snap-stanford/GEARS

Issues

• IndexError: index 0 is out of bounds for axis 0 with size 0

  #73 opened 12 days ago by XinMakise
  0

• Custom PertData ``new_data_process`` error

  #62 opened 3 months ago by Yonggie
  1

• KeyError: 'val'

  #71 opened a month ago by xiaomaolxc
  3

• simulation_single option with pert_data.prepare_split gives ValueError

  #72 opened 25 days ago by murthy1770
  0

• Environments (versions of packages) to run GEARS

  #70 opened a month ago by wcanisay-y
  0

• About the preparation of split

  #40 opened 7 months ago by GoldenRain-Su
  4

• Duplicated gene names in replogle_k562_essential

  #68 opened a month ago by zhan8855
  4

• Mixup in hyperparameters for H_pert H_gene?

  #69 opened a month ago by mhorlacher
  0

• Missing `torch_geometric` in `requirements.txt`

  #65 opened 2 months ago by jamesbraza
  1

• Moving `torch.device` to work in Google Colab

  #66 opened 2 months ago by jamesbraza
  1

• Are there pretrained weights available?

  #67 opened 2 months ago by jamesbraza
  1

• error about prepare_split

  #64 opened 2 months ago by oahux28
  4

• differences between papers and implementations

  #61 opened 2 months ago by sheunbaek
  1

• Question about how to generate condition colname?

  #63 opened 3 months ago by yanwuanxin
  3

• Trouble using the outputs obtained from the GEARS model

  #49 opened 4 months ago by fratajcz
  4

• custom GO graph location

  #60 opened 3 months ago by Jiahao-Gao
  1

• result of gears_model.GI_predict: ['mag', 'dcor', 'corr_fit', 'dominance', 'eq_contr']

  #59 opened 3 months ago by yanwuanxin
  1

• Questions about split and the experiment results

  #55 opened 3 months ago by yu3jun
  0

• Questions about reproduction of Figure2f and Figure2cd

  #58 opened 3 months ago by yu3jun
  0

• How to obtain more top_non_dropout_de?

  #57 opened 3 months ago by yanwuanxin
  1

• KeyError: 'val'

  #56 opened 3 months ago by yanwuanxin
  5

• Perturbations are not in the GO graph

  #54 opened 4 months ago by niklasbinder
  4

• Publication of model parameters

  #50 opened 4 months ago by fratajcz
  2

• Questions about reproduction of Figure2cd

  #51 opened 4 months ago by zhoummmin
  2

• Directly implementing gears on scRNA-seq data

  #53 opened 4 months ago by XiaoMi93
  1

• Question on data pre-processing

  #28 opened 9 months ago by cbirchsy
  8

• A question about directional loss.

  #52 opened 4 months ago by Bunnybeibei
  1

• Interpretation of Prediction

  #47 opened 4 months ago by uddamvathanak
  4

• perturbation coexpression

  #48 opened 4 months ago by xinghao-1210
  1

• Issue with new_data_process function

  #45 opened 4 months ago by carversh
  3

• prediction interpretation

  #46 opened 5 months ago by Gianl-msi
  1

• tutorial_inference_Norman.ipynb is out-of-date

  #44 opened 5 months ago by jzqin
  0

• How to define pertubation?

  #43 opened 5 months ago by Larrycpan
  2

• MLP module last layer activation is always set to ReLU

  #42 opened 6 months ago by dparkSonata
  1

• Matching to Different Set of Controls

  #41 opened 6 months ago by GordianArnav
  1

• no_test option for data split yields error

  #29 opened 6 months ago by ekernf01
  6

• Issue loading custom data

  #39 opened 7 months ago by docmab23
  1

• A question about the direction loss

  #36 opened 7 months ago by zhan8855
  3

• error: model_initialize() got an unexpected keyword argument 'cell_fitness_pred' when running "Using Trained Model" tutorial

  #37 opened 7 months ago by xwanaf
  2

• No file in https://dataverse.harvard.edu/api/accsess/datafile/6934319

  #38 opened 8 months ago by hzlllll
  2

• Any suggestions for the HPC requirement

  #35 opened 8 months ago by Marsrocky
  5

• Very long import time

  #34 opened 8 months ago by dzyim
  1

• traing stack using the v0.10.0 gears

  #33 opened 8 months ago by weizhiting
  5

• How many epochs should take when training the model using the Replogle K562 essential dataset.

  #31 opened 8 months ago by weizhiting
  1

• Error when trying to load the pre-trained model

  #32 opened 8 months ago by moghra
  1

• Predictions: expression or delta expression?

  #30 opened 8 months ago by ekernf01
  2

• A question about selecting genes

  #27 opened 9 months ago by HelloWorldLTY
  1

• Bug in new_data_process

  #24 opened 10 months ago by pckinnunen
  3

• IndexError: index 0 is out of bounds for axis 0 with size 0

  #26 opened 10 months ago by taffy-miao
  5

• Questions on pert_data.prepare_split

  #25 opened 10 months ago by taffy-miao
  2