Table 1 .

Summary of major scHi-C embedding techniques

Family of embedding methods	Linearity	Primary reference	Special scHi-C pre-processing	Special measure of similarity/difference between cells	Explicit usage of contacts co-occurrence patterns
PCA	Linear	[100]	Raw binned matrix	–	No
		[76]	Interchromosomal interactions profile	–	No
		[60]	TAD profile	–	No
		[87]	Compartment score profile	–	No
t-SNE	Non-linear	[85]	20 PCs of compartment score profiles	–	No
Spectral embedding	Non-linear	[69]	Distance decays	Symmetric KL	No
MDS	Non-linear	[65]	Distance decay	Jensen–Shannon divergence	No
		[100]	scHi-C binned matrix after smoothing and random-walk imputation	SCC	No
UMAP	Non-linear	[16]	TAD contact profiles	–	No
		[49]	Cell-topic matrix after LDA	–	Yes
		[99]	Hypergraph embedding	–	Yes

MDS indicates multidimensional scaling; SCC, stratum-adjusted correlation coefficient; UMAP, uniform manifold approximation and projection.