Commit History

Upload annotation_human_G029.gtf with huggingface_hub
7dc70e4

jarrydmartinx commited on

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5d61a87

pytorch-survival commited on

Moved metric-tabular code and notebooks into main branch of metric-tabular repo. Consolidated notebooks for datasets in notebooks/ leaving only dataset files in top level dir.
35dfebc

pytorch-survival commited on

Added padding to PerceiverTabularTokenizer.
6e90a4a

pytorch-survival commited on

Added padding to PerceiverTabularTokenizer.
ad8fa4c

pytorch-survival commited on

Added padding to PerceiverTabularTokenizer.
1f60c5d

pytorch-survival commited on

Tokenizer and TPM finished. Still designing dataset object.
1496d6b

pytorch-survival commited on

Added logic for converting to llvm using scipy. This can surely be done faster outside of python, but don't overoptimize. Strangely, the libsvm, svmlite file for BRCA is larger than the dense csv. This may be because we're storing large integers. May be less after normalization. It may simplly be that the count data is not as sparse as imagined. We really need to reduce to the subset of genes available for gene2vec intersection HiG2Vec, and that will greatly reduce the size of both. The libsvm format is good for text processing, I think but csr matrices or even dense matrices could be just as good if the sparsity is not so bad.
81aebce

pytorch-survival commited on

Rename tcga_cancer2filepath.json to tcga_index.json
d278bf2

jarrydmartinx commited on

Rename gtex_tissue2filepath.json to gtex_index.json
c2f5f58

jarrydmartinx commited on

Added .json files mapping study/tissue/cancer ids to sra/gtex/tcga filepaths in recount3-opendata bucket.
ea5c6f0

pytorch-survival commited on