theislab/chemCPA

Issues

• Request: pre-trained models weight checkpoints

  #153 opened a year ago by Tigerrr07
  2

• Errors running default manual_seml_sweep.py

  #165 opened 5 months ago by ArturDev42
  2

• Differential expression evaluated by rank_genes_groups using t-test vs. wilcoxon method

  #164 opened 8 months ago by ceesu
  0

• How to download drugbank_all.csv?

  #163 opened 8 months ago by wangyucheng1234
  0

• Pretraining and running model

  #162 opened 9 months ago by xianglin226
  2

• what did you intend to do with drug_name.split("+")]

  #132 opened a year ago by bhomass
  8

• two types of validation data for fine tuning experiment

  #150 opened a year ago by bhomass
  1

• how to obtain delta r2 in table 4?

  #155 opened 9 months ago by bhomass
  3

• K562 cell type not in L1000. what did you do during fine-tuning?

  #156 opened 9 months ago by bhomass
  1

• Initial gene embedding for chemcpa

  #158 opened 10 months ago by sepidism
  4

• Clarifications about LINCS data / evaluation

  #159 opened 10 months ago by rvinas
  2

• what exactly is your baseline?

  #146 opened a year ago by bhomass
  9

• chemCPA vs chemCPA pretrained

  #147 opened 10 months ago by bhomass
  2

• Can't find drugbank_all.csv

  #117 opened a year ago by sumanabasu
  4

• how was lincs_trapnell.smiles generated?

  #141 opened 10 months ago by bhomass
  1

• the uncertainty equation

  #154 opened 10 months ago by bhomass
  1

• Is your R2 variance result published anywhere

  #152 opened 10 months ago by bhomass
  1

• Preprocessing notebooks

  #157 opened a year ago by sepidism
  0

• ood drug belinostat leaks to pretraining dataset

  #149 opened a year ago by bhomass
  1

• File location of seml_sweep_icb.py

  #151 opened a year ago by Tigerrr07
  1

• Split setting for your experimental reimplementation

  #148 opened a year ago by sheunbaek
  1

• Reproducibility issues

  #121 opened a year ago by regloeb
  2

• where is trapnell_final_V7.h5ad?

  #128 opened a year ago by bhomass
  2

• LINCS pretrained model weights and configs

  #123 opened a year ago by jasperhyp
  9

• Did the extended gene dataset (2000 genes) perform better than the 977 gene dataset?

  #142 opened a year ago by bhomass
  1

• which molecular embedding was ultimately chosen?

  #143 opened a year ago by bhomass
  2

• entanglement score

  #139 opened a year ago by bhomass
  1

• is de_genes keyed on condition only or cell_drug_dose_comb

  #144 opened a year ago by bhomass
  1

• Provide dataset to run an individual training round

  #115 opened a year ago by ggonzalezp
  2

• what is config_hash for?

  #140 opened a year ago by bhomass
  2

• cell_id or cell_type for dataset.data_params.covariate_keys

  #129 opened a year ago by bhomass
  2

• bug in embedding.py

  #136 opened a year ago by bhomass
  2

• when do you ever want exp = ExperimentWrapper(init_all=False)?

  #137 opened a year ago by bhomass
  1

• `compute_prediction()` function does not work for a batch size of 1

  #130 opened a year ago by sumanabasu
  0

• Clarification of data preprocessing/normalisation

  #120 opened a year ago by cbirchsy
  0

• LINCS data preprocessing: `treatment time` averaged? Normalization?

  #125 opened a year ago by jasperhyp
  2

• KeyError: 'assinex' on lincs.ipynb with lincs_full.h5ad

  #116 opened a year ago by sumanabasu
  4

• bug in lincs.ipynb

  #124 opened a year ago by bhomass
  0

• where is GSE92742_Broad_LINCS_pert_info.txt

  #126 opened a year ago by bhomass
  1

• Can not find “lincs_full.h5ad” file

  #106 opened 2 years ago by Dean-98543
  4

• mongodb credentials

  #122 opened a year ago by bhomass
  1

• question about reproducing the result

  #114 opened a year ago by huawen-poppy
  2

• Usage of control cell gene expression in evaluation of chemCPA

  #111 opened a year ago by Dean-98543
  9

• Fold-change prediction on novel SMILES

  #109 opened a year ago by michal-pikusa
  3

• fail in running the rdkit hparam for lincs

  #113 opened 2 years ago by huawen-poppy
  2

• what's the differences between lincs_full.h5ad and lincs.h5ad?

  #110 opened 2 years ago by huawen-poppy
  3

• How to calculate the uncertainty

  #112 opened 2 years ago by tuln128
  2

• Finetuning to SciPlex dataset.

  #108 opened 2 years ago by reem12345
  4

• Creating chemCPA environemnt

  #105 opened 2 years ago by v-mahughes
  2

• Get things ready for publication

  #98 opened 3 years ago by siboehm
  3