snap-stanford GEARS issues

snap-stanford / GEARS

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

MIT License

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issues

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Questions about creating pertdata with own data files

#79 HelloWorldLTY opened 1 week ago
1
Address a potential problem while creating a training dataset with dense array inputs

#78 HelloWorldLTY opened 1 week ago
0
Question about "Using Trained Model"

#77 incase-1 closed 1 week ago
1
Unpickling Error in gene_set_path

#76 bioinfonewguy opened 2 weeks ago
1
Value error in loading the dataset

#75 bboyrush117 opened 3 weeks ago
1
Beginner question: GEARS on un-perturbed data

#74 bioinfonewguy closed 3 weeks ago
1
IndexError: index 0 is out of bounds for axis 0 with size 0

#73 XinMakise closed 1 month ago
0
simulation_single option with pert_data.prepare_split gives ValueError

#72 murthy1770 opened 1 month ago
0
KeyError: 'val'

#71 xiaomaolxc opened 1 month ago
3
Environments (versions of packages) to run GEARS

#70 wcanisay-y opened 2 months ago
0
Mixup in hyperparameters for H_pert H_gene?

#69 mhorlacher opened 2 months ago
0
Duplicated gene names in replogle_k562_essential

#68 zhan8855 closed 2 months ago
4
Are there pretrained weights available?

#67 jamesbraza closed 2 months ago
1
Moving `torch.device` to work in Google Colab

#66 jamesbraza closed 2 months ago
1
Missing `torch_geometric` in `requirements.txt`

#65 jamesbraza closed 2 months ago
1
error about prepare_split

#64 oahux28 closed 3 months ago
4
Question about how to generate condition colname?

#63 yanwuanxin closed 3 months ago
3
Custom PertData ``new_data_process`` error

#62 Yonggie opened 3 months ago
1
differences between papers and implementations

#61 sheunbaek closed 3 months ago
1
custom GO graph location

#60 Jiahao-Gao opened 3 months ago
1
result of gears_model.GI_predict: ['mag', 'dcor', 'corr_fit', 'dominance', 'eq_contr']

#59 yanwuanxin closed 3 months ago
1
Questions about reproduction of Figure2f and Figure2cd

#58 yu3jun opened 4 months ago
0
How to obtain more top_non_dropout_de?

#57 yanwuanxin opened 4 months ago
1
KeyError: 'val'

#56 yanwuanxin closed 4 months ago
5
Questions about split and the experiment results

#55 yu3jun closed 4 months ago
0
Perturbations are not in the GO graph

#54 niklasbinder closed 4 months ago
4
Directly implementing gears on scRNA-seq data

#53 XiaoMi93 opened 4 months ago
1
A question about directional loss.

#52 Bunnybeibei closed 4 months ago
1
Questions about reproduction of Figure2cd

#51 zhoummmin closed 4 months ago
2
Publication of model parameters

#50 fratajcz closed 4 months ago
2
Trouble using the outputs obtained from the GEARS model

#49 fratajcz closed 5 months ago
4
perturbation coexpression

#48 xinghao-1210 closed 5 months ago
1
Interpretation of Prediction

#47 uddamvathanak closed 5 months ago
4
prediction interpretation

#46 Gianl-msi closed 5 months ago
1
Issue with new_data_process function

#45 carversh closed 5 months ago
3
tutorial_inference_Norman.ipynb is out-of-date

#44 jzqin opened 6 months ago
0
How to define pertubation?

#43 Larrycpan closed 6 months ago
2
MLP module last layer activation is always set to ReLU

#42 dparkSonata opened 7 months ago
1
Matching to Different Set of Controls

#41 GordianArnav closed 7 months ago
1
About the preparation of split

#40 GoldenRain-Su closed 7 months ago
4
Issue loading custom data

#39 docmab23 opened 8 months ago
1
No file in https://dataverse.harvard.edu/api/accsess/datafile/6934319

#38 hzlllll closed 8 months ago
2
error: model_initialize() got an unexpected keyword argument 'cell_fitness_pred' when running "Using Trained Model" tutorial

#37 xwanaf closed 8 months ago
2
A question about the direction loss

#36 zhan8855 closed 7 months ago
3
Any suggestions for the HPC requirement

#35 Marsrocky closed 8 months ago
5
Very long import time

#34 dzyim closed 9 months ago
1
traing stack using the v0.10.0 gears

#33 weizhiting closed 9 months ago
5
Error when trying to load the pre-trained model

#32 moghra closed 9 months ago
1
How many epochs should take when training the model using the Replogle K562 essential dataset.

#31 weizhiting closed 9 months ago
1
Predictions: expression or delta expression?

#30 ekernf01 closed 9 months ago
2