snap-stanford/GEARS

Issues

• Missing files for reproducing Fig 3c

  #89 opened 2 months ago by chinaliye
  0

• tutorial_inference_Norman.ipynb is out-of-date

  #44 opened 4 months ago by jzqin
  2

• uncertainty score question

  #88 opened 2 months ago by ernesto-iacucci
  2

• Interpreting the results of GI_predict()

  #87 opened 2 months ago by ManuelMoradiellos
  2

• MLP module last layer activation is always set to ReLU

  #42 opened 2 months ago by dparkSonata
  1

• How to obtain more top_non_dropout_de?

  #57 opened 2 months ago by yanwuanxin
  2

• How is the adamson data generated?

  #83 opened 2 months ago by YOU-k
  1

• Question about loss function of direction

  #86 opened 2 months ago by ChangxiChi
  1

• test

  #85 opened 3 months ago by oscarpitcho
  0

• Unpickling Error in gene_set_path

  #76 opened 6 months ago by bioinfonewguy
  3

• How canI generate go_essential_all for mouse

  #84 opened 4 months ago by mabaoweireadingene
  0

• Question about mean baseline

  #82 opened 4 months ago by Leafaeolian
  0

• Directly implementing gears on scRNA-seq data

  #53 opened 4 months ago by XiaoMi93
  3

• custom GO graph location

  #60 opened 4 months ago by Jiahao-Gao
  1

• Issue loading custom data

  #39 opened 4 months ago by docmab23
  2

• Trouble using the outputs obtained from the GEARS model

  #49 opened 10 months ago by fratajcz
  5

• Questions about creating pertdata with own data files

  #79 opened 5 months ago by HelloWorldLTY
  3

• KeyError: 'val'

  #71 opened 5 months ago by xiaomaolxc
  4

• Value error in loading the dataset

  #75 opened 5 months ago by bboyrush117
  2

• simulation_single option with pert_data.prepare_split gives ValueError

  #72 opened 7 months ago by murthy1770
  1

• KeyError 'val' when creating dataloader with split='single'

  #81 opened 5 months ago by domcke
  1

• Pretrained Reploge2022 model

  #80 opened 5 months ago by Jiahao-Gao
  0

• Question about "Using Trained Model"

  #77 opened 5 months ago by incase-1
  1

• Beginner question: GEARS on un-perturbed data

  #74 opened 6 months ago by bioinfonewguy
  1

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

  #73 opened 6 months ago by XinMakise
  0

• Custom PertData ``new_data_process`` error

  #62 opened 9 months ago by Yonggie
  1

• Environments (versions of packages) to run GEARS

  #70 opened 7 months ago by wcanisay-y
  0

• About the preparation of split

  #40 opened a year ago by GoldenRain-Su
  4

• Duplicated gene names in replogle_k562_essential

  #68 opened 7 months ago by zhan8855
  4

• Mixup in hyperparameters for H_pert H_gene?

  #69 opened 7 months ago by mhorlacher
  0

• Missing `torch_geometric` in `requirements.txt`

  #65 opened 8 months ago by jamesbraza
  1

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

  #66 opened 8 months ago by jamesbraza
  1

• Are there pretrained weights available?

  #67 opened 8 months ago by jamesbraza
  1

• error about prepare_split

  #64 opened 8 months ago by oahux28
  4

• differences between papers and implementations

  #61 opened 8 months ago by sheunbaek
  1

• Question about how to generate condition colname?

  #63 opened 8 months ago by yanwuanxin
  3

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

  #59 opened 9 months ago by yanwuanxin
  1

• Questions about split and the experiment results

  #55 opened 9 months ago by yu3jun
  0

• Questions about reproduction of Figure2f and Figure2cd

  #58 opened 9 months ago by yu3jun
  0

• KeyError: 'val'

  #56 opened 9 months ago by yanwuanxin
  5

• Perturbations are not in the GO graph

  #54 opened 9 months ago by niklasbinder
  4

• Publication of model parameters

  #50 opened 10 months ago by fratajcz
  2

• Questions about reproduction of Figure2cd

  #51 opened 10 months ago by zhoummmin
  2

• A question about directional loss.

  #52 opened 10 months ago by Bunnybeibei
  1

• Interpretation of Prediction

  #47 opened 10 months ago by uddamvathanak
  4

• perturbation coexpression

  #48 opened 10 months ago by xinghao-1210
  1

• Issue with new_data_process function

  #45 opened 10 months ago by carversh
  3

• prediction interpretation

  #46 opened 10 months ago by Gianl-msi
  1

• How to define pertubation?

  #43 opened a year ago by Larrycpan
  2

• Matching to Different Set of Controls

  #41 opened a year ago by GordianArnav
  1