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Geneformer

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Geneformer / geneformer

Commit History

  1. Fix bug in selecting a gene with "aggregate_data" option

    davidjwen
    Verified signature
    92b62f4

  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. change doc formatting

    Christina Theodoris
    17f036a

  5. 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

  1. tokenizer-uncropped-input_ids (#275)⁠

    ctheodoris +1: jamieb-nvs
    8df5dc1

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

    ctheodoris +1: tpob
    1366905

  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. Add memory-efficient method for computing emb summary statistics

    Christina Theodoris
    6caf480

  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. Rename heatmap legend to be correct label

    Christina Theodoris
    badcca6

  3. Add function to extract and plot cell embeddings

    Christina Theodoris
    d154fee

  4. Add error for no files found and suppress loompy import warning

    Christina Theodoris
    abdf980

  1. Add sorting for aggregating data for goal state shifts

    Christina Theodoris
    50e921d

  2. Fix min_genes to be >= tokens to perturb as a group

    Christina Theodoris
    268e566

  1. Update tokenizer to allow tokenization without custom cell attributes

    Christina Theodoris
    57b9778

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

    Christina Theodoris
    acd253c

  1. Update internal format of anchor token to list for consistency with genes to perturb

    Christina Theodoris
    b36d210

  1. Add filtering for start state cells prior to in silico perturbation when modeling cell states

    Christina Theodoris
    bb217cf

  1. Correct order of state dict in in silico perturber stats and tensor dims of alt state emb in in silico perturber

    Christina Theodoris
    3d06203

  2. Add explanation of output columns and sort by largest shift

    Christina Theodoris
    3072225

  1. Modify tokenizer to allow renaming attr names btwn loom and .dataset

    Christina Theodoris
    e78c44d

  2. Modify quant_layers to convert layer nums to integers before calculating max

    Christina Theodoris
    2181aa4

  1. Modify documentation for modeling only 2 cell states

    Christina Theodoris
    019165f