_hominis
s__Streptococcus_salivarius
s__Veillonella_parvula
s__Victivallis_vadensis

Total ML models: 2913

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

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

Fold 1 (1 retrainings)
	Error rate: 0.16883116883116883
	Accuracy: 0.8462
	F1: 0.8441
	Precision: 0.8607
	Recall: 0.8462
	Matthews Corr. Coeff.: 0.7057
	Confusion Matrix:
		TN: 19
		FP: 1
		FN: 5
		TP: 14

Fold 2 (0 retrainings)
	Error rate: 0.15584415584415584
	Accuracy: 0.7436
	F1: 0.7436
	Precision: 0.7436
	Recall: 0.7436
	Matthews Corr. Coeff.: 0.4868
	Confusion Matrix:
		TN: 15
		FP: 5
		FN: 5
		TP: 14

Fold 3 (0 retrainings)
	Error rate: 0.21428571428571427
	Accuracy: 0.9231
	F1: 0.9232
	Precision: 0.9245
	Recall: 0.9231
	Matthews Corr. Coeff.: 0.8470
	Confusion Matrix:
		TN: 19
		FP: 2
		FN: 1
		TP: 17

Fold 4 (0 retrainings)
	Error rate: 0.15483870967741936
	Accuracy: 0.7895
	F1: 0.7895
	Precision: 0.7939
	Recall: 0.7895
	Matthews Corr. Coeff.: 0.5833
	Confusion Matrix:
		TN: 15
		FP: 5
		FN: 3
		TP: 15

Fold 5 (0 retrainings)
	Error rate: 0.15483870967741936
	Accuracy: 0.7632
	F1: 0.7627
	Precision: 0.7718
	Recall: 0.7632
	Matthews Corr. Coeff.: 0.5356
	Confusion Matrix:
		TN: 14
		FP: 6
		FN: 3
		TP: 15

Retrainings: 0.2000 (0.4472 stdev)
Error Rate: 0.1697 (0.0256 stdev)
Accuracy: 0.8131 (0.0726 stdev)
F1: 0.8126 (0.0725 stdev)
Precision: 0.8189 (0.0732 stdev)
Recall: 0.8131 (0.0726 stdev)
Matthews Corr. Coeff.: 0.6317 (0.1452 stdev)
Total elapsed time: 242s
