...

Makefile

@@ -7,7 +7,7 @@ PYTHON_VERSION = 3.8
 PYTHON_INTERPRETER = python
 
 # --- CLI flag 变量 ---
-MPNN_FLAG = $(if $(USE_MPNN),--use-mpnn,)
+MPNN_FLAG = $(if $(NO_MPNN),,--use-mpnn)
 DEVICE_FLAG = $(if $(DEVICE),--device $(DEVICE),)
 SEED_FLAG = $(if $(SEED),--seed $(SEED),)
 N_TRIALS_FLAG = $(if $(N_TRIALS),--n-trials $(N_TRIALS),)

data/processed/benchmark/feature_columns.txt

@@ -0,0 +1,55 @@
+smiles
+Cationic_Lipid_to_mRNA_weight_ratio
+Cationic_Lipid_Mol_Ratio
+Phospholipid_Mol_Ratio
+Cholesterol_Mol_Ratio
+PEG_Lipid_Mol_Ratio
+Purity_Pure
+Purity_Crude
+Mix_type_Microfluidic
+Mix_type_Pipetting
+Cargo_type_mRNA
+Cargo_type_pDNA
+Cargo_type_siRNA
+Target_or_delivered_gene_FFL
+Target_or_delivered_gene_Peptide_barcode
+Target_or_delivered_gene_hEPO
+Target_or_delivered_gene_FVII
+Target_or_delivered_gene_GFP
+Helper_lipid_ID_DOPE
+Helper_lipid_ID_DOTAP
+Helper_lipid_ID_DSPC
+Helper_lipid_ID_MDOA
+Model_type_A549
+Model_type_BDMC
+Model_type_BMDM
+Model_type_HBEC_ALI
+Model_type_HEK293T
+Model_type_HeLa
+Model_type_IGROV1
+Model_type_Mouse
+Model_type_RAW264p7
+Delivery_target_body
+Delivery_target_dendritic_cell
+Delivery_target_generic_cell
+Delivery_target_liver
+Delivery_target_lung
+Delivery_target_lung_epithelium
+Delivery_target_macrophage
+Delivery_target_muscle
+Delivery_target_spleen
+Route_of_administration_in_vitro
+Route_of_administration_intramuscular
+Route_of_administration_intratracheal
+Route_of_administration_intravenous
+Batch_or_individual_or_barcoded_Barcoded
+Batch_or_individual_or_barcoded_Individual
+Value_name_log_luminescence
+Value_name_luminescence
+Value_name_FFL_silencing
+Value_name_Peptide_abundance
+Value_name_hEPO
+Value_name_FVII_silencing
+Value_name_GFP_delivery
+Value_name_Discretized_luminescence
+quantified_delivery

models/benchmark/config.json

@@ -0,0 +1,15 @@
+{
+  "d_model": 256,
+  "num_heads": 8,
+  "n_attn_layers": 4,
+  "fusion_strategy": "attention",
+  "head_hidden_dim": 128,
+  "dropout": 0.1,
+  "use_mpnn": false,
+  "mpnn_ensemble_paths": null,
+  "lr": 0.0001,
+  "weight_decay": 1e-05,
+  "batch_size": 64,
+  "epochs": 50,
+  "patience": 10
+}