Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering

Table 5 Comparison of clustering results with the Reference Atlas annotations at developmental ontology Level 5

Measures	Clustering	E11.5	E13.5	E15.5	E18.5	P4	P14	P28	Average
	k-means	0.5932	0.5264	0.5009	0.4493	0.4210	0.4165	0.3885	0.4708
NMI	PCA₂	0.3429	0.2243	0.2269	0.2781	0.2390	0.2931	0.2877	0.2703
NMI	PCA₁₀	0.5354	0.4481	0.4299	0.4011	0.3815	0.3796	0.3720	0.4211
	t-SNE₂	0.6267	0.5593	0.5331	0.4932	0.4222	0.4100	0.4228	0.4953
	t-SNE₁₀	0.6321	0.5736	0.5279	0.5062	0.4600	0.4089	0.4564	0.5093
	k-means	0.5822	0.6408	0.6675	0.6727	0.7024	0.7380	0.7234	0.6753
S-index	PCA₂	0.8000	0.8380	0.8329	0.8017	0.8161	0.7819	0.8128	0.8119
S-index	PCA₁₀	0.6712	0.7064	0.7288	0.7258	0.7398	0.7506	0.7392	0.7231
	t-SNE₂	0.5562	0.6257	0.6670	0.6714	0.6901	0.7441	0.7318	0.6695
	t-SNE₁₀	0.5603	0.6096	0.6515	0.6685	0.6997	0.7077	0.7112	0.6584
	k-means	0.1380	0.0839	0.0634	0.0467	0.0331	0.0318	0.0272	0.0606
ARI	PCA₂	0.0428	0.0135	0.0108	0.0211	0.0124	0.0169	0.0214	0.0199
ARI	PCA₁₀	0.1132	0.0660	0.0488	0.0384	0.0264	0.0238	0.0252	0.0488
	t-SNE₂	0.1698	0.0946	0.0675	0.0631	0.0337	0.0316	0.0306	0.0701
	t-SNE₁₀	0.1765	0.1087	0.0618	0.0709	0.0448	0.0304	0.0444	0.0768
	k-means	0.4961	0.6097	0.6437	0.6192	0.7062	0.7663	0.7272	0.6526
Purity	PCA₂	0.2842	0.3640	0.4556	0.5260	0.5929	0.6666	0.6545	0.5063
Purity	PCA₁₀	0.4314	0.5330	0.5947	0.6006	0.6882	0.7430	0.7199	0.6158
	t-SNE₂	0.5346	0.6254	0.6729	0.6515	0.6943	0.7533	0.7465	0.6684
	t-SNE₁₀	0.5383	0.6456	0.6711	0.6609	0.7309	0.7480	0.7623	0.6796

ISSN: 1471-2105