Commit History

Update geneformer/perturber_utils.py
cec6545
verified

hchen725 commited on

fix overexpression with anchor genes and add perturbation batch with special tokens
9154763
verified

hchen725 commited on

add isp for perturb all with cls
bcaf65e
verified

hchen725 commited on

define ncells for clearing memory
428e3b0
verified

ctheodoris commited on

update isp for cls perturb set
99f40b4
verified

ctheodoris commited on

Update geneformer/in_silico_perturber.py
3e24216
verified

ctheodoris commited on

update with isp changes to account for cls from prior PR
d6e949b
verified

ctheodoris commited on

account for more than 1 gene being overexpressed
0f1a805
verified

ctheodoris commited on

Update geneformer/perturber_utils.py
43bb5ab
verified

hchen725 commited on

update to account for set of perturbed genes with aggregate_data
eb038a6

ctheodoris commited on

update to enable cls emb
b2bbd7c

ctheodoris commited on

update tokenizer to include eos token
ead0550

Christina Theodoris commited on

fix cell state gene embeddings bug (#345)
c0e7b19
verified

ctheodoris commited on

patch datasets save_to_disk
75c67a1

Christina Theodoris commited on

update kwargs for pretrainer
fb130e6

Christina Theodoris commited on

refer to token dictionary in self
86fe0dd

Christina Theodoris commited on

Update with gene classifier, custom token dict, and str validate options (#329)
0568479
verified

ctheodoris hchen725 commited on

add option for hyperparameter tuning to cc.validate
4bddd45

Christina Theodoris commited on

correct typo
5a43832
verified

ctheodoris commited on

update examples for predict_eval and handle roc for 2 cell classes
eeba323

Christina Theodoris commited on

Update readthedocs for classifier
f75f5ac

Christina Theodoris commited on

Get the gene keys and gene list keys from the token dictionary instead of medians (#304)
b294421
verified

ctheodoris hchen725 commited on

Prevent ruff/isort on init
941390d

Christina Theodoris commited on

Add classifier module and examples
9e9cca9

Christina Theodoris commited on

Add option for variable input_size and to add CLS/SEP Tokens (#299)
aa25cd2
verified

ctheodoris hchen725 commited on

add load model for train and fix validate anchor gene error
0d675a3

Christina Theodoris commited on

Handle case of single gene del for isp modeling of gene embs
316d817

Christina Theodoris commited on

edit docstring format to highlight options
e3330a6

Christina Theodoris commited on

edit docstring codeblock highlighting
d1931b1

Christina Theodoris commited on

update type of null_dict_list in docstring
79788b6

Christina Theodoris commited on

add readthedocs link to model card
cf0d7d4

Christina Theodoris commited on

update doc css
f91f132

Christina Theodoris commited on

change doc formatting
17f036a

Christina Theodoris commited on

update readthedocs.yaml
e04975c

Christina Theodoris commited on

add readthedocs yaml and req
142fe6f

Christina Theodoris commited on

add sphinx docs
2a0dcbe

Christina Theodoris commited on

update dependencies, reinstate compatibility with python<3.9 with typing for List
10d3f10

Christina Theodoris commited on

Add option for modified batch size for loom tokenizer
0960cf6

Christina Theodoris commited on

Add functions for extracting gene embeddings, move state_embs_dict outside isp, fix bugs in isp
2f25aea

Christina Theodoris commited on

Add option for modifying chunk size for anndata tokenizer
fd93ebf

Christina Theodoris commited on

Add pre-commit config
5d0082c

Christina Theodoris commited on

Update model card to emphasize need to install git-lfs and suggest https method
dbfac41

ctheodoris commited on

Add option to output embs as tensor
624349c

Christina Theodoris commited on