Christina Theodoris

#355 opened 18 days ago by

New activity in ctheodoris/Geneformer 4 days ago

Update geneformer/perturber_utils.py

#354 opened 18 days ago by

GPU Requirement for Cell State Classifier

#360 opened 4 days ago by

cparsonage

New activity in ctheodoris/Geneformer 6 days ago

Update geneformer/emb_extractor.py

#356 opened 17 days ago by

New activity in ctheodoris/Geneformer 7 days ago

Update geneformer/emb_extractor.py

#352 opened 18 days ago by

New activity in ctheodoris/Geneformer 9 days ago

Error: Can't load tokenizer using from_pretrained

4

#359 opened 9 days ago by

lomi280

New activity in ctheodoris/Geneformer 11 days ago

all cells for training

#349 opened 24 days ago by

cstrlln

New activity in ctheodoris/Geneformer 15 days ago

Availbable datasets for reproducing results

#357 opened 15 days ago by

vaknavidru

New activity in ctheodoris/Geneformer 17 days ago

Difference between tokenizing anndata vs loom

#351 opened 19 days ago by

alandenadel

Error when running in_silico_perturber example

#293 opened 5 months ago by

nlapier2

New activity in ctheodoris/Geneformer 23 days ago

Update geneformer/emb_extractor.py

#350 opened 23 days ago by

New activity in ctheodoris/Geneformer 29 days ago

In silico perturbation

#344 opened about 1 month ago by

Renqing

Upload in_silico_perturber_stats.py

#313 opened 4 months ago by

davidjwen

fix cell state gene embeddings bug

#345 opened about 1 month ago by

davidjwen

Need advice getting started

#348 opened 29 days ago by

cstrlln

New activity in ctheodoris/Geneformer about 1 month ago

Error when tokenizing large datasets

10

#80 opened about 1 year ago by

yanwu2014

pyarrow.lib.ArrowInvalid: Value 2147483705 too large to fit in C integer type

#347 opened about 1 month ago by

alandenadel

AssertionError in classifier_utils.py

#343 opened about 1 month ago by

lhl1bit

Calculating the direction of gene shifts after perturbation

#342 opened about 2 months ago by

cmdn

New activity in ctheodoris/Geneformer about 2 months ago

TypeError: argument of type PosixPath is not iterable

#339 opened 2 months ago by

romerm16

patch_save_to_disk

#340 opened about 2 months ago by

SidMahesh

Pretraining error reported

#341 opened about 2 months ago by

babykai

genetransformer

#324 opened 3 months ago by

sofiaztj

New activity in ctheodoris/Geneformer 3 months ago

Effect of gene knock-out during in-silico perturbations on gene embeddings

#337 opened 3 months ago by

jamieb-nvs

in_silico_perturber ERROR

#326 opened 3 months ago by

zxh1210

In_silico_perturbation : out of memory error + GPU size

#338 opened 3 months ago by

melanieblr

TypeError in calling classifier.py

#336 opened 3 months ago by

nicomakii

Number of cells recommended for fine tuning

#335 opened 3 months ago by

schhina

Geneformer prerequisite

#318 opened 4 months ago by

onader01

How to reproduce the results of overexpressing OSKM genes?

10

#333 opened 3 months ago by

weilangchan

Input files for examples

#332 opened 3 months ago by

yb1996

Update for gene classification

#330 opened 3 months ago by

Update with gene classifier, custom token dict, and str validate options

#329 opened 3 months ago by

in-silico_perturbation/IndexError: Dimension out of range (expected to be in range of [-1, 0], but got 1)

9

#291 opened 6 months ago by

miladmrv

Further network analysis examples

#325 opened 3 months ago by

as8020

Can "cell_types" be more than three?

#323 opened 3 months ago by

module 'geneformer' has no attribute 'perturber_utils'

#322 opened 3 months ago by

yehuicheng

a tiny bug fix missing default_training_args

#320 opened 3 months ago by

icefire080

Found dtype Long but expected Float

#321 opened 3 months ago by

yehuicheng

New activity in ctheodoris/Geneformer 4 months ago

Question about data splitting

#317 opened 4 months ago by

MinieRosie

Is used for bulk RNA with tumor celline?

#316 opened 4 months ago by

mengcheng-yao

There was a problem preparing the pre-training corpus

#315 opened 4 months ago by

babykai

Performance Evaluation: 12-Layer vs. 6-Layer Geneformer

#314 opened 4 months ago by

Qianaqian

How to do pre-training with my own 500,000 dataset

#309 opened 4 months ago by

yehuicheng

Error in function `TranscriptomeTokenizer`

#308 opened 4 months ago by

giuliaelgarcia

Classifier.validate() got an unexpected keyword argument 'predict'

#307 opened 4 months ago by

New activity in ctheodoris/Genecorpus-30M 4 months ago

The labels in Gene Function Classification are not Mutually Exclusive

4

#19 opened 4 months ago by

Linear-Matrix-Probability

New activity in ctheodoris/Geneformer 4 months ago

Pre-trained corpus processing consulting

#306 opened 4 months ago by

babykai

How to determine the number of the genes in the final result of perturbation？

#305 opened 4 months ago by

Get the gene keys and gene list keys from the token dictionary instead of medians

#304 opened 4 months ago by

Upload 15 files

#267 opened 9 months ago by

tigerdeF

InSilicoPerturberStats can't handle 2 classes

#296 opened 5 months ago by

MinieRosie

Add emb_mode required argument into load_model

#302 opened 4 months ago by

Update geneformer/emb_extractor.py

#303 opened 4 months ago by

About multi gpu for cell classification finetune

#300 opened 4 months ago by

Eyulaochen

Fix typo

#301 opened 4 months ago by

Add option for variable input_size and to add CLS/SEP Tokens

#299 opened 4 months ago by

New activity in ctheodoris/Geneformer 5 months ago

error in perturbation with anchor gene

#298 opened 5 months ago by

Help for model interpretation

#295 opened 5 months ago by

MinieRosie

torch.cuda.OutOfMemoryError when runing embex.get_state_embs