Initial release containing two independent datasets: one for gene dependency model training and prediction (based on DepMap Achilles data), and another for benchmarking drug sensitivity capabilities (based on GDSC2 data).

An important caveat: don’t use the drug training sets to train for the gene dependency test or the other way around! It will leak data into the holdout sets, invalidating your results.

Also, if you assemble your own train sets to test for these benchmark targets, make sure the drugs’ targets don’t overlap with any genes in the GEX test set and vice versa, genes in your training set shouldn’t overlap with drugs’ targets in the DEX test set.

Primary test All train and test sets Evaluation scripts Publication

Drug dataset:

Cell lines in TRAIN (& DEX): 555
Cell lines in CEX (& AEX): 139
Drugs in TRAIN (& CEX): 117
Drugs in DEX (& AEX): 18

Total set sizes:

	split 0 (primary)	split 1	split 2
TRAIN	46.038	42.896	42.654
CEX	14.334	13.460	13.427
DEX	9.479	13.579	13.821
AEX	2.424	3.396	3.489

CRISPR KO dataset:

Cell lines in TRAIN (& GEX): 803
Cell lines in CEX (& AEX): 201
Genes in TRAIN (& CEX): 1036
Genes in GEX (& AEX): 258
Genes in extended GEX: 6052

Total set sizes:

	split 0 (primary)	split 1	split 2
TRAIN	665.430	662.953	657.971
CEX	208.196	211.308	217.520
GEX	207.150	206.364	204.828
AEX	51.850	52.620	54.172
EXT_GEX	4.859.048	4.840.880	4.804.580
EXT_AEX	1.216.216	1.234.368	1.270.684