Christina Theodoris

#337 opened 19 days ago by

jamieb-nvs

in_silico_perturber ERROR

#326 opened about 1 month ago by

zxh1210

In_silico_perturbation : out of memory error + GPU size

#338 opened 18 days ago by

melanieblr

New activity in ctheodoris/Geneformer 21 days ago

TypeError in calling classifier.py

#336 opened 21 days ago by

nicomakii

New activity in ctheodoris/Geneformer 25 days ago

Number of cells recommended for fine tuning

#335 opened 25 days ago by

schhina

New activity in ctheodoris/Geneformer 27 days ago

Geneformer prerequisite

#318 opened about 2 months ago by

onader01

New activity in ctheodoris/Geneformer 28 days ago

How to reproduce the results of overexpressing OSKM genes?

10

#333 opened 28 days ago by

weilangchan

New activity in ctheodoris/Geneformer 29 days ago

Input files for examples

#332 opened 29 days ago by

yb1996

Update for gene classification

#330 opened about 1 month ago by

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

#329 opened about 1 month ago by

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

9

#291 opened 4 months ago by

miladmrv

New activity in ctheodoris/Geneformer about 1 month ago

Further network analysis examples

#325 opened about 1 month ago by

as8020

Can "cell_types" be more than three?

#323 opened about 1 month ago by

module 'geneformer' has no attribute 'perturber_utils'

#322 opened about 1 month ago by

yehuicheng

a tiny bug fix missing default_training_args

#320 opened about 1 month ago by

icefire080

Found dtype Long but expected Float

#321 opened about 1 month ago by

yehuicheng

New activity in ctheodoris/Geneformer about 2 months ago

Question about data splitting

#317 opened about 2 months ago by

Is used for bulk RNA with tumor celline?

#316 opened about 2 months ago by

mengcheng-yao

There was a problem preparing the pre-training corpus

#315 opened about 2 months ago by

babykai

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

#314 opened about 2 months ago by

Qianaqian

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

#309 opened about 2 months ago by

yehuicheng

New activity in ctheodoris/Geneformer 2 months ago

Error in function `TranscriptomeTokenizer`

#308 opened 2 months ago by

giuliaelgarcia

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

#307 opened 2 months ago by

New activity in ctheodoris/Genecorpus-30M 2 months ago

The labels in Gene Function Classification are not Mutually Exclusive

4

#19 opened 2 months ago by

Linear-Matrix-Probability

New activity in ctheodoris/Geneformer 2 months ago

Pre-trained corpus processing consulting

#306 opened 2 months ago by

babykai

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

#305 opened 2 months ago by

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

#304 opened 2 months ago by

Upload 15 files

#267 opened 7 months ago by

tigerdeF

InSilicoPerturberStats can't handle 2 classes

#296 opened 3 months ago by

Add emb_mode required argument into load_model

#302 opened 2 months ago by

Update geneformer/emb_extractor.py

#303 opened 2 months ago by

About multi gpu for cell classification finetune

#300 opened 2 months ago by

Eyulaochen

Fix typo

#301 opened 2 months ago by

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

#299 opened 2 months ago by

New activity in ctheodoris/Geneformer 3 months ago

error in perturbation with anchor gene

#298 opened 3 months ago by

Error when running in_silico_perturber example

#293 opened 3 months ago by

nlapier2

Help for model interpretation

#295 opened 3 months ago by

torch.cuda.OutOfMemoryError when runing embex.get_state_embs

#297 opened 3 months ago by

Jonyyqn

No <cls> token is added in tokenizer -> suboptimal cell classification?

#294 opened 3 months ago by

aribenjamin

Replicating results for Figure 6

10

#246 opened 8 months ago by

Upload in_silico_perturber.py

#292 opened 4 months ago by

davidjwen

New activity in ctheodoris/Geneformer 4 months ago

Seeking Geneformer related help

#289 opened 4 months ago by

rongguangda

How can I know the lable names of the fine tunned model geneformer-6L-30M_CellClassifier_cardiomyopathies_220224?

#290 opened 4 months ago by

dynastyteng

In silico perturbation errors when perturbing a single gene

8

#288 opened 4 months ago by

sarudak

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

Inquiry about Missing Columns in Sample Dataset

#18 opened 4 months ago by

mizu0426

New activity in ctheodoris/Geneformer 4 months ago

Requirements.txt or conda.yaml for env missing

#281 opened 5 months ago by

yardenko

Error in calculating cosine similarity in perturber_utils and solutions

#287 opened 4 months ago by

davidliwei

How to output p-value and FDR and perturbation result of gene embedding when doing single-gene perturbation

5

#285 opened 4 months ago by

Jonyyqn

New activity in ctheodoris/Geneformer 5 months ago

A bug when loading the new gene embeddings extractor

#284 opened 5 months ago by

iLOVE2D

New activity in ctheodoris/Genecorpus-30M 5 months ago

Example of cell type prediction

#17 opened 5 months ago by

dynastyteng

New activity in ctheodoris/Geneformer 5 months ago

RuntimeError: The expanded size of the tensor (2048) must match the existing size (512) at non-singleton dimension 1.

#247 opened 8 months ago by

LZW150

how to concatenate mulitple arrow format datasets into one big arrow format datasets?

#282 opened 5 months ago by

fczqx

Update geneformer/in_silico_perturber.py

#283 opened 5 months ago by

itsAnnieeeeee

torch.cuda.OutOfMemoryError: CUDA out of memory in in_silico_perturbation

#276 opened 6 months ago by

kchen360

Error adding deletions through inSilicoPerturber

4

#260 opened 7 months ago by

AMCalejandro

How to output gene embeddings after single gene perturbation, similar to Fig5a/b?

#256 opened 7 months ago by

junguyen

[In silico perturbation] RuntimeError: No active exception to reraise