Geneformer / geneformer

Commit History

Upload in_silico_perturber.py
9f0fa5d
verified

davidjwen commited on

change default emb to cls
9ee140a
verified

ctheodoris commited on

CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling (#416)
b6d28c3
verified

ctheodoris madhavanvenkatesh commited on

move dict loading to function in eval utils
57bc17e

ctheodoris commited on

edit docs formatting
ef094b2

ctheodoris commited on

update tokenizer to defaults for 95M models for special token and input size
da8cf3d
verified

ctheodoris commited on

sync token_dictionary variable name w/ classifier
a021deb
verified

ctheodoris commited on

fix imports mtl/eval_utils
eab1878

ctheodoris commited on

allow model_type valid options to take params model_type : {"Pretrained", "GeneClassifier", "CellClassifier", "MTLCellClassifier", "MTLCellClassifier-Quantized"} (#390)
47e0ef8
verified

ctheodoris madhavanvenkatesh commited on

comment out "def save_model_without_heads(original_model_save_directory)"; redundant for ISP/Emb extractor (#382)
22bf20f
verified

ctheodoris madhavanvenkatesh commited on

fixed bug related to dynamic ranges in dictionary with 'min' and 'max' value mismatch in optuna suggest fn (#380)
fe1640b
verified

ctheodoris madhavanvenkatesh commited on

precommit formatting
f07bfd7

ctheodoris commited on

update with 12L and 20L i4096 gc95M models, multitask and quantiz code
933ca80

ctheodoris commited on

rename for consistency
ec19834
verified

ctheodoris commited on

delete old gene name dict
817eca2
verified

ctheodoris commited on

update to only have gene names as keys in gene_name_id_dict
e61485e
verified

ctheodoris commited on

add typing list import
42053dc

ctheodoris commited on

move dicts to init
ea428cb

ctheodoris commited on

add random state to umap
eb2a04b

ctheodoris commited on

update get_embs with token_gene_dict arg
ace12e9
verified

ctheodoris commited on

update refs to get_model_emb_dims
3fe35ba
verified

ctheodoris commited on

clone embs_i to resolve memory leak in cls embs
57f02a4

ctheodoris commited on

update perturber stats to reflect cos sim and emb_extractor to suppress warnings for non-cls
25dd1da

ctheodoris 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