https://github.com/exitare/vae-subtype-sample-generation

https://github.com/exitare/vae-subtype-sample-generation

Last synced: 23 days ago
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• Host: GitHub
• URL: https://github.com/exitare/vae-subtype-sample-generation
• Owner: Exitare
• Created: 2022-07-28T16:32:21.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2022-10-12T03:28:52.000Z (over 2 years ago)
• Last Synced: 2023-03-05T13:31:16.171Z (almost 2 years ago)
• Language: Jupyter Notebook
• Size: 2.51 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md

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README

        
# VAE-Subtype-Sample-Generation operations

### Goal: Generate TCGA cohort samples

    based on encoding of all TCGA samples

    use gene expression data type only

pip install -r requirements.txt  

python3 -m venv venv  

source venv/bin/activate  

### 2022-10-04  

VAE_smpl_gen_04.ipynb pushed, connected to UMAP now  

2022-08-08

test on 1000 x 100 make_classification fabricated data

Use latent space dimension of 10 b/c order mag < 100

sbatch fbrctd.sh 10 fbrctd_00 data/1000_100_X.tsv

2022-08-03

file prepped with 8009 samples and 99 subtypes

labels encoded

to /VAE-Subtype-Sample-Generation/data on Exacloud

sbatch sample_gen_data.sh 1000 v0.2 data/cmbnd_25_lbl_xfrm.tsv

* expecting out_of_memory fail

2022-08-02

sbatch sample_gen.sh -lt 1000 -p v00 --data data/BRCA_feat_ntrsct_25.tsv

sbatch sample_gen.sh 1000 v0.1 path_to_file

sbatch sample_gen_data.sh 1000 v0.1 data/BRCA_feat_ntrsct_25.tsv

next actions:

    clone into Exacloud

    upload gene expression extraction from molecular file scripts

    read direct from GDAN TMP dir (?)

2022-07-28

output and error report directories setup

25 is latent space column dimension

v03 is result dir name

sbatch sample_gen.sh 25 v03 data/trn_v00.tsv data/val_v00.tsv data/tst_v00.tsv