Table 4 Parameters and performance (as measured by (10) and manual gating as ground truth) of the best results obtained by optimalFlowTemplates + optimalFlowClassification on \(\mathcal {TS}\)
From: optimalFlow: optimal transport approach to flow cytometry gating and population matching
\({\mathcal {C}}^2\) | \({\mathcal {C}}^{5}\) | \({\mathcal {C}}^{7}\) | |
|---|---|---|---|
Median F-measure | 0.9441931 | 0.8530806 | 0.957045 |
Database Clustering | Complete linkage | HDBSCAN | Complete linkage |
Template Formation | Pooling | Pooling | HDBSCAN |
Assigned Cluster | 1 | 6 | 2 |
Sample Clustering | tclust | tclust | tclust |
Supervised Classification | QDA | QDA from template | Random forest |
Assigned Cytometry | \({\mathcal {C}}^{1}\) | \({\mathcal {C}}^{8}\) |
\({\mathcal {C}}^{9}\) | \({\mathcal {C}}^{14}\) | \({\mathcal {C}}^{15}\) | |
|---|---|---|---|
Median F-measure | 0.9458429 | 0.9254252 | 0.8807339 |
Database Clustering | HDBSCAN | HDBSCAN | HDBSCAN |
Template Formation | Pooling | k-barycenter | k-barycenter |
Assigned Cluster | 9 | 1 | 1 |
Sample Clustering | tclust | tclust | tclust |
Supervised Classification | QDA | Label transfer with (6) | Random forest |
Assigned Cytometry | \({\mathcal {C}}^{13}\) | \({\mathcal {C}}^{1}\) |
\({\mathcal {C}}^{17}\) | \({\mathcal {C}}^{18}\) | \({\mathcal {C}}^{26}\) | |
|---|---|---|---|
Median F-measure | 0.9679446 | 0.9575489 | 0.8316279 |
Database Clustering | HDBSCAN | HDBSCAN | Complete linkage |
Template Formation | HDBSCAN | HDBSCAN | HDBSCAN |
Assigned Cluster | 7 | 7 | 4 |
Sample Clustering | tclust | flowMeans | tclust |
Supervised Classification | Random forest | Random forest | Random forest |
Assigned Cytometry | \({\mathcal {C}}^{20}\) | \({\mathcal {C}}^{20}\) | \({\mathcal {C}}^{24}\) |
\({\mathcal {C}}^{27}\) | \({\mathcal {C}}^{29}\) | \({\mathcal {C}}^{31}\) | |
|---|---|---|---|
Median F-measure | 0.9312977 | 0.9259644 | 0.931515 |
Database Clustering | Complete linkage | Complete linkage | HDBSCAN |
Template Formation | Pooling | k-barycenter | Pooling |
Assigned Cluster | 5 | 6 | 4 |
Sample Clustering | tclust | flowMeans | tclust |
Supervised Classification | Random forest | Random forest | QDA from template |
Assigned Cytometry | \({\mathcal {C}}^{28}\) | \({\mathcal {C}}^{33}\) |
\({\mathcal {C}}^{40}\) | |||
|---|---|---|---|
Median F-measure | 0.8240522 | ||
Database Clustering | Complete linkage | ||
Template Formation | Pooling | ||
Assigned Cluster | 6 | ||
Sample Clustering | tclust | ||
Supervised Classification | Random forest | ||
Assigned Cytometry | \({\mathcal {C}}^{30}\) | ||