Christina Theodoris

#372 opened 12 days ago by

dimstef

Multiprocessing in InSilicoPerturber

4

#369 opened 17 days ago by

nlapier2

New activity in ctheodoris/Geneformer 13 days ago

AssertionError in classifier_utils.py

#343 opened 2 months ago by

lhl1bit

Need to add import to in_silico_perturber.py: from typing import List

#371 opened 14 days ago by

lhl1bit

New activity in ctheodoris/Geneformer 17 days ago

Error Generating State Embeddings Dictionary

#370 opened 17 days ago by

cparsonage

New activity in ctheodoris/Geneformer 18 days ago

Error in in_silico_perturbation example: get_model_embedding_dimensions

4

#368 opened 18 days ago by

nlapier2

New activity in ctheodoris/Genecorpus-30M 18 days ago

human_dcm_hcm_nf.dataset does not contain cardiomyocytes cell type

#22 opened 19 days ago by

saranyabalachandran

Count matrix

#23 opened 18 days ago by

sinabooeshaghi

test

#20 opened 20 days ago by

saranyabalachandran

New activity in ctheodoris/Geneformer 19 days ago

In Silico perturbation consumes all the GPU memory - OutofMemoryError: CUDA out of memory.

#365 opened 20 days ago by

vivekanand4

Need a Gene Name Dictionary for Mouse Gene Names

#366 opened 19 days ago by

bbutaney

New activity in ctheodoris/Genecorpus-30M 19 days ago

ArrowInvalid: Not an Arrow file

#21 opened 19 days ago by

sinabooeshaghi

New activity in ctheodoris/Geneformer 19 days ago

embs_df with all model embeddings

#363 opened 20 days ago by

Add function to get number of model embeddings

#364 opened 20 days ago by

New activity in ctheodoris/Geneformer 21 days ago

cosine shift

#346 opened 2 months ago by

qubug

New activity in ctheodoris/Geneformer 25 days ago

Update geneformer/in_silico_perturber.py

#355 opened about 1 month ago by

New activity in ctheodoris/Geneformer 26 days ago

Update geneformer/perturber_utils.py

#354 opened about 1 month ago by

GPU Requirement for Cell State Classifier

#360 opened 26 days ago by

cparsonage

New activity in ctheodoris/Geneformer 29 days ago

Update geneformer/emb_extractor.py

#356 opened about 1 month ago by

New activity in ctheodoris/Geneformer 30 days ago

Update geneformer/emb_extractor.py

#352 opened about 1 month ago by

New activity in ctheodoris/Geneformer about 1 month ago

Error: Can't load tokenizer using from_pretrained

4

#359 opened about 1 month ago by

lomi280

all cells for training

#349 opened about 2 months ago by

cstrlln

Availbable datasets for reproducing results

#357 opened about 1 month ago by

vaknavidru

Difference between tokenizing anndata vs loom

#351 opened about 1 month ago by

alandenadel

Error when running in_silico_perturber example

#293 opened 6 months ago by

nlapier2

Update geneformer/emb_extractor.py

#350 opened about 1 month ago by

New activity in ctheodoris/Geneformer about 2 months ago

In silico perturbation

#344 opened 2 months ago by

Renqing

Upload in_silico_perturber_stats.py

#313 opened 5 months ago by

davidjwen

fix cell state gene embeddings bug

#345 opened 2 months ago by

davidjwen

Need advice getting started

#348 opened about 2 months ago by

cstrlln

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 2 months ago by

alandenadel

New activity in ctheodoris/Geneformer 2 months ago

Calculating the direction of gene shifts after perturbation

#342 opened 2 months ago by

cmdn

TypeError: argument of type PosixPath is not iterable

#339 opened 3 months ago by

romerm16

patch_save_to_disk

#340 opened 3 months ago by

SidMahesh

Pretraining error reported

#341 opened 2 months ago by

babykai

New activity in ctheodoris/Geneformer 3 months ago

genetransformer

#324 opened 4 months ago by

sofiaztj

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 4 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

New activity in ctheodoris/Geneformer 4 months ago

Number of cells recommended for fine tuning

#335 opened 4 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 4 months ago by

weilangchan

Input files for examples

#332 opened 4 months ago by

yb1996

Update for gene classification

#330 opened 4 months ago by

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

#329 opened 4 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 4 months ago by

as8020

Can "cell_types" be more than three?

#323 opened 4 months ago by

jialei233

module 'geneformer' has no attribute 'perturber_utils'

#322 opened 4 months ago by

yehuicheng

a tiny bug fix missing default_training_args

#320 opened 4 months ago by

icefire080

Found dtype Long but expected Float

#321 opened 4 months ago by

yehuicheng

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 5 months ago by

Qianaqian

New activity in ctheodoris/Geneformer 5 months ago

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

#309 opened 5 months ago by

yehuicheng

Error in function `TranscriptomeTokenizer`

#308 opened 5 months ago by

giuliaelgarcia

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