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Geneformer

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Geneformer / examples

15 contributors

History: 28 commits

ricomnl's picture

Added anndata tokenizer and switched to Dataset.from_generator

b6ca566 over 1 year ago

pretraining_new_model
Update links including unsorted example lengths file over 1 year ago
cell_classification.ipynb

96.1 kB

Add note to recommend tuning hyperparameters for downstream applications over 1 year ago
extract_and_plot_cell_embeddings.ipynb

1.13 MB

Fixed error with perturbing individual genes and updated ways to specify cell_states_to_model (#146) over 1 year ago
gene_classification.ipynb

168 kB

Add note to recommend tuning hyperparameters for downstream applications over 1 year ago
hyperparam_optimiz_for_disease_classifier.py

6.78 kB

Change list of individual IDs to set to ensure unique before subsetting into train/valid/test sets over 1 year ago
in_silico_perturbation.ipynb

3.65 kB

Fixed error with perturbing individual genes and updated ways to specify cell_states_to_model (#146) over 1 year ago
tokenizing_scRNAseq_data.ipynb

3.32 kB

Added anndata tokenizer and switched to Dataset.from_generator over 1 year ago