Table 3

Performance evaluation with AUC (A), precision (P), and recall (R) (with the standard mean error in brackets)

ComparisonMethodEW-T2DLCC-T2DIBDObesity
A. Taxonomic featuresRFA78.2%(3.2%)95.1%(1.5%)75.1%(2.6%)92.6%(2.2%)65.3%(4.4%)
P71.3%(2.3%)92.6%(1.7%)66.9%(1.9%)70.0%(20.0%)64.1%(0.4%)
R80.0%(3.4%)82.5%(3.6%)62.9%(3.9%)20.0%(6.3%)97.6%(1.5%)
SVMA75.5%(3.1%)89.4%(2.2%)71.6%(2.4%)92.0%(2.6%)64.2%(3.8%)
P75.2%(3.6%)81.9%(3.3%)65.7%(3.5%)66.7%(18.3%)70.9%(2.5%)
R69.1%(6.2%)75.0%(4.2%)61.8%(4.7%)36.0%(9.8%)77.0%(3.1%)
MLPA74.1%(5.1%)90.0%(1.5%)72.3%(2.2%)86.4%(5.0%)52.3%(3.0%)
P86.4%(6.9%)79.3%(2.1%)67.3%(2.0%)86.3%(2.3%)67.2%(1.5%)
R69.1%(6.8%)86.1%(3.2%)64.1%(5.8%)94.1%(2.6%)70.3%(1.5%)
FT-TransformerA78.4%(3.6%)90.4%(2.4%)73.2%(3.0%)93.6%(2.0%)66.1%(1.7%)
P71.4%(4.7%)84.8%(6.2%)66.8%(3.2%)70.1%(7.7%)75.9%(2.5%)
R69.1%(6.8%)85.8%(3.4%)64.1%(3.3%)72.0%(4.9%)67.3%(6.9%)
DeepMicro [7]A82.9%(3.9%)88.8%(1.1%)72.5%(2.5%)87.3%(3.0%)67.4%(3.4%)
P
R
EnsDeepDP [4]A86.7%(N/A)94.3%(N/A)77.6%(N/A)95.8%(N/A)72.3%(N/A)
P
R
B. Taxonomic features with external knowledgeMeta-Signer [15]A90.5%(5.0%)79.4(15.9%)60.0%(13.5%)
P
R
TaxoNN [16]A91.1%(N/A)73.3%(N/A)
P
R
PopPhy-CNN [14]A90.1%(N/A)58.9%(N/A)
P
R
MicroKPNN [18]A85.8(6.7%)96.9%(0.9%)75.5%(3.2%)95.4%(3.7%)72.8%(4.8%)
P
R
C. Taxonomic features and functional featuresMDL4MicrobiomeA76.8%(5.7%)92.5%(1.3%)74.7%(1.3%)88.0%(0.6%)54.1%(2.0%)
P76.3%(7.5%)78.1%(1.4%)67.6%(1.9%)86.0%(1.7%)69.3%(1.9%)
R69.1%(4.6%)89.1%(5.4%)66.5%(4.2%)92.9%(2.9%)72.1%(3.2%)
MVIB [29]A85.9%(2.3%)92.5%(0.5%)75.8%(1.2%)93.6%(1.4%)66.6%(2.7%)
P
R
FT-ConcatA82.6%(3.1%)91.7%(1.7%)77.5%(1.9%)92.0%(2.4%)61.5%(4.2%)
P77.8%(4.0%)89.4%(3.2%)68.9%(2.2%)79.3%(9.7%)75.1%(3.3%)
R80.0%(7.3%)76.7%(4.5%)68.2%(6.1%)64.0%(7.5%)57.6%(12.4%)
FT-VoteA82.2%(2.1%)91.4%(1.4%)76.6%(1.6%)94.6%(1.7%)61.0%(3.3%)
P70.5%(5.4%)84.4%(4.0%)68.3%(1.5%)77.7%(6.1%)70.4%(2.1%)
R80.0%(6.0%)87.5%(2.9%)63.5%(4.3%)56.0%(11.7%)63.0%(11.9%)
T-MBTA83.2%(4.2%)91.7%(2.3%)76.6%(1.6%)95.5%(2.1%)62.2%(3.3%)
P80.0%(2.8%)87.1%(4.2%)69.7%(2.8%)81.7%(7.6%)73.1%(2.6%)
R67.3%(6.2%)80.8%(6.0%)70.0%(1.7%)68.0%(8.0%)60.6%(7.3%)
MSFT-TransformerA87.5%(4.1%)94.1%(1.2%)77.6%(1.6%)97.4%(1.8%)67.7%(2.9%)
P80.5%(7.0%)88.7%(3.9%)70.8%(2.8%)100.0%(0.0%)72.7%(2.9%)
R83.6%(6.0%)89.2%(3.4%)65.3%(2.5%)72.0%(13.6%)69.7%(10.5%)
ComparisonMethodEW-T2DLCC-T2DIBDObesity
A. Taxonomic featuresRFA78.2%(3.2%)95.1%(1.5%)75.1%(2.6%)92.6%(2.2%)65.3%(4.4%)
P71.3%(2.3%)92.6%(1.7%)66.9%(1.9%)70.0%(20.0%)64.1%(0.4%)
R80.0%(3.4%)82.5%(3.6%)62.9%(3.9%)20.0%(6.3%)97.6%(1.5%)
SVMA75.5%(3.1%)89.4%(2.2%)71.6%(2.4%)92.0%(2.6%)64.2%(3.8%)
P75.2%(3.6%)81.9%(3.3%)65.7%(3.5%)66.7%(18.3%)70.9%(2.5%)
R69.1%(6.2%)75.0%(4.2%)61.8%(4.7%)36.0%(9.8%)77.0%(3.1%)
MLPA74.1%(5.1%)90.0%(1.5%)72.3%(2.2%)86.4%(5.0%)52.3%(3.0%)
P86.4%(6.9%)79.3%(2.1%)67.3%(2.0%)86.3%(2.3%)67.2%(1.5%)
R69.1%(6.8%)86.1%(3.2%)64.1%(5.8%)94.1%(2.6%)70.3%(1.5%)
FT-TransformerA78.4%(3.6%)90.4%(2.4%)73.2%(3.0%)93.6%(2.0%)66.1%(1.7%)
P71.4%(4.7%)84.8%(6.2%)66.8%(3.2%)70.1%(7.7%)75.9%(2.5%)
R69.1%(6.8%)85.8%(3.4%)64.1%(3.3%)72.0%(4.9%)67.3%(6.9%)
DeepMicro [7]A82.9%(3.9%)88.8%(1.1%)72.5%(2.5%)87.3%(3.0%)67.4%(3.4%)
P
R
EnsDeepDP [4]A86.7%(N/A)94.3%(N/A)77.6%(N/A)95.8%(N/A)72.3%(N/A)
P
R
B. Taxonomic features with external knowledgeMeta-Signer [15]A90.5%(5.0%)79.4(15.9%)60.0%(13.5%)
P
R
TaxoNN [16]A91.1%(N/A)73.3%(N/A)
P
R
PopPhy-CNN [14]A90.1%(N/A)58.9%(N/A)
P
R
MicroKPNN [18]A85.8(6.7%)96.9%(0.9%)75.5%(3.2%)95.4%(3.7%)72.8%(4.8%)
P
R
C. Taxonomic features and functional featuresMDL4MicrobiomeA76.8%(5.7%)92.5%(1.3%)74.7%(1.3%)88.0%(0.6%)54.1%(2.0%)
P76.3%(7.5%)78.1%(1.4%)67.6%(1.9%)86.0%(1.7%)69.3%(1.9%)
R69.1%(4.6%)89.1%(5.4%)66.5%(4.2%)92.9%(2.9%)72.1%(3.2%)
MVIB [29]A85.9%(2.3%)92.5%(0.5%)75.8%(1.2%)93.6%(1.4%)66.6%(2.7%)
P
R
FT-ConcatA82.6%(3.1%)91.7%(1.7%)77.5%(1.9%)92.0%(2.4%)61.5%(4.2%)
P77.8%(4.0%)89.4%(3.2%)68.9%(2.2%)79.3%(9.7%)75.1%(3.3%)
R80.0%(7.3%)76.7%(4.5%)68.2%(6.1%)64.0%(7.5%)57.6%(12.4%)
FT-VoteA82.2%(2.1%)91.4%(1.4%)76.6%(1.6%)94.6%(1.7%)61.0%(3.3%)
P70.5%(5.4%)84.4%(4.0%)68.3%(1.5%)77.7%(6.1%)70.4%(2.1%)
R80.0%(6.0%)87.5%(2.9%)63.5%(4.3%)56.0%(11.7%)63.0%(11.9%)
T-MBTA83.2%(4.2%)91.7%(2.3%)76.6%(1.6%)95.5%(2.1%)62.2%(3.3%)
P80.0%(2.8%)87.1%(4.2%)69.7%(2.8%)81.7%(7.6%)73.1%(2.6%)
R67.3%(6.2%)80.8%(6.0%)70.0%(1.7%)68.0%(8.0%)60.6%(7.3%)
MSFT-TransformerA87.5%(4.1%)94.1%(1.2%)77.6%(1.6%)97.4%(1.8%)67.7%(2.9%)
P80.5%(7.0%)88.7%(3.9%)70.8%(2.8%)100.0%(0.0%)72.7%(2.9%)
R83.6%(6.0%)89.2%(3.4%)65.3%(2.5%)72.0%(13.6%)69.7%(10.5%)

The reported results of cited methods are based on previous works that use the same datasets. There are a total of nine methods (uncited) evaluated with our framework for five trails, including MSFT-Transformer. N/A indicates that the corresponding study did not provide the standard mean error. The best performance of each dataset is highlighted in bold while the second-high underlined.

Table 3

Performance evaluation with AUC (A), precision (P), and recall (R) (with the standard mean error in brackets)

ComparisonMethodEW-T2DLCC-T2DIBDObesity
A. Taxonomic featuresRFA78.2%(3.2%)95.1%(1.5%)75.1%(2.6%)92.6%(2.2%)65.3%(4.4%)
P71.3%(2.3%)92.6%(1.7%)66.9%(1.9%)70.0%(20.0%)64.1%(0.4%)
R80.0%(3.4%)82.5%(3.6%)62.9%(3.9%)20.0%(6.3%)97.6%(1.5%)
SVMA75.5%(3.1%)89.4%(2.2%)71.6%(2.4%)92.0%(2.6%)64.2%(3.8%)
P75.2%(3.6%)81.9%(3.3%)65.7%(3.5%)66.7%(18.3%)70.9%(2.5%)
R69.1%(6.2%)75.0%(4.2%)61.8%(4.7%)36.0%(9.8%)77.0%(3.1%)
MLPA74.1%(5.1%)90.0%(1.5%)72.3%(2.2%)86.4%(5.0%)52.3%(3.0%)
P86.4%(6.9%)79.3%(2.1%)67.3%(2.0%)86.3%(2.3%)67.2%(1.5%)
R69.1%(6.8%)86.1%(3.2%)64.1%(5.8%)94.1%(2.6%)70.3%(1.5%)
FT-TransformerA78.4%(3.6%)90.4%(2.4%)73.2%(3.0%)93.6%(2.0%)66.1%(1.7%)
P71.4%(4.7%)84.8%(6.2%)66.8%(3.2%)70.1%(7.7%)75.9%(2.5%)
R69.1%(6.8%)85.8%(3.4%)64.1%(3.3%)72.0%(4.9%)67.3%(6.9%)
DeepMicro [7]A82.9%(3.9%)88.8%(1.1%)72.5%(2.5%)87.3%(3.0%)67.4%(3.4%)
P
R
EnsDeepDP [4]A86.7%(N/A)94.3%(N/A)77.6%(N/A)95.8%(N/A)72.3%(N/A)
P
R
B. Taxonomic features with external knowledgeMeta-Signer [15]A90.5%(5.0%)79.4(15.9%)60.0%(13.5%)
P
R
TaxoNN [16]A91.1%(N/A)73.3%(N/A)
P
R
PopPhy-CNN [14]A90.1%(N/A)58.9%(N/A)
P
R
MicroKPNN [18]A85.8(6.7%)96.9%(0.9%)75.5%(3.2%)95.4%(3.7%)72.8%(4.8%)
P
R
C. Taxonomic features and functional featuresMDL4MicrobiomeA76.8%(5.7%)92.5%(1.3%)74.7%(1.3%)88.0%(0.6%)54.1%(2.0%)
P76.3%(7.5%)78.1%(1.4%)67.6%(1.9%)86.0%(1.7%)69.3%(1.9%)
R69.1%(4.6%)89.1%(5.4%)66.5%(4.2%)92.9%(2.9%)72.1%(3.2%)
MVIB [29]A85.9%(2.3%)92.5%(0.5%)75.8%(1.2%)93.6%(1.4%)66.6%(2.7%)
P
R
FT-ConcatA82.6%(3.1%)91.7%(1.7%)77.5%(1.9%)92.0%(2.4%)61.5%(4.2%)
P77.8%(4.0%)89.4%(3.2%)68.9%(2.2%)79.3%(9.7%)75.1%(3.3%)
R80.0%(7.3%)76.7%(4.5%)68.2%(6.1%)64.0%(7.5%)57.6%(12.4%)
FT-VoteA82.2%(2.1%)91.4%(1.4%)76.6%(1.6%)94.6%(1.7%)61.0%(3.3%)
P70.5%(5.4%)84.4%(4.0%)68.3%(1.5%)77.7%(6.1%)70.4%(2.1%)
R80.0%(6.0%)87.5%(2.9%)63.5%(4.3%)56.0%(11.7%)63.0%(11.9%)
T-MBTA83.2%(4.2%)91.7%(2.3%)76.6%(1.6%)95.5%(2.1%)62.2%(3.3%)
P80.0%(2.8%)87.1%(4.2%)69.7%(2.8%)81.7%(7.6%)73.1%(2.6%)
R67.3%(6.2%)80.8%(6.0%)70.0%(1.7%)68.0%(8.0%)60.6%(7.3%)
MSFT-TransformerA87.5%(4.1%)94.1%(1.2%)77.6%(1.6%)97.4%(1.8%)67.7%(2.9%)
P80.5%(7.0%)88.7%(3.9%)70.8%(2.8%)100.0%(0.0%)72.7%(2.9%)
R83.6%(6.0%)89.2%(3.4%)65.3%(2.5%)72.0%(13.6%)69.7%(10.5%)
ComparisonMethodEW-T2DLCC-T2DIBDObesity
A. Taxonomic featuresRFA78.2%(3.2%)95.1%(1.5%)75.1%(2.6%)92.6%(2.2%)65.3%(4.4%)
P71.3%(2.3%)92.6%(1.7%)66.9%(1.9%)70.0%(20.0%)64.1%(0.4%)
R80.0%(3.4%)82.5%(3.6%)62.9%(3.9%)20.0%(6.3%)97.6%(1.5%)
SVMA75.5%(3.1%)89.4%(2.2%)71.6%(2.4%)92.0%(2.6%)64.2%(3.8%)
P75.2%(3.6%)81.9%(3.3%)65.7%(3.5%)66.7%(18.3%)70.9%(2.5%)
R69.1%(6.2%)75.0%(4.2%)61.8%(4.7%)36.0%(9.8%)77.0%(3.1%)
MLPA74.1%(5.1%)90.0%(1.5%)72.3%(2.2%)86.4%(5.0%)52.3%(3.0%)
P86.4%(6.9%)79.3%(2.1%)67.3%(2.0%)86.3%(2.3%)67.2%(1.5%)
R69.1%(6.8%)86.1%(3.2%)64.1%(5.8%)94.1%(2.6%)70.3%(1.5%)
FT-TransformerA78.4%(3.6%)90.4%(2.4%)73.2%(3.0%)93.6%(2.0%)66.1%(1.7%)
P71.4%(4.7%)84.8%(6.2%)66.8%(3.2%)70.1%(7.7%)75.9%(2.5%)
R69.1%(6.8%)85.8%(3.4%)64.1%(3.3%)72.0%(4.9%)67.3%(6.9%)
DeepMicro [7]A82.9%(3.9%)88.8%(1.1%)72.5%(2.5%)87.3%(3.0%)67.4%(3.4%)
P
R
EnsDeepDP [4]A86.7%(N/A)94.3%(N/A)77.6%(N/A)95.8%(N/A)72.3%(N/A)
P
R
B. Taxonomic features with external knowledgeMeta-Signer [15]A90.5%(5.0%)79.4(15.9%)60.0%(13.5%)
P
R
TaxoNN [16]A91.1%(N/A)73.3%(N/A)
P
R
PopPhy-CNN [14]A90.1%(N/A)58.9%(N/A)
P
R
MicroKPNN [18]A85.8(6.7%)96.9%(0.9%)75.5%(3.2%)95.4%(3.7%)72.8%(4.8%)
P
R
C. Taxonomic features and functional featuresMDL4MicrobiomeA76.8%(5.7%)92.5%(1.3%)74.7%(1.3%)88.0%(0.6%)54.1%(2.0%)
P76.3%(7.5%)78.1%(1.4%)67.6%(1.9%)86.0%(1.7%)69.3%(1.9%)
R69.1%(4.6%)89.1%(5.4%)66.5%(4.2%)92.9%(2.9%)72.1%(3.2%)
MVIB [29]A85.9%(2.3%)92.5%(0.5%)75.8%(1.2%)93.6%(1.4%)66.6%(2.7%)
P
R
FT-ConcatA82.6%(3.1%)91.7%(1.7%)77.5%(1.9%)92.0%(2.4%)61.5%(4.2%)
P77.8%(4.0%)89.4%(3.2%)68.9%(2.2%)79.3%(9.7%)75.1%(3.3%)
R80.0%(7.3%)76.7%(4.5%)68.2%(6.1%)64.0%(7.5%)57.6%(12.4%)
FT-VoteA82.2%(2.1%)91.4%(1.4%)76.6%(1.6%)94.6%(1.7%)61.0%(3.3%)
P70.5%(5.4%)84.4%(4.0%)68.3%(1.5%)77.7%(6.1%)70.4%(2.1%)
R80.0%(6.0%)87.5%(2.9%)63.5%(4.3%)56.0%(11.7%)63.0%(11.9%)
T-MBTA83.2%(4.2%)91.7%(2.3%)76.6%(1.6%)95.5%(2.1%)62.2%(3.3%)
P80.0%(2.8%)87.1%(4.2%)69.7%(2.8%)81.7%(7.6%)73.1%(2.6%)
R67.3%(6.2%)80.8%(6.0%)70.0%(1.7%)68.0%(8.0%)60.6%(7.3%)
MSFT-TransformerA87.5%(4.1%)94.1%(1.2%)77.6%(1.6%)97.4%(1.8%)67.7%(2.9%)
P80.5%(7.0%)88.7%(3.9%)70.8%(2.8%)100.0%(0.0%)72.7%(2.9%)
R83.6%(6.0%)89.2%(3.4%)65.3%(2.5%)72.0%(13.6%)69.7%(10.5%)

The reported results of cited methods are based on previous works that use the same datasets. There are a total of nine methods (uncited) evaluated with our framework for five trails, including MSFT-Transformer. N/A indicates that the corresponding study did not provide the standard mean error. The best performance of each dataset is highlighted in bold while the second-high underlined.

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