Metrics

Average Silhouette Width

Higher is better

sklearn.metrics.silhouette_score

Davies–Bouldin Index

Lower is better

sklearn.metrics.davies_bouldin_score

Calinski–Harabasz Index

Higher is better

sklearn.metrics.calinski_harabasz_score

Spearman distance corr (latent vs UMAP)

DRE.evaluate_dimensionality_reduction

Coranking Q_NX local average over the selected neighbourhood range

DRE Lee & Verleysen 2009

Coranking Q_NX global average

DRE

Argmax of Q_NX(k) — optimal neighbourhood scale

DRE

Weighted composite of Q_local + Q_global

DRE

Spearman dist corr (latent vs tSNE)

DRE

Coranking Q_NX local (tSNE)

DRE

Coranking Q_NX global (tSNE)

DRE

Argmax Q_NX(k) in tSNE

DRE

Weighted composite (tSNE)

DRE

Intrinsic manifold dimensionality score

LSE.SingleCellLatentSpaceEvaluator

PCA eigenvalue decay rate

LSE

Effective latent dim (1/Σ w_i² when Σ w_i=1)

LSE

Covariance eigenvalue anisotropy

LSE

Primary developmental axis strength

LSE

Perturbation robustness score

LSE

Weighted composite (trajectory-aware)

LSE