Table 1 Hyperparameter tuning.
Cuda | TRUE | TRUE2 | TRUE3 |
|---|---|---|---|
Seed | 43 | 43 | 43 |
num_workers | 4 | 4 | 4 |
num_class | 2 | 2 | 2 |
Kmer | 3 | 3 | 3 |
heatmap_seq | |||
save_figure_type | png | png | png |
Mode | train-test | train-test | train-test |
Type | prot | prot | prot |
Model | TRANSFORMERS | GAT | RNN-CNN |
datatype | userprovide | userprovide | userprovide |
interval_log | 10 | 10 | 10 |
interval_valid | 1 | 1 | 1 |
interval_test | 1 | 1 | 1 |
Epoch | 50 | 50 | 50 |
Optimizer | Adam | Adam | Adam |
loss_func | C.E. | C.E. | C.E. |
batch_size | 4 | 8 | 32 |
L.R. | 1.00E-05 | 0.0001 | 0.0001 |
Reg | 0.0025 | 0.0025 | 0.0025 |
Gamma | 2 | 2 | 2 |
Alpha | 0.25 | 0.25 | 0.25 |
max_len | 35 | 207 | 52 |
dim_embedding | 32 | 32 | 32 |
minimode | modelCompare | modelCompare | modelCompare |
if_use_FL | 0 | 0 | 0 |
if_data_aug | 0 | 0 | 0 |
if_data_enh | 0 | 0 | 0 |
CDHit | [‘1’] | [‘1’] | [‘1’] |
