All metrics listed¶

“Applying Deep Learning algorithm to perform lung cells annotation”, A. Collin, 2020¶

Clustering¶

silhouette coefficient

davies_bouldin index

dunn index

density_based_clustering_validation

rand_index

fowlkes_mallows_score

mutual information

v_measure

Dimensionality Reduction¶

kruskal_stress

spearman’s rho

local_continuity_meta_criterion

trustworthiness_and_continuity

Specificity¶

one-vs-all

one-vs-max

shannon's entropy

gini_coefficient

kendall's tau

Open Problems¶

SCIB

Batch integration // Leucken et. al (2022)¶

adjusted_rand_index

average_silhouetta_width

lisi

cell_cycle_conservation

graph connectivity

high_gene_variability

isolated_label_f1_score

kbet

normalized_mutual_information

principal_component_regression

Denoising // Batson et. al. (2019)¶

mean-squared error

poisson loss

Spatial Decomposition // Miles et. al. (2005)¶

coefficient of determination

Spatially variable genes // Kendall (1938)¶

kendall correlation

Dimensionality reduction for visualisation¶

Global¶

Distance correlation

Density preservation

co-KNN AUC

global co-kNN

Graph Edit Distance

Local¶

trustworthiness

continuity

local_continuity_meta_criterion

co-KNN size

local co-KNN

Entourage

Average Jaccard Distance