Table 3.
Performance metrics for the tuned extra trees model for predicting drugs’ activity against each of the 40 gut bacterial strains. AUROC: receiver operating characteristic area under the curve.
| Bacterium | AUROC | Precision | Recall | F1 |
|---|---|---|---|---|
| Akkermansia muciniphila (NT5021) | 0.93 | 0.73 | 0.65 | 0.69 |
| Bacteroides caccae (NT5050) | 0.88 | 0.74 | 0.54 | 0.62 |
| Bacteroides fragilis (ET) (NT5033) | 0.84 | 0.61 | 0.50 | 0.55 |
| Bacteroides fragilis (NT) (NT5003) | 0.82 | 0.72 | 0.58 | 0.64 |
| Bacteroides ovatus (NT5054) | 0.87 | 0.76 | 0.55 | 0.64 |
| Bacteroides thetaiotaomicron (NT5004) | 0.79 | 0.72 | 0.52 | 0.60 |
| Bacteroides uniformis (NT5002) | 0.79 | 0.66 | 0.58 | 0.62 |
| Bacteroides vulgatus (NT5001) | 0.77 | 0.69 | 0.69 | 0.69 |
| Bacteroides xylanisolvens (NT5064) | 0.81 | 0.77 | 0.37 | 0.50 |
| Bifidobacterium adolescentis (NT5022) | 0.86 | 0.88 | 0.58 | 0.70 |
| Bifidobacterium longum (NT5028) | 0.86 | 0.94 | 0.64 | 0.76 |
| Bilophila wadsworthia (NT5036) | 0.94 | 0.90 | 0.53 | 0.67 |
| Blautia obeum (NT5069) | 0.84 | 0.79 | 0.68 | 0.73 |
| Clostridium bolteae (NT5026) | 0.85 | 0.74 | 0.52 | 0.61 |
| Clostridium difficile (NT5083) | 0.86 | 0.83 | 0.37 | 0.51 |
| Clostridium perfringens (NT5032) | 0.89 | 0.78 | 0.79 | 0.78 |
| Clostridium ramosum (NT5006) | 0.91 | 0.89 | 0.61 | 0.72 |
| Clostridium saccharolyticum (NT5037) | 0.84 | 0.84 | 0.55 | 0.67 |
| Collinsella aerofaciens (NT5073) | 0.82 | 0.77 | 0.69 | 0.73 |
| Coprococcus comes (NT5048) | 0.80 | 0.81 | 0.66 | 0.73 |
| Dorea formicigenerans (NT5076) | 0.84 | 0.73 | 0.67 | 0.70 |
| Eggerthella lenta (NT5024) | 0.89 | 0.90 | 0.66 | 0.76 |
| Escherichia coli ED1a (NT5078) | 0.91 | 1.00 | 0.53 | 0.69 |
| Escherichia coli IAI1 (NT5077) | 0.95 | 1.00 | 0.61 | 0.76 |
| Eubacterium eligens (NT5075) | 0.80 | 0.65 | 0.65 | 0.65 |
| Eubacterium rectale (NT5009) | 0.81 | 0.69 | 0.75 | 0.72 |
| Fusobacterium nucleatum (NT5025) | 0.87 | 0.79 | 0.60 | 0.68 |
| Lactobacillus paracasei (NT5042) | 0.77 | 0.71 | 0.57 | 0.63 |
| Odoribacter splanchnicus (NT5081) | 0.93 | 0.86 | 0.71 | 0.77 |
| Parabacteroides distasonis (NT5074) | 0.81 | 0.72 | 0.57 | 0.64 |
| Parabacteroides merdae (NT5071) | 0.70 | 0.59 | 0.47 | 0.52 |
| Prevotella copri (NT5019) | 0.82 | 0.69 | 0.50 | 0.58 |
| Roseburia hominis (NT5079) | 0.89 | 0.84 | 0.68 | 0.75 |
| Roseburia intestinalis (NT5011) | 0.82 | 0.78 | 0.77 | 0.77 |
| Ruminococcus bromii (NT5045) | 0.85 | 0.69 | 0.67 | 0.68 |
| Ruminococcus gnavus (NT5046) | 0.83 | 0.75 | 0.63 | 0.69 |
| Ruminococcus torques (NT5047) | 0.75 | 0.67 | 0.54 | 0.60 |
| Streptococcus parasanguinis (NT5072) | 0.82 | 0.85 | 0.55 | 0.67 |
| Streptococcus salivarius (NT5038) | 0.89 | 0.86 | 0.60 | 0.71 |
| Veillonella parvula (NT5017) | 0.91 | 0.95 | 0.66 | 0.78 |