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It is a measurement to determine the quality of clustering, which is between 0 (no mutual information) and 1 (perfect correlation).\n \n ![](images/nmi.png)\n \n-Figure 3: Performance comparison among VAE, t-SNE and PCA under different simulation parameters. \n+Figure 3: Performance comparison among VAE, t-SNE and PCA under different simulation parameters.\n+\n+#### VAE performance on real single cell datasets\n+\n+##### 1. real single cell datasets:\n+\n+To evaluate the performance of VAE and the other dimension reduction approaches, we selected 8 real single cell datasets with true cell type labels.\n+\n+| dataset | ncells | ngenes | tissue | organism | cell types | Accesion number | Platform | celltype annotation |\n+| ------- | ------ | ------ | ------ | -------- | --------- | --------- | ------------------ | -------------------------------------- |\n+| yan | 90 | 20214 | Embryo Devel | human | 6 | GSE36552 | Illumina HiSeq 2000 | from different embryonic developmental time points |\n+| goolam | 124 | 41428 | Embryo Devel | mouse | 5 | E-MTAB-3321 | | from different embryonic developmental time points |\n+| pollen | 301 | 23730 | Developing Cerebral Cortex | human | 11 | SRP041736 | Illumina HiSeq 2000 | from different celllines |\n+| patel | 430 | 5948 | Glioblastoma | human | 12 | GSE57249 | Illumina HiSeq 2000 | from five primary glioblastomas |\n+| nestorowa | 1656 | 4773 | Glioblastoma | human | 12 | GSE81682 | Illumina HiSeq 2500 | defined by sorting |\n+| Petropoulos | 1529 | 26178 | Embryo Devel | human | 6 | E-MTAB-3929 | Illumina HiSeq 2000 | defined by developmental stages |\n+| HCA melanoma data | 6639 | 22489 | Lymph node | mouse | 9 | HCA release | Smart-seq2 |\n+| baron-human | 8569 | 20125 | Pancreas | human | 14 | GSE84133 | Illumina HiSeq 2500 | from expression profiles and cell origin |\n+\n+##### 2. 2-dimensional projection of real single cell data based on differnt structure of VAE: VAE_depth3 (3 hidden layer), VAE_depth2 (2 hidden layer), VAE_depth1 (1 hidden layer), t-SNE, ZIFA, UMAP and PCA\n+\n+We tested the performance of VAE and another 4 methods (t-SNE, ZIFA, UMAP and PCA) on these real datasets with different number of cells, genes and cell types. ","path":"content/03.aim1.md","position":65,"original_position":65,"commit_id":"063b3db4a6f178341446fa94316fa25ff357d6de","original_commit_id":"063b3db4a6f178341446fa94316fa25ff357d6de","user":{"login":"cgreene","id":542643,"node_id":"MDQ6VXNlcjU0MjY0Mw==","avatar_url":"https://avatars2.githubusercontent.com/u/542643?v=4","gravatar_id":"","url":"https://api.github.com/users/cgreene","html_url":"https://github.com/cgreene","followers_url":"https://api.github.com/users/cgreene/followers","following_url":"https://api.github.com/users/cgreene/following{/other_user}","gists_url":"https://api.github.com/users/cgreene/gists{/gist_id}","starred_url":"https://api.github.com/users/cgreene/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cgreene/subscriptions","organizations_url":"https://api.github.com/users/cgreene/orgs","repos_url":"https://api.github.com/users/cgreene/repos","events_url":"https://api.github.com/users/cgreene/events{/privacy}","received_events_url":"https://api.github.com/users/cgreene/received_events","type":"User","site_admin":false},"body":"Also, might want to add refs for these methods 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