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Geneformer

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Geneformer

Commit History

  1. Update for gene classification (#330)⁠

    ctheodoris +1: hchen725
    Verified signature
    94095d1

  2. Update with gene classifier, custom token dict, and str validate options (#329)⁠

    ctheodoris +1: hchen725
    Verified signature
    0568479

  1. add option for hyperparameter tuning to cc.validate

    Christina Theodoris
    4bddd45

  1. correct typo

    ctheodoris
    Verified signature
    5a43832

  1. update examples for predict_eval and handle roc for 2 cell classes

    Christina Theodoris
    eeba323

  1. Update readthedocs for classifier

    Christina Theodoris
    f75f5ac

  1. Get the gene keys and gene list keys from the token dictionary instead of medians (#304)⁠

    ctheodoris +1: hchen725
    Verified signature
    b294421

  2. Prevent ruff/isort on init

    Christina Theodoris
    941390d

  3. Add classifier module and examples

    Christina Theodoris
    9e9cca9

  1. Update geneformer/emb_extractor.py (#303)⁠

    ctheodoris +1: hchen725
    Verified signature
    d6c634c

  1. Fix typo (#301)⁠

    ctheodoris +1: hchen725
    Verified signature
    075bd53

  1. Add option for variable input_size and to add CLS/SEP Tokens (#299)⁠

    ctheodoris +1: hchen725
    Verified signature
    aa25cd2

  1. add load model for train and fix validate anchor gene error

    Christina Theodoris
    0d675a3

  1. Handle case of single gene del for isp modeling of gene embs

    Christina Theodoris
    316d817

  1. edit docstring format to highlight options

    Christina Theodoris
    e3330a6

  2. edit docstring codeblock highlighting

    Christina Theodoris
    d1931b1

  3. update type of null_dict_list in docstring

    Christina Theodoris
    79788b6

  4. add readthedocs link to model card

    Christina Theodoris
    cf0d7d4

  5. update doc css

    Christina Theodoris
    f91f132

  6. change doc formatting

    Christina Theodoris
    17f036a

  7. update readthedocs.yaml

    Christina Theodoris
    e04975c

  8. add readthedocs yaml and req

    Christina Theodoris
    142fe6f

  9. add sphinx docs

    Christina Theodoris
    2a0dcbe

  1. update dependencies, reinstate compatibility with python<3.9 with typing for List

    Christina Theodoris
    10d3f10

  1. Add option for modified batch size for loom tokenizer

    Christina Theodoris
    0960cf6

  1. Add functions for extracting gene embeddings, move state_embs_dict outside isp, fix bugs in isp

    Christina Theodoris
    2f25aea

  2. Add option for modifying chunk size for anndata tokenizer

    Christina Theodoris
    fd93ebf

  3. Add pre-commit config

    Christina Theodoris
    5d0082c

  1. tokenizer-uncropped-input_ids (#275)⁠

    ctheodoris +1: jamieb-nvs
    8df5dc1

  1. fix: incorrect condition control flow (#261)⁠

    ctheodoris +1: tpob
    1366905

  1. Update model card to emphasize need to install git-lfs and suggest https method

    ctheodoris
    dbfac41

  1. Add option to output embs as tensor

    Christina Theodoris
    624349c

  1. anndata_tokenizer (#170)⁠

    ctheodoris +1: ricomnl
    4302f48

  1. Fixed bugs related to overexpressing genes (#229)⁠

    ctheodoris +1: davidjwen
    39ab62e

  1. Update installation instructions to include git lfs install and ssh method

    ctheodoris
    4ce81ab

  1. Config head node runtime via IP (#234)⁠

    ctheodoris +1: madhavanvenkatesh
    b8fda63

  1. Add memory-efficient method for computing emb summary statistics

    Christina Theodoris
    6caf480

  1. Adding `safetensors` variant of this model (#209)⁠

    ctheodoris +1: SFconvertbot
    61f15d2

  1. Fixed bug with the double removing of indices when cell_states_to_model is false (#188)⁠

    ctheodoris +1: davidjwen
    0adfe67

  2. Upload in_silico_perturber.py (#187)⁠

    ctheodoris +1: davidjwen
    8180caa

  1. Added feature to perturb a set of indices to help with debugging and with very large runtimes (#175)⁠

    ctheodoris +1: davidjwen
    f115e8f

  1. Re-update stats to handle case of empty alt_states

    Christina Theodoris
    78517d8

  2. Add handling for case of alt_states being empty list

    Christina Theodoris
    9e8dbe5

  1. Remove print statement from PR

    ctheodoris
    c4b1f94

  2. Fixed bug in gen_attention_mask with len > max_len (#158)⁠

    ctheodoris +1: davidjwen
    3a94209

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

    ctheodoris +1: davidjwen
    9169bfd

  1. Add error message for "gene" embedding extraction under development.

    Christina Theodoris
    65b4915

  2. Update README.md⁠

    ctheodoris
    e820326

  3. Rename heatmap legend to be correct label

    Christina Theodoris
    badcca6

  4. Add function to extract and plot cell embeddings

    Christina Theodoris
    d154fee