# ${TRAIN_FILE}${GPU_PER_TRIAL}${NUM_SAMPLES}${N_FOLDS}${DATA_TYPES}${NAME_TAG}${SUBSET_TYPE}${STRATIFY}${BOTTLENECK}${FULL}${ENCODER_TRAIN}
require(utils)
require(data.table)
all_combos <- c(
# "gnndrug mut exp",
# "gnndrug cnv exp",
# "gnndrug exp prot",
# "gnndrug exp rppa",
# "gnndrug exp hist",
# "gnndrug exp metab",
# "gnndrug exp mirna",
# "gnndrug prot rppa",
# "gnndrug cnv prot",
"gnndrug mut cnv",
# "gnndrug mirna metab",
# "gnndrug metab hist",
# "gnndrug metab rppa",
# "drug cnv exp metab"
# "gnndrug cnv exp prot",
# "gnndrug cnv exp prot mirna metab hist rppa",
# "gnndrug exp rppa hist prot",
# "gnndrug exp prot hist rppa",
# "gnndrug exp prot rppa",
# "gnndrug exp rppa prot",
# "gnndrug mirna metab hist rppa",
# "gnndrug mut cnv exp prot"
# "gnndrug mut cnv exp prot mirna metab hist rppa"
# "gnndrug mut cnv exp",
# "gnndrug cnv exp prot metab"
# "drug cnv exp prot metab"
# "drug mut cnv exp",
# "drug mut cnv exp prot",
# "drug cnv exp prot",
# "drug exp rppa prot",
# "drug exp rppa hist prot",
# "drug mirna metab hist rppa",
# "drug mut cnv exp prot mirna metab hist rppa",
# "drug cnv exp prot mirna metab hist rppa"
# "gnndrug mut prot",
# "gnndrug mut mirna",
# "gnndrug mut metab",
# "gnndrug mut hist",
# "gnndrug mut rppa",
# "gnndrug cnv mirna",
# "gnndrug cnv metab",
# "gnndrug cnv hist",
# "gnndrug cnv rppa",
# "gnndrug prot mirna",
# "gnndrug prot metab",
# "gnndrug prot hist",
"gnndrug mirna hist",
"gnndrug mirna rppa",
"gnndrug hist rppa",
# "drug mut prot",
# "drug mut mirna",
# "drug mut metab",
# "drug mut hist",
# "drug mut rppa",
# "drug cnv mirna",
"drug cnv metab",
# "drug cnv hist",
# "drug cnv rppa",
# "drug prot mirna",
# "drug prot metab",
# "drug prot hist",
# "drug mirna hist",
# "drug mirna rppa",
# "drug hist rppa",
#
# "drug mut exp",
# "drug cnv exp",
# "drug exp prot",
# "drug exp rppa",
# "drug exp hist",
# "drug exp metab",
# "drug exp mirna",
# "drug prot rppa",
# "drug cnv prot",
# "drug mut cnv",
# "drug mirna metab",
# "drug metab hist",
# "drug metab rppa"
# "gnndrug exp",
"gnndrug mut",
"gnndrug cnv",
"gnndrug prot",
"gnndrug mirna"
# "gnndrug metab",
# "gnndrug hist",
# "gnndrug rppa"
#
# "drug exp",
# "drug mut",
# "drug cnv",
# "drug prot",
# "drug mirna",
# "drug metab"
# "drug hist",
# "drug rppa"
# "gnndrug mut exp hist",
# "gnndrug cnv exp hist",
# "gnndrug exp prot hist",
# "gnndrug exp mirna hist",
# "gnndrug exp metab hist",
# "gnndrug exp hist rppa"
# "gnndrug cnv exp metab"
)
# ${TRAIN_FILE} ${N_FOLDS} ${DATA_TYPES} ${NAME_TAG} ${SUBSET_TYPE} ${STRATIFY} ${FULL} ${ENCODER_TRAIN}
all_grids <- vector(mode = "list")
for (combo in all_combos) {
ENCODER_TRAIN <- "1"
NUM_SAMPLES <- "40"
if (grepl("cnv", combo)) {
GPU_PER_TRIAL <- "1"
} else if (combo == "gnndrug prot" | combo == "drug prot") {
GPU_PER_TRIAL <- "0.5"
# NUM_SAMPLES <- "32"
} else if (combo == "gnndrug exp" |
combo == "gnndrug exp prot" |
combo == "gnndrug mut" |
combo == "drug mut" |
combo == "drug exp" | combo == "drug exp prot") {
GPU_PER_TRIAL <- "0.5"
# NUM_SAMPLES <- "8"
} else if (combo == "gnndrug mirna" |
combo == "gnndrug metab" |
combo == "gnndrug hist" | combo == "gnndrug rppa" |
combo == "drug mirna" |
combo == "drug metab" |
combo == "drug hist" | combo == "drug rppa") {
GPU_PER_TRIAL <- "0.2"
# NUM_SAMPLES <- "40"
} else {
GPU_PER_TRIAL <- "1"
# NUM_SAMPLES <- "8"
}
# LOSS_TYPE = "rmse"
# loss_type_name = "RMSELoss"
# LOSS_TYPE = "weighted_rmse"
# loss_type_name = "WeightedRMSELoss"
for (LOSS_TYPE in c("rmse", "weighted_rmse")) {
if (LOSS_TYPE == "rmse") {
loss_type_name = "RMSELoss"
} else {
loss_type_name = "WeightedRMSELoss"
}
for (ONE_HOT_DRUGS in c("0", "1")) {
if (ONE_HOT_DRUGS == "1") {
one_hot_drugs_name = "OneHotDrugs"
} else {
if (grepl("gnndrug", combo) == TRUE) {
one_hot_drugs_name = "GNNDrugs"
} else {
one_hot_drugs_name = "MorganDrugs"
}
}
for (MERGE_METHOD in c("sum", "concat", "lmf")) {
if (MERGE_METHOD == "sum") {
merge_method_name = "MergeBySum"
} else if (MERGE_METHOD == "concat") {
merge_method_name = "MergeByConcat"
} else if (MERGE_METHOD == "lmf") {
merge_method_name = "MergeByLMF"
}
for (BOTTLENECK in c("0", "1")) {
# for (TRAIN_FILE in c("CTRP_AAC_MORGAN_1024.hdf")) {
# for (TRAIN_FILE in c("CTRP_AAC_SMILES.txt", "GDSC1_AAC_SMILES.txt", "GDSC2_AAC_SMILES.txt")) {
# for (TRAIN_FILE in c("CTRP_AAC_MORGAN_1024.hdf", "GDSC1_AAC_MORGAN_1024.hdf", "GDSC2_AAC_MORGAN_1024.hdf")) {
# for (TRAIN_FILE in c("CTRP_AAC_SMILES.txt")) {
if (grepl("gnn", combo)) {
TRAIN_FILE = "CTRP_AAC_SMILES.txt"
} else {
TRAIN_FILE = "CTRP_AAC_MORGAN_1024.hdf"
}
train_set_name <- "CTRP"
for (SUBSET_TYPE in c("cell_line", "drug", "lineage", "both")) {
if (SUBSET_TYPE == "both") {
N_FOLDS <- "5"
} else {
N_FOLDS <- "5"
}
for (FULL in c("0", "1")) {
if (FULL == "1") {
cur_pretrain <- "0"
# train_set_name <- gsub("\\_.+", "", TRAIN_FILE)
full <- "FullModel"
encoder <- "EncoderTrain"
split <- toupper(SUBSET_TYPE)
data_types <- gsub(" ", "_", combo)
if (BOTTLENECK == "0") {
bottleneck <- "NoBottleNeck"
} else {
bottleneck <- "WithBottleNeck"
}
if (cur_pretrain == "0") {
pretrain <- "NoTCGAPretrain"
} else {
pretrain <- "WithTCGAPretrain"
}
NAME_TAG <-
paste(
"HyperOpt_DRP",
train_set_name,
full,
encoder,
"Split",
split,
bottleneck,
pretrain,
merge_method_name,
loss_type_name,
one_hot_drugs_name,
data_types,
sep = "_"
)
cur_grid <- data.table(
TRAIN_FILE = TRAIN_FILE,
GPU_PER_TRIAL = GPU_PER_TRIAL,
NUM_SAMPLES = NUM_SAMPLES,
N_FOLDS = N_FOLDS,
DATA_TYPES = combo,
NAME_TAG = NAME_TAG,
SUBSET_TYPE = SUBSET_TYPE,
STRATIFY = "1",
BOTTLENECK = BOTTLENECK,
FULL = FULL,
ENCODER_TRAIN = ENCODER_TRAIN,
PRETRAIN = cur_pretrain,
MERGE_METHOD = MERGE_METHOD,
LOSS_TYPE = LOSS_TYPE,
ONE_HOT_DRUGS = ONE_HOT_DRUGS
)
all_grids <- append(all_grids, list(cur_grid))
} else {
if (grepl("cnv", combo) | grepl("exp", combo)) {
for (PRETRAIN in c("0", "1")) {
cur_encoder_train <- "1"
encoder <- "EncoderTrain"
# train_set_name <- gsub("\\_.+", "", TRAIN_FILE)
full <- "ResponseOnly"
split <- toupper(SUBSET_TYPE)
data_types <- gsub(" ", "_", combo)
if (BOTTLENECK == "0") {
bottleneck <- "NoBottleNeck"
} else {
bottleneck <- "WithBottleNeck"
}
if (PRETRAIN == "0") {
pretrain <- "NoTCGAPretrain"
} else {
pretrain <- "WithTCGAPretrain"
}
NAME_TAG <-
paste(
"HyperOpt_DRP",
train_set_name,
full,
encoder,
"Split",
split,
bottleneck,
pretrain,
merge_method_name,
loss_type_name,
one_hot_drugs_name,
data_types,
sep = "_"
)
cur_grid <- data.table(
TRAIN_FILE = TRAIN_FILE,
GPU_PER_TRIAL = GPU_PER_TRIAL,
NUM_SAMPLES = NUM_SAMPLES,
N_FOLDS = N_FOLDS,
DATA_TYPES = combo,
NAME_TAG = NAME_TAG,
SUBSET_TYPE = SUBSET_TYPE,
STRATIFY = "1",
BOTTLENECK = BOTTLENECK,
FULL = FULL,
ENCODER_TRAIN = cur_encoder_train,
PRETRAIN = PRETRAIN,
MERGE_METHOD = MERGE_METHOD,
LOSS_TYPE = LOSS_TYPE,
ONE_HOT_DRUGS = ONE_HOT_DRUGS
)
all_grids <- append(all_grids, list(cur_grid))
}
} else {
cur_encoder_train <- "1"
encoder <- "EncoderTrain"
# train_set_name <- gsub("\\_.+", "", TRAIN_FILE)
full <- "ResponseOnly"
split <- toupper(SUBSET_TYPE)
data_types <- gsub(" ", "_", combo)
if (BOTTLENECK == "0") {
bottleneck <- "NoBottleNeck"
} else {
bottleneck <- "WithBottleNeck"
}
cur_pretrain <- "0"
pretrain <- "NoTCGAPretrain"
NAME_TAG <-
paste(
"HyperOpt_DRP",
train_set_name,
full,
encoder,
"Split",
split,
bottleneck,
pretrain,
merge_method_name,
loss_type_name,
one_hot_drugs_name,
data_types,
sep = "_"
)
cur_grid <- data.table(
TRAIN_FILE = TRAIN_FILE,
GPU_PER_TRIAL = GPU_PER_TRIAL,
NUM_SAMPLES = NUM_SAMPLES,
N_FOLDS = N_FOLDS,
DATA_TYPES = combo,
NAME_TAG = NAME_TAG,
SUBSET_TYPE = SUBSET_TYPE,
STRATIFY = "1",
BOTTLENECK = BOTTLENECK,
FULL = FULL,
ENCODER_TRAIN = cur_encoder_train,
PRETRAIN = cur_pretrain,
MERGE_METHOD = MERGE_METHOD,
LOSS_TYPE = LOSS_TYPE,
ONE_HOT_DRUGS = ONE_HOT_DRUGS
)
all_grids <- append(all_grids, list(cur_grid))
}
}
}
}
}
}
}
}
}
all_param_combos <- rbindlist(all_grids)
# ==== Bi-Modal split by DRUG (ALL) ====
combos <- all_param_combos[PRETRAIN == 0 & SUBSET_TYPE == "drug" & MERGE_METHOD == "concat" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
# combos <- all_param_combos[PRETRAIN == 0 & SUBSET_TYPE == "drug" & MERGE_METHOD == "lmf" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- all_param_combos[PRETRAIN == 0 & SUBSET_TYPE == "drug" & MERGE_METHOD == "concat" & LOSS_TYPE == "rmse" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
# fwrite(combos, "DRP/slurm/grids/drp_cv_split_by_DRUG_grid.csv", col.names = F)
# fwrite(combos, "DRP/slurm/grids/drp_cv_lmf_split_by_DRUG_grid.csv", col.names = F)
# fwrite(combos, "DRP/slurm/grids/drp_validate_lmf_split_by_DRUG_grid.csv", col.names = F)
fwrite(combos, "DRP/slurm/grids/drp_validate_split_by_DRUG_grid.csv", col.names = F)
# ==== Bi-Modal split by CELL_LINE (ALL) ====
combos <- all_param_combos[PRETRAIN == 0 & SUBSET_TYPE == "cell_line" & (MERGE_METHOD == "concat" | MERGE_METHOD == "lmf") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_cv_split_by_CELL_LINE_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & SUBSET_TYPE == "cell_line" & (MERGE_METHOD == "concat" | MERGE_METHOD == "lmf") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
# fwrite(combos, "DRP/slurm/grids/drp_validate_split_by_CELL_LINE_grid.csv", col.names = F)
# ==== (GDSC) Bi-modal with GNN + LMF ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/drp_opt_gdsc_grid.csv", col.names = F)
# ==== Bi-modal Baseline (Morgan + Concat + RMSE) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & LOSS_TYPE == "rmse" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_cell_line_drug_grid.csv", col.names = F)
# ==== Bi-modal Baseline + LDS (Morgan + Concat + WeightedRMSE) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_grid.csv", col.names = F)
# combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_with_lds_cell_line_drug_grid.csv", col.names = F)
# ==== Bi-modal Baseline + LMF (Morgan + LMF + RMSE) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0 & LOSS_TYPE == "rmse"]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_with_lmf_grid.csv", col.names = F)
# combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & SUBSET_TYPE != "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0 & LOSS_TYPE == "rmse"]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_with_lmf_cell_line_drug_grid.csv", col.names = F)
# ==== Bi-modal Baseline + LMF (Morgan + LMF + RMSE) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "sum") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0 & LOSS_TYPE == "rmse"]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_with_sum_grid.csv", col.names = F)
# combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "sum") & SUBSET_TYPE != "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0 & LOSS_TYPE == "rmse"]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_with_sum_cell_line_drug_grid.csv", col.names = F)
# ==== Bi-modal Baseline + GNN (GNN + concat + RMSE) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0 & LOSS_TYPE == "rmse"]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_with_gnn_grid.csv", col.names = F)
# combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & SUBSET_TYPE != "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0 & LOSS_TYPE == "rmse"]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_with_gnn_cell_line_drug_grid.csv", col.names = F)
# fwrite(combos, "DRP/slurm/grids/drp_opt_baseline_with_gnn_cell_line_drug_grid_extra.csv", col.names = F)
# ==== Bi-modal with GNN + LMF but no LDS ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/drp_opt_noLDS_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/drp_opt_noLDS_cell_line_drug_grid.csv", col.names = F)
# ==== Bi-modal GNN + Concatenation (non-LMF) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "weighted_rmse" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_concat_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_concat_cell_line_drug_grid.csv", col.names = F)
# combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & SUBSET_TYPE == "drug" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
# combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
# fwrite(combos, "DRP/slurm/drp_opt_concat_drug_grid.csv", col.names = F)
# ==== Bi-modal GNN + Sum (non-LMF) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "sum") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/drp_opt_sum_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "sum") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_sum_cell_line_drug_grid.csv", col.names = F)
# ==== Bi-modal GNN + LMF + LDS (trifecta) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_bi_lmf_lds_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
# combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_bi_lmf_lds_cell_line_drug_grid.csv", col.names = F)
# ==== Bi-modal GNN + LMF without LDS (trifecta - LDS) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "rmse" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_bi_trifecta_without_lds_grid.csv", col.names = F)
# combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
# ==== Bi-modal LDS + GNN without LMF (trifecta - LMF) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & LOSS_TYPE == "weighted_rmse" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_bi_trifecta_without_lds_grid.csv", col.names = F)
# combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
# ==== Bi-modal LMF + LDS without GNN ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" &
SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_morgan_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & (SUBSET_TYPE == "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_morgan_cell_line_drug_grid.csv", col.names = F)
# ==== Bi-modal Trifecta ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_bimodal_trifecta_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE == "drug" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_bimodal_trifecta_cell_line_drug_grid.csv", col.names = F)
# ==== Bi-Modal Bottleneck (Cell Line Splitting/Grouping) ====
baseline_combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" &
TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE == "cell_line" &
BOTTLENECK == 1 & FULL == 1 & ONE_HOT_DRUGS == 0]
baseline_combos <- baseline_combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(baseline_combos, "DRP/slurm/grids/drp_opt_bimodal_baseline_bottleneck_cell_line_grid.csv", col.names = F)
trifecta_combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" &
TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE == "cell_line" &
BOTTLENECK == 1 & FULL == 1 & ONE_HOT_DRUGS == 0]
trifecta_combos <- trifecta_combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(trifecta_combos, "DRP/slurm/grids/drp_opt_bimodal_trifecta_bottleneck_cell_line_grid.csv", col.names = F)
# ==== Tri-modal Trifecta (initial) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_trimodal_trifecta_other_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & DATA_TYPES %like% "gnn" & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE == "cell_line" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_trimodal_trifecta_other_cell_line_drug_grid.csv", col.names = F)
# ==== Tri-modal Trifecta (remainders) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_trimodal_trifecta_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & (SUBSET_TYPE == "cell_line" | SUBSET_TYPE == "cell_line") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_trimodal_trifecta_cell_line_drug_grid.csv", col.names = F)
# ==== Tri-modal Trifecta, split by lineage ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE == "lineage" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_trimodal_trifecta_lineage_grid.csv", col.names = F)
# ==== Tri-modal baseline (remainders) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_trimodal_baseline_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE != "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_trimodal_baseline_cell_line_drug_grid.csv", col.names = F)
# ==== Tri-modal baseline (remainders) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_trimodal_baseline_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE != "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_trimodal_baseline_cell_line_drug_grid.csv", col.names = F)
# ==== Tri-Modal Bottleneck (Cell Line Splitting/Grouping) ====
baseline_combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" &
TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE == "cell_line" &
BOTTLENECK == 1 & FULL == 1 & ONE_HOT_DRUGS == 0]
baseline_combos <- baseline_combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(baseline_combos, "DRP/slurm/grids/drp_opt_trimodal_baseline_bottleneck_cell_line_grid.csv", col.names = F)
trifecta_combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" &
TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE == "cell_line" &
BOTTLENECK == 1 & FULL == 1 & ONE_HOT_DRUGS == 0]
trifecta_combos <- trifecta_combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(trifecta_combos, "DRP/slurm/grids/drp_opt_trimodal_trifecta_bottleneck_cell_line_grid.csv", col.names = F)
# EXP_HIST
# MIRNA_RPPA
# ==== Multi-modal Trifecta with EXP_HIST ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_exp_hist_trifecta_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE != "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_exp_hist_trifecta_cell_line_drug_grid.csv", col.names = F)
# ==== Multi-modal Trifecta with CNV_EXP_METAB ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
combos$GPU_PER_TRIAL <- 0.5
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_cnv_exp_metab_trifecta_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE != "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
combos$GPU_PER_TRIAL <- 0.5
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_cnv_exp_metab_trifecta_cell_line_drug_grid.csv", col.names = F)
# ==== Multi-modal Trifecta with CNV_EXP_PROT_METAB ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
combos$GPU_PER_TRIAL <- 1
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_cnv_exp_metab_trifecta_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
combos$GPU_PER_TRIAL <- 1
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_cnv_exp_prot_metab_trifecta_cell_line_drug_grid.csv", col.names = F)
# ==== Multi-modal Baseline ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_baseline_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE != "cell_line" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_baseline_cell_line_drug_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_baseline_all_grid.csv", col.names = F)
# ==== Multi-modal Baseline + LMF ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_baseline_with_lmf_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE != "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_baseline_with_lmf_cell_line_drug_grid.csv", col.names = F)
# ==== Multi-modal Baseline + LDS ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_baseline_with_lds_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "rmse" & TRAIN_FILE == "CTRP_AAC_MORGAN_1024.hdf" & SUBSET_TYPE != "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_baseline_with_lmf_cell_line_drug_grid.csv", col.names = F)
# ==== Multi-modal GNN + LMF + LDS (trifecta) ====
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_trifecta_grid.csv", col.names = F)
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & TRAIN_FILE == "CTRP_AAC_SMILES.txt" & SUBSET_TYPE != "lineage" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_multimodal_trifecta_cell_line_drug_grid.csv", col.names = F)
table(all_param_combos$DATA_TYPES)
all_param_combos[PRETRAIN == 0]
all_param_combos[PRETRAIN == 1]
unique(all_param_combos[, .SD, .SDcols = !c("PRETRAIN")])
all_param_combos[PRETRAIN == 0 & FULL == 1]
all_param_combos[PRETRAIN == 0 & FULL == 1]
all_param_combos[FULL == 1]
table(all_param_combos[FULL == 1]$DATA_TYPES)
table(all_param_combos[FULL == 1 & PRETRAIN == 0]$DATA_TYPES)
all_param_combos[FULL == 1 & PRETRAIN == 0 & MERGE_METHOD == "concat" & SUBSET_TYPE == "drug"]
all_param_combos[FULL == 0 & PRETRAIN == 0 & MERGE_METHOD == "concat" & SUBSET_TYPE == "drug"]
# 2 data types including exp
combos <- all_param_combos[PRETRAIN == 0 & MERGE_METHOD == "sum" & SUBSET_TYPE == "drug" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
fwrite(combos, "DRP/slurm/drp_opt_grid.csv", col.names = F)
# unimodal + bimodal with exp + lmf + gnndrug
combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
combos <- combos[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/drp_opt_grid.csv", col.names = F)
# fwrite(combos, "DRP/slurm/drp_opt_grid_sub.csv", col.names = F)
combos_1 <- all_param_combos[PRETRAIN == 0 & MERGE_METHOD == "sum" & SUBSET_TYPE == "drug" & BOTTLENECK == 0 & FULL == 1]
combos_2 <- all_param_combos[PRETRAIN == 0 & MERGE_METHOD == "sum" & SUBSET_TYPE == "drug" & BOTTLENECK == 0 & FULL == 0 & DATA_TYPES == "drug cnv"]
combos_3 <- all_param_combos[PRETRAIN == 0 & MERGE_METHOD == "sum" & SUBSET_TYPE == "drug" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 1]
fwrite(unique(rbindlist(list(combos_1, combos_2, combos_3))), "DRP/slurm/drp_opt_grid.csv", col.names = F)
fwrite(all_param_combos[PRETRAIN == 0 & MERGE_METHOD == "sum" & SUBSET_TYPE == "drug" & BOTTLENECK == 0], "DRP/slurm/drp_opt_grid.csv", col.names = F)
fwrite(all_param_combos[PRETRAIN == 0 & MERGE_METHOD == "sum" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & ONE_HOT_DRUGS == 0], "DRP/slurm/drp_opt_grid.csv", col.names = F)
fwrite(all_param_combos[PRETRAIN == 0 & FULL == 0 & MERGE_METHOD == "concat" & SUBSET_TYPE == "drug" & ONE_HOT_DRUGS == 0], "DRP/slurm/drp_opt_grid.csv", col.names = F)
fwrite(all_param_combos[PRETRAIN == 0 & FULL == 1], "DRP/slurm/drp_opt_extra_grid.csv", col.names = F)
fwrite(all_param_combos[PRETRAIN == 0 & FULL == 1][1], "DRP/slurm/drp_opt_test_grid.csv", col.names = F)
fwrite(all_param_combos[PRETRAIN == 0 & FULL == 1], "DRP/slurm/drp_opt_drug_grid.csv", col.names = F)
colnames(all_param_combos)
# "TRAIN_FILE" "GPU_PER_TRIAL" "NUM_SAMPLES" "N_FOLDS" "DATA_TYPES" "NAME_TAG" "SUBSET_TYPE" "STRATIFY" "BOTTLENECK"
# "FULL" "ENCODER_TRAIN" "PRETRAIN" "MERGE_METHOD" "LOSS_TYPE" "ONE_HOT_DRUGS"
# ==== CV Grid ====
# require(data.table)
# cur_opt_grid <- fread("DRP/slurm/drp_opt_grid.csv")
# # ${TRAIN_FILE} ${N_FOLDS} ${DATA_TYPES} ${NAME_TAG} ${SUBSET_TYPE} ${STRATIFY} ${FULL} ${ENCODER_TRAIN}
# cur_cv_grid <- unique(cur_opt_grid[, c(1, 4, 5, 6, 7, 8, 10, 11, 13, 14, 15)])
# fwrite(cur_cv_grid, "DRP/slurm/drp_cv_grid.csv", col.names = F)
#
# cur_cv_grid[V6 %like% ".*ResponseOnly.*"]
# fwrite(cur_cv_grid[V6 %like% ".*ResponseOnly.*" & V5 != "drug cnv" & V15 == 0], "DRP/slurm/drp_cv_grid.csv", col.names = F)
# fwrite(cur_cv_grid[!(V6 %like% ".*ResponseOnly.*" & V5 == "drug cnv")], "DRP/slurm/drp_cv_grid.csv", col.names = F)
# fwrite(cur_cv_grid[!(V6 %like% ".*ResponseOnly.*" & V5 == "drug cnv") & !(V6 %like% "OneHotDrugs")], "DRP/slurm/drp_infer_grid.csv", col.names = F)
#
# cur_cv_grid <- fread("DRP/slurm/drp_cv_grid.csv")
# cur_cv_grid$V1 <- gsub(pattern = "CTRP", replacement = "GDSC2", cur_cv_grid$V1)
# cur_cv_grid$V4 <- gsub(pattern = "CTRP", replacement = "GDSC2", cur_cv_grid$V4)
#
#
#
# fwrite(cur_cv_grid, "DRP/slurm/drp_cv_grid.csv", col.names = F)
# Remaining CV Runs ====
cnv_metab_base <- all_param_combos[DATA_TYPES == "drug cnv metab" & PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "rmse" &
SUBSET_TYPE == "cell_line" & BOTTLENECK == 1 & FULL == 0 & ONE_HOT_DRUGS == 0]
cnv_sum_lds_gnn <- all_param_combos[DATA_TYPES == "gnndrug cnv" & PRETRAIN == 0 & (MERGE_METHOD == "sum") & LOSS_TYPE == "weighted_rmse" &
SUBSET_TYPE == "cell_line" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
cnv_lmf_base_gnn <- all_param_combos[DATA_TYPES == "gnndrug cnv" & PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "rmse" &
SUBSET_TYPE == "drug" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
hist_rppa_trifecta <- all_param_combos[DATA_TYPES == "gnndrug hist rppa" & PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" &
SUBSET_TYPE %in% c("cell_line", "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
mirna_hist_trifecta <- all_param_combos[DATA_TYPES == "gnndrug mirna hist" & PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" &
SUBSET_TYPE %in% c("cell_line") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
mirna_lmf_base_gnn <- all_param_combos[DATA_TYPES == "gnndrug mirna" & PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "rmse" &
SUBSET_TYPE == "drug" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
mirna_rppa_trifecta <- all_param_combos[DATA_TYPES == "gnndrug mirna rppa" & PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" &
SUBSET_TYPE %in% c("cell_line", "drug") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
mut_cnv_trifecta <- all_param_combos[DATA_TYPES == "gnndrug mut cnv" & PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" &
SUBSET_TYPE %in% c("both") & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
mut_base_lds_gnn <- all_param_combos[DATA_TYPES == "gnndrug mut" & PRETRAIN == 0 & (MERGE_METHOD == "concat") & LOSS_TYPE == "weighted_rmse" &
SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
prot_lmf_base_gnn <- all_param_combos[DATA_TYPES == "gnndrug prot" & PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "rmse" &
SUBSET_TYPE == "drug" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
stragglers <- rbindlist(
list(
cnv_metab_base,
cnv_sum_lds_gnn,
cnv_lmf_base_gnn,
hist_rppa_trifecta,
mirna_hist_trifecta,
mirna_lmf_base_gnn,
mirna_rppa_trifecta,
mut_cnv_trifecta,
mut_base_lds_gnn,
prot_lmf_base_gnn
)
)
# combos <- all_param_combos[PRETRAIN == 0 & (MERGE_METHOD == "lmf") & LOSS_TYPE == "weighted_rmse" & SUBSET_TYPE == "both" & BOTTLENECK == 0 & FULL == 0 & ONE_HOT_DRUGS == 0]
stragglers <- stragglers[, !c("ENCODER_TRAIN", "ONE_HOT_DRUGS")]
fwrite(combos, "DRP/slurm/grids/drp_opt_stragglers.csv", col.names = F)
Datasets
Models
