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Geneformer

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594
Geneformer

Commit History

  1. Use dynamic CUDA check instead of hardcoded device in perturber_utils.py (#594)⁠

    ctheodoris +1: dlgenomics
    1f7fbae

  1. Update README.md

    ctheodoris
    Verified signature
    04c2b2e

  1. Update geneformer/mtl/model.py (#585)⁠

    ctheodoris +1: MajorasMeow
    ad8f66d

  1. update readme citations

    ctheodoris
    Verified signature
    fcd26c4

  1. Update geneformer/mtl/train.py (#582)⁠

    ctheodoris +1: MajorasMeow
    05fcbeb

  1. default id_class_dict to None for gene classifiers

    Christina Theodoris
    f45a6c7

  1. track metadata in predictions

    Christina Theodoris
    be98543

  2. add emb extractor option for saving all gene embs

    Christina Theodoris
    fb6abe0

  3. add pickle suffix option to isp stats

    Christina Theodoris
    5cada60

  4. Fix TypeError in make_perturbation_batch_special (#567)⁠

    ctheodoris +1: so298
    Verified signature
    05a3a20

  1. add empty tokenized_counts for loom to pass until keep_counts implemented

    ctheodoris
    Verified signature
    7ec90d6

  1. subsample heatmap with max_ncells_to_plot when max_ncells is None

    ctheodoris
    Verified signature
    9187fee

  1. tokenizer zarr integration (#561)⁠

    ctheodoris
    Verified signature
    91215c4

  1. Update geneformer/perturber_utils.py to be compatible with different versions of the datasets package. (#553)⁠

    ctheodoris +1: IchigoJiken
    Verified signature
    1930588

  2. Update geneformer/evaluation_utils.py to be compatible with different versions of the datasets package. (#552)⁠

    ctheodoris +1: IchigoJiken
    Verified signature
    b2dc06c

  1. add input_identifier to tokenize specific matched files

    Christina Theodoris
    ac59e36

  1. plot umap for all labels in same view

    Christina Theodoris
    ff551ee

  2. Update README.md

    ctheodoris
    Verified signature
    13cd541

  1. silence tensor copy warning

    Christina Theodoris
    9d8d2f0

  2. clone rather than wrap tensors

    Christina Theodoris
    aea4988

  3. update collator with dummy save fn for transformers compatibility

    Christina Theodoris
    f17618a

  1. fix to properly move model after checking device

    Christina Theodoris
    f953554

  2. move model to device after checking

    Christina Theodoris
    efc403d

  3. update V1 token dict usage to self attr

    Christina Theodoris
    f26136d

  4. move V1 autoformatting to after validate_options

    Christina Theodoris
    4364d31

  1. add option for relabeling data from prior label class dict, update dict paths in manifest

    Christina Theodoris
    76a78a0

  1. delete first version of dist multitask example

    ctheodoris
    Verified signature
    a67c9c0

  1. update dist multitask example name

    Christina Theodoris
    596f1c2

  2. Add example notebook for distributed multi-task cell classification (#543)⁠

    ctheodoris +1: madhavanvvs
    Verified signature
    f3ff19d

  1. specify bitsandbites version

    Christina Theodoris
    6a50f33

  2. add V2 models

    Christina Theodoris
    7cf49a3

  3. update with V2 models

    Christina Theodoris
    d319fef

  1. edit docs to remove backend isp functions

    Christina Theodoris
    31bf641

  1. fix TypeError: TrainingArguments.__init__() got an unexpected keyword argument 'evaluation_strategy' (#539)⁠

    ctheodoris +1: jackkuo
    Verified signature
    42dbf0a

  1. add fallback task_type for LoraConfig to support different PEFT versions (#538)⁠

    ctheodoris +1: madhavanvvs
    Verified signature
    d471d1b

  1. update eval_strategy for new transformers version

    Christina Theodoris
    18a2ca6

  2. move import wandb to conditional

    Christina Theodoris
    7e4697d

  1. fully qualified imports to resolve name-space conflicts (#532)⁠

    ctheodoris +1: madhavanvvs
    Verified signature
    5f07ec8

  1. ddp_mtl_nccl_support (#524)⁠

    ctheodoris
    Verified signature
    e2efe2b

  1. edit imports in perturber_utils

    Christina Theodoris
    c6d04a6

  1. fix exact_mean subselection to be for index rather than col name

    Christina Theodoris
    a13a2cf

  2. fix exact_mean and exact_median to subselect dataframe emb cols, not cell rows

    Christina Theodoris
    cfc8cdb

  3. add quantization for pretrained model

    Christina Theodoris
    7b591f6

  1. Prepare data cell level pass cell state dict instead of genes (#483)⁠

    ctheodoris +1: hchen725
    Verified signature
    69e6887

  2. ensure gene class dict only inverted when using gene classifier

    Christina Theodoris
    54b408b

  1. make plot roc compatible with eval-only metrics

    Christina Theodoris
    ae4867d

  2. Merge remote-tracking branch 'origin/main'

    Christina Theodoris
    5760b30

  3. fix gene class dict labeling

    Christina Theodoris
    bfcada4

  1. Fix how mappings and train and val data are returned (#473)⁠

    ctheodoris +1: hchen725
    Verified signature
    c81f6f9

  1. Upload gene_name_id_dict_gc95M.pkl (#470)⁠

    ctheodoris +1: hchen725
    Verified signature
    01d3ea8