Extended Data Table 4 Benchmarking cell embeddings, using scGraph

Method	HVG	Brain	Breast	COVID	Eye	Gut (F)	Heart	Lung (F,D)	Lung (F,O)	Lung	Pancreas	Skin
Harmony		0.168	0.739	0.770	0.405	0.538	0.763	0.511	0.284	0.700	0.520	0.465
Harmony	✓	0.427	0.736	0.804	0.515	0.696	0.552	0.570	0.356	0.781	0.431	0.694
Scanorama		0.239	0.645	0.776	0.522	0.706	0.628	0.594	0.263	0.351	0.439	0.559
Scanorama	✓	0.250	0.694	0.760	0.534	0.635	0.554	0.622	0.201	0.309	0.291	0.465
BBKNN		0.091	0.644	0.775	0.524	0.596	0.684	0.579	0.314	0.685	0.563	0.626
BBKNN	✓	0.166	0.658	0.771	0.456	0.736	0.627	0.693	0.550	0.689	0.445	0.690
scVI		0.065	0.632	0.719	0.393	0.650	0.316	0.493	0.478	0.704	0.378	0.387
scVI	✓	0.254	0.690	0.752	0.314	0.649	0.588	0.499	0.453	0.674	0.506	0.567
scANVI		0.116	0.647	0.757	0.408	0.626	0.350	0.567	0.552	0.672	0.390	0.386
scANVI	✓	0.396	0.735	0.763	0.517	0.600	0.569	0.585	0.509	0.678	0.394	0.436
scGen	✓	0.217	0.600	0.779	0.436	0.526	0.606	0.331	0.161	0.337	0.354	0.692
scPoli		-	-	0.573	0.431	0.588	0.679	0.394	0.572	0.588	0.311	0.462
scPoli	✓	0.295	0.519	0.672	0.360	0.594	0.706	0.455	0.590	0.518	0.401	0.422
Geneformer		-	-	-	0.524	0.747	0.449	0.604	0.265	0.479	-	0.540
scGPT	✓	-	-	0.535	0.256	0.447	0.487	0.552	0.388	0.390	-	0.378
Author’s		0.295	0.689	-	0.284	0.641	0.702	0.500	-	0.640	-	0.472
Islander		-0.071	-0.032	0.361	-0.335	0.098	0.013	-0.011	0.022	-0.061	0.234	-0.093

“F”, “D” and “O” represents fetal, donor and organoid, respectively. “-” means the embeddings are not available, due to memory limitations (>500 G in RAM) or unavailability of raw counts or ensembl ids (used in Geneformer and scGPT). We bold the highest and underline the lowest scores for each dataset.

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