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Geneformer / examples

Commit History

  1. Fixed error with perturbing individual genes and updated ways to specify cell_states_to_model (#146)⁠

    ctheodoris +1: davidjwen
    9169bfd

  1. Rename heatmap legend to be correct label

    Christina Theodoris
    badcca6

  2. Add function to extract and plot cell embeddings

    Christina Theodoris
    d154fee

  1. Update isp to allow modeling single perturbation in multiple cells as batches

    Christina Theodoris
    acd253c

  1. Change list of individual IDs to set to ensure unique before subsetting into train/valid/test sets

    Christina Theodoris
    45b9d69

  1. Add note to recommend tuning hyperparameters for downstream applications

    Christina Theodoris
    98ce6d7

  1. Add instructions to convert gene annotations w/ Ensembl Biomart

    Christina Theodoris
    77eb432

  1. Remove unused evalset variable from cell classification example

    Christina Theodoris
    879a878

  1. Update links including unsorted example lengths file

    Christina Theodoris
    f0b6641

  1. Add uniform max len for padding for predictions

    Christina Theodoris
    67f674c

  1. Add example code for obtaining non-zero median digests

    Christina Theodoris
    67b7f01

  1. Add further explanation regarding input file format for transcriptome tokenizer

    Christina Theodoris
    c34ead6

  1. Update instructions in tokenizing example to clarify requirement for Ensembl ID

    Christina Theodoris
    d468697

  2. Update instructions in tokenizing example to clarify requirement for Ensembl ID

    Christina Theodoris
    e606e1c

  1. Add further explanation to tokenizer example script and updated tokenizer to match loompy raised error

    Christina Theodoris
    78dd83b

  1. Move example input files to dataset repository to include example datasets for fine-tuning

    Christina Theodoris
    875ef33

  2. Add example for tokenizing .loom dataset

    Christina Theodoris
    f89f796

  3. Update gene classification example to create directory after training arguments are defined

    Christina Theodoris
    ebe5ee8

  4. Subclass collator for cell classification

    Christina Theodoris
    402ba9b

  1. Update pretrainer for transformers==4.28.0

    Christina Theodoris
    b925dcc

  1. Add example input labels for distinguishing bivalent promoters.

    Christina Theodoris
    996d3e5

  2. Add in silico perturbation example notebook.

    Christina Theodoris
    1c2f864

  1. Add example input files for gene classification of TF dosage sensitivity

    Christina Theodoris
    0710c44

  1. Add example for hyperparameter optimization for disease classifier

    Christina Theodoris
    79a0c41

  1. Add data collator for gene classification and example for gene classification

    Christina Theodoris
    edacd12

  1. Add data collator for cell classification and example for cell classification

    Christina Theodoris
    088ea6e

  1. Add Geneformer trainer and pretraining example

    Christina Theodoris
    bcc03e8