Commit History
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correct typo
Verified signature5a43832
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Update readthedocs for classifier
Christina Theodorisf75f5ac
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Get the gene keys and gene list keys from the token dictionary instead of medians (#304)
Verified signature- Get the gene keys and gene list keys from the token dictionary instead of medians (faab0d7678ab0347fae033a620c388ca970b59e0) Co-authored-by: Han Chen <hchen725@users.noreply.huggingface.co>b294421 -
Add classifier module and examples
Christina Theodoris9e9cca9
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Fix typo (#301)
Verified signature- Fix typo (d1bbf272387475f1c413cca8679150549abd8bed) Co-authored-by: Han Chen <hchen725@users.noreply.huggingface.co>075bd53
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Add option for variable input_size and to add CLS/SEP Tokens (#299)
Verified signature- Add option for variable input_size and to add CLS/SEP Tokens (944c98c4ed4fa9bd539c2a7d8db5351161d85012) Co-authored-by: Han Chen <hchen725@users.noreply.huggingface.co>aa25cd2
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edit docstring format to highlight options
Christina Theodorise3330a6 -
change doc formatting
Christina Theodoris17f036a -
add sphinx docs
Christina Theodoris2a0dcbe
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Add option for modified batch size for loom tokenizer
Christina Theodoris0960cf6
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Add option for modifying chunk size for anndata tokenizer
Christina Theodorisfd93ebf
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tokenizer-uncropped-input_ids (#275)
- Adding option to keep uncropped input_ids as a feature (caec2855ca523f772b903115267a9d5468349da4) Co-authored-by: Jamie Boylan <jamieb-nvs@users.noreply.huggingface.co>8df5dc1
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anndata_tokenizer (#170)
- Added anndata tokenizer and switched to Dataset.from_generator (b6ca56647a16de97f6f95785eb76cb1a965f9960) - Generalized (5cb733f4fed85e1568ba9671e5b1f9babd7b8491) - Addressed issues for tokenizer, anndata tokenizer now uses a fraction of memory (b24676d0956565ff7b4f8b57d1e936ad17f8740e) - Fixed issues (94e8d231c41a89232a55c064e5c8ea95edd51d2e) - Fixed issue, loom and h5ad now produce same checksums (9c62f4c6e3ab0afd1943079306655bd20eba2246) - Rename loom tokenizer function and modify example notebook for adata. (4fdb85061180ccf022ab761c2557be6ba67d848e) Co-authored-by: Rico Meinl <ricomnl@users.noreply.huggingface.co>4302f48
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Add error for no files found and suppress loompy import warning
Christina Theodorisabdf980
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Update tokenizer to allow tokenization without custom cell attributes
Christina Theodoris57b9778
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Modify tokenizer to allow renaming attr names btwn loom and .dataset
Christina Theodorise78c44d
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Add further explanation regarding input file format for transcriptome tokenizer
Christina Theodorisc34ead6
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Add further explanation to tokenizer example script and updated tokenizer to match loompy raised error
Christina Theodoris78dd83b
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Fix bug with metadata when processing multiple .loom files (#3)
- Fix bug with metadata when processing multiple .loom files (36a4b0619fa47023cfdd4f842c0850c5a4b7305b) Co-authored-by: David Wen <davidjwen@users.noreply.huggingface.co>044d737
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Add data collator for cell classification and example for cell classification
Christina Theodoris088ea6e
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Add Geneformer tokenizer and updated model card
Christina Theodoris5426788