Table 1 Comparison of direct application of k-means and SIMLR clustering on raw gene expression data with autoencoder-based k-means and SIMLR ensemble
From: Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis
| Â | Raw | Autoencoder | ||||||
|---|---|---|---|---|---|---|---|---|
| Â | ARI | NMI | FM | Jaccard | ARI | NMI | FM | Jaccard |
k-means | Â | Â | Â | Â | Â | |||
Mouse neurons | 0.22 ±0.02 | 0.36 ±0.03 | 0.39 ±0.02 | 0.22 ±0.01 | 0.38 ±0.02 | 0.56 ±0.01 | 0.53 ±0.02 | 0.34 ±0.02 |
Mouse striatum | 0.36 ±0.07 | 0.69 ±0.06 | 0.51 ±0.06 | 0.31 ±0.05 | 0.45 ±0.01 | 0.75 ±0.01 | 0.58 ±0.01 | 0.37 ±0.01 |
Human archived brain | 0.29 ±0.01 | 0.49 ±0.01 | 0.35 ±0.01 | 0.21 ±0.01 | 0.37 ±0.01 | 0.56 ±0 | 0.43 ±0.01 | 0.27 ±0.01 |
Mouse archived brain | 0.32 ±0.01 | 0.49 ±0 | 0.35 ±0.01 | 0.21 ±0.01 | 0.43 ±0.01 | 0.58 ±0 | 0.46 ±0.01 | 0.3 ±0.01 |
SIMLR | Â | Â | Â | Â | Â | |||
Mouse neurons | 0.44 ±0 | 0.65 ±0 | 0.58 ±0 | 0.39 ±0 | 0.71 ±0 | 0.7 ±0 | 0.81 ±0 | 0.67 ±0 |
Mouse striatum | 0.55 ±0 | 0.81 ±0 | 0.67 ±0 | 0.34 ±0 | 0.8 ±0.02 | 0.87 ±0.01 | 0.85 ±0.02 | 0.74 ±0.03 |