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config.yaml
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config.yaml
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# data_dir:
data_dir: '/home/andyb/project_in_bioinformatics/data'
# data_dir: '/home/andy/Projects/pib/data'
# study: ["TCGA", "GTEx"]
study: ["TCGA", "GTEx"]
# type: ["gene", "exon"]
type: ["gene"]
# size: ["full", r"[0-9]+x[0-9]+"]
size: ["full"]
# filter: ["pca", "naive"]
filter: ["pca", "naive"]
# architecture: ["9662", r"[0-9]+(-[0-9]+)*"]
architecture: ["9662", "966", "96", "9", "966-10", "96-10", "96-10-10", "96-100"]
# max_training_time: "60"
max_training_time: "90000"
# pathways
pathways: '/home/andyb/project_in_bioinformatics/data/from_lasse/pathways_df.tsv'
# max_epochs
max_epochs: "250"
# batch_size
batch_size: "100"
# nn: ["ff", "pw"]
nn: ["ff"]
# labels
labels: ["stages", "samples"]
# analysis_type:
analysis_type: [
"naive/ff_57992-26/samples",
"naive/ff_57992-5/stages",
"naive/ff_9662-26/samples",
"naive/ff_9662-5/stages",
"pca/ff_9662-26/samples",
"pca/ff_9662-5/stages",
"naive/ff_186-26/samples",
"naive/ff_186-5/stages",
"pca/ff_186-26/samples",
"pca/ff_186-5/stages",
"naive/pw_186-26/samples",
"naive/pw_186-5/stages",
"naive/ff_57992-100-26/samples",
"naive/ff_57992-100-5/stages",
"naive/ff_9662-100-26/samples",
"naive/ff_9662-100-5/stages",
"pca/ff_9662-100-26/samples",
"pca/ff_9662-100-5/stages",
"naive/ff_186-100-26/samples",
"naive/ff_186-100-5/stages",
"pca/ff_186-100-26/samples",
"pca/ff_186-100-5/stages",
"naive/pw_186-100-26/samples",
"naive/pw_186-100-5/stages",
]