theislab chemCPA issues

theislab / chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

https://arxiv.org/abs/2204.13545

MIT License

88 stars 23 forks source link

issues

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Errors running default manual_seml_sweep.py

#165 ArturDev42 opened 4 days ago
0
Differential expression evaluated by rank_genes_groups using t-test vs. wilcoxon method

#164 ceesu opened 3 months ago
0
How to download drugbank_all.csv?

#163 wangyucheng1234 opened 3 months ago
0
Pretraining and running model

#162 xianglin226 opened 3 months ago
2
Data loading

#161 B1RO closed 4 months ago
1
Biroscak/esm2 embedding computation

#160 B1RO closed 4 months ago
1
Clarifications about LINCS data / evaluation

#159 rvinas opened 4 months ago
2
Initial gene embedding for chemcpa

#158 sepidism opened 5 months ago
4
Preprocessing notebooks

#157 sepidism closed 5 months ago
0
K562 cell type not in L1000. what did you do during fine-tuning?

#156 bhomass closed 3 months ago
1
how to obtain delta r2 in table 4?

#155 bhomass closed 3 months ago
3
the uncertainty equation

#154 bhomass closed 5 months ago
1
Request: pre-trained models weight checkpoints

#153 Tigerrr07 opened 7 months ago
1
Is your R2 variance result published anywhere

#152 bhomass closed 5 months ago
1
File location of seml_sweep_icb.py

#151 Tigerrr07 closed 7 months ago
1
two types of validation data for fine tuning experiment

#150 bhomass opened 8 months ago
1
ood drug belinostat leaks to pretraining dataset

#149 bhomass closed 7 months ago
1
Split setting for your experimental reimplementation

#148 sheunbaek closed 8 months ago
1
chemCPA vs chemCPA pretrained

#147 bhomass closed 5 months ago
2
what exactly is your baseline?

#146 bhomass closed 8 months ago
9
Update README.md

#145 MxMstrmn closed 9 months ago
0
is de_genes keyed on condition only or cell_drug_dose_comb

#144 bhomass opened 9 months ago
1
which molecular embedding was ultimately chosen?

#143 bhomass closed 8 months ago
2
Did the extended gene dataset (2000 genes) perform better than the 977 gene dataset?

#142 bhomass closed 8 months ago
1
how was lincs_trapnell.smiles generated?

#141 bhomass closed 5 months ago
1
what is config_hash for?

#140 bhomass closed 9 months ago
2
entanglement score

#139 bhomass closed 8 months ago
1
Address reproducibility issues

#138 MxMstrmn closed 8 months ago
1
when do you ever want exp = ExperimentWrapper(init_all=False)?

#137 bhomass closed 10 months ago
1
bug in embedding.py

#136 bhomass closed 10 months ago
2
Unsqueeze tensors if batch size is 1

#135 MxMstrmn closed 10 months ago
0
Make cell_type a required covariate_key

#134 MxMstrmn closed 10 months ago
0
Clarification of data preprocessing/normalisation

#133 MxMstrmn closed 10 months ago
0
what did you intend to do with drug_name.split("+")]

#132 bhomass opened 10 months ago
8
Fix slicing for lincs_full.h5ad in `lincs.ipynb`

#131 MxMstrmn closed 10 months ago
1
`compute_prediction()` function does not work for a batch size of 1

#130 sumanabasu closed 10 months ago
0
cell_id or cell_type for dataset.data_params.covariate_keys

#129 bhomass closed 10 months ago
2
where is trapnell_final_V7.h5ad?

#128 bhomass closed 8 months ago
2
Fix manual training

#127 MxMstrmn closed 10 months ago
0
where is GSE92742_Broad_LINCS_pert_info.txt

#126 bhomass closed 10 months ago
1
LINCS data preprocessing: `treatment time` averaged? Normalization?

#125 jasperhyp closed 10 months ago
2
bug in lincs.ipynb

#124 bhomass closed 10 months ago
0
LINCS pretrained model weights and configs

#123 jasperhyp closed 8 months ago
9
mongodb credentials

#122 bhomass closed 10 months ago
1
Reproducibility issues

#121 regloeb closed 8 months ago
2
Clarification of data preprocessing/normalisation

#120 cbirchsy closed 10 months ago
0
change readme

#119 Doosheck closed 1 year ago
0
Readme update

#118 Doosheck closed 1 year ago
1
Can't find drugbank_all.csv

#117 sumanabasu closed 10 months ago
4
KeyError: 'assinex' on lincs.ipynb with lincs_full.h5ad

#116 sumanabasu closed 10 months ago
4