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theislab
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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
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Errors running default manual_seml_sweep.py
#165
ArturDev42
opened
4 months ago
2
Differential expression evaluated by rank_genes_groups using t-test vs. wilcoxon method
#164
ceesu
opened
7 months ago
0
How to download drugbank_all.csv?
#163
wangyucheng1234
opened
8 months ago
1
Pretraining and running model
#162
xianglin226
opened
8 months ago
2
Data loading
#161
B1RO
closed
8 months ago
1
Biroscak/esm2 embedding computation
#160
B1RO
closed
8 months ago
1
Clarifications about LINCS data / evaluation
#159
rvinas
opened
9 months ago
2
Initial gene embedding for chemcpa
#158
sepidism
opened
10 months ago
4
Preprocessing notebooks
#157
sepidism
closed
10 months ago
0
K562 cell type not in L1000. what did you do during fine-tuning?
#156
bhomass
closed
8 months ago
1
how to obtain delta r2 in table 4?
#155
bhomass
closed
8 months ago
3
the uncertainty equation
#154
bhomass
closed
9 months ago
1
Request: pre-trained models weight checkpoints
#153
Tigerrr07
opened
1 year ago
2
Is your R2 variance result published anywhere
#152
bhomass
closed
9 months ago
1
File location of seml_sweep_icb.py
#151
Tigerrr07
closed
1 year ago
1
two types of validation data for fine tuning experiment
#150
bhomass
opened
1 year ago
1
ood drug belinostat leaks to pretraining dataset
#149
bhomass
closed
1 year ago
1
Split setting for your experimental reimplementation
#148
sheunbaek
closed
1 year ago
1
chemCPA vs chemCPA pretrained
#147
bhomass
closed
9 months ago
2
what exactly is your baseline?
#146
bhomass
closed
1 year ago
9
Update README.md
#145
MxMstrmn
closed
1 year ago
0
is de_genes keyed on condition only or cell_drug_dose_comb
#144
bhomass
opened
1 year ago
1
which molecular embedding was ultimately chosen?
#143
bhomass
closed
1 year ago
2
Did the extended gene dataset (2000 genes) perform better than the 977 gene dataset?
#142
bhomass
closed
1 year ago
1
how was lincs_trapnell.smiles generated?
#141
bhomass
closed
9 months ago
1
what is config_hash for?
#140
bhomass
closed
1 year ago
2
entanglement score
#139
bhomass
closed
1 year ago
1
Address reproducibility issues
#138
MxMstrmn
closed
1 year ago
1
when do you ever want exp = ExperimentWrapper(init_all=False)?
#137
bhomass
closed
1 year ago
1
bug in embedding.py
#136
bhomass
closed
1 year ago
2
Unsqueeze tensors if batch size is 1
#135
MxMstrmn
closed
1 year ago
0
Make cell_type a required covariate_key
#134
MxMstrmn
closed
1 year ago
0
Clarification of data preprocessing/normalisation
#133
MxMstrmn
closed
1 year ago
0
what did you intend to do with drug_name.split("+")]
#132
bhomass
opened
1 year ago
8
Fix slicing for lincs_full.h5ad in `lincs.ipynb`
#131
MxMstrmn
closed
1 year ago
1
`compute_prediction()` function does not work for a batch size of 1
#130
sumanabasu
closed
1 year ago
0
cell_id or cell_type for dataset.data_params.covariate_keys
#129
bhomass
closed
1 year ago
2
where is trapnell_final_V7.h5ad?
#128
bhomass
closed
1 year ago
2
Fix manual training
#127
MxMstrmn
closed
1 year ago
0
where is GSE92742_Broad_LINCS_pert_info.txt
#126
bhomass
closed
1 year ago
1
LINCS data preprocessing: `treatment time` averaged? Normalization?
#125
jasperhyp
closed
1 year ago
2
bug in lincs.ipynb
#124
bhomass
closed
1 year ago
0
LINCS pretrained model weights and configs
#123
jasperhyp
closed
1 year ago
9
mongodb credentials
#122
bhomass
closed
1 year ago
1
Reproducibility issues
#121
regloeb
closed
1 year ago
2
Clarification of data preprocessing/normalisation
#120
cbirchsy
closed
1 year 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
1 year ago
4
KeyError: 'assinex' on lincs.ipynb with lincs_full.h5ad
#116
sumanabasu
closed
1 year ago
4
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