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Geneformer

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Geneformer

Commit History

  1. Update geneformer/perturber_utils.py

    yuz299
    Verified signature
    566111f

  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

  1. Add checks for custom attributes and n_counts prior to sum ensembl id (#461)⁠

    ctheodoris +1: hchen725
    Verified signature
    09de197

  2. further emphasize different token dictionaries in examples

    Christina Theodoris
    e2ee685

  3. remove unused imports while no longer using distributed sampler

    ctheodoris
    Verified signature
    b9028ba

  4. Raise error for train and validation mismatch (#459)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    9af94b8

  1. Upload in_silico_perturber.py (#432)⁠

    ctheodoris +1: davidjwen
    Verified signature
    cb89107

  1. Update geneformer/emb_extractor.py (#453)⁠

    ctheodoris +1: hchen725
    Verified signature
    ebc1e09

  2. Update geneformer/tokenizer.py (#450)⁠

    ctheodoris +1: hchen725
    Verified signature
    664f71e

  1. update isp default mode to cls

    ctheodoris
    Verified signature
    0c99403

  1. Adding tags to the model (#448)⁠

    ctheodoris +1: canergen
    Verified signature
    3a68669

  1. update transformers version to match pretrainer using accelerate

    ctheodoris
    Verified signature
    3d62bb9

  2. update pretrainer to not use distributed sampler (Trainer uses accelerate)

    ctheodoris
    Verified signature
    8140c51

  1. update function for N_Detections for mixture_model without anchor_token

    Christina Theodoris
    df297bc

  1. add check to ensure emb_label is None for getting state embs dict

    Christina Theodoris
    39b4444

  1. change default emb to cls

    ctheodoris
    Verified signature
    9ee140a

  1. include install time in model card

    ctheodoris
    Verified signature
    21d36cd

  1. Update trainer output dir (#427)⁠

    ctheodoris +1: hchen725
    Verified signature
    dc23c5f

  1. Update geneformer/tokenizer.py (#415)⁠

    ctheodoris +1: hchen725
    Verified signature
    63275a8

  2. Create multi-task_cell_classification.ipynb (#418)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    b138ba5

  1. CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling (#416)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    b6d28c3

  1. Add find_packages to automatically include mtl and subpackages in setup.py (#410)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    3b78204

  2. adding tensorboard to setup.py (#409)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    94d98d1

  3. tensorboard add to reqs (#407)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    e8fa43a

  1. dictionaries from parent dir (#405)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    85f295e

  2. remove token dictionary and unpickling from init (#403)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    7eca269

  1. move dict loading to function in eval utils

    ctheodoris
    57bc17e

  2. edit doc formatting

    ctheodoris
    fce3f6e

  3. edit docs formatting

    ctheodoris
    ef094b2

  4. add mtl_classifier to docs

    ctheodoris
    bedb3b7

  5. add input size tip to instructions

    ctheodoris
    Verified signature
    2732369

  6. update tokenizer to defaults for 95M models for special token and input size

    ctheodoris
    Verified signature
    da8cf3d

  7. update instructions to include reminder about token dictionary

    ctheodoris
    Verified signature
    cb1b0d5

  1. pointing dictionaries from the mtl module's init (#397)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    7470753

  2. Refactored token dictionary loading and encapsulated dictionary (#398)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    beb62a4

  3. Refactor: Convert mask_token_id, pad_token_id, and all_special_ids to properties (#395)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    2e06f1a

  1. sync token_dictionary variable name w/ classifier

    ctheodoris
    Verified signature
    a021deb

  1. update setup with req and manifest with updated filenames

    ctheodoris
    a34fbc2

  1. fix imports mtl/eval_utils

    ctheodoris
    eab1878

  1. allow model_type valid options to take params model_type : {"Pretrained", "GeneClassifier", "CellClassifier", "MTLCellClassifier", "MTLCellClassifier-Quantized"} (#390)⁠

    ctheodoris +1: madhavanvenkatesh
    Verified signature
    47e0ef8