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fix_seed: 0
checkpoints_every: 64
tensorboard_log: True
tqdm_progress_bar: False
result_path: ./results/stability/
resume:
resume: False
resume_path: /path/to/checkpoint.pth
restart_optimizer: True
handle_shape_missmatch: True
prot2token_model:
compile_model: True
positional_encoding_type: learned # absolute, learned
protein_encoder:
model_name: facebook/esm2_t33_650M_UR50D # facebook/esm2_t33_650M_UR50D, facebook/esm2_t30_150M_UR50D, facebook/esm2_t12_35M_UR50D, facebook/esm2_t6_8M_UR50D, Rostlab/prot_t5_base_mt_uniref50
max_len: 1024
drop_positional_encoding: True
quantization_4_bit: False # use with tune_embedding enabled
tune_embedding: False
fine_tune:
enable: True
last_layers_trainable: 6
lora:
enable: False
r: 8
lora_alpha: 32
lora_dropout: 0.05
molecule_encoder:
enable: False
model_name: gayane/BARTSmiles
max_len: 128
drop_positional_encoding: True
tune_embedding: False
fine_tune:
enable: False
last_layers_trainable: 2
decoder:
dimension: 640
dim_feedforward: 1280
num_heads: 8
num_layers: 8
max_len: 32
activation_function: gelu
train_settings:
skip: False
data_path: /mnt/hdd8/mehdi/datasets/Joint_training/
num_epochs: 48
start_metric_epoch: 2
shuffle: True
loss: crossentropy # crossentropy or focal
sample_weight: True
task_weight: False
mixed_precision: bf16 # no, fp16, bf16, fp8
device: cuda
batch_size: 16
random_masking: 0.15 # 0 to 1.0
num_workers: 0
grad_accumulation: 32
max_task_samples: 250000
valid_settings:
data_path: /mnt/hdd8/mehdi/datasets/Joint_training/
do_every: 1
batch_size: 1
num_workers: 0
test_settings:
enable: True
data_path: /mnt/hdd8/mehdi/datasets/Joint_training/
batch_size: 1
num_workers: 0
monitoring_metrics:
fluorescence: spearman
stability: spearman
protein_ligand_affinity: rmse
human_ppi: f1
structure_similarity: spearman
protein_protein_interface: auc
enzyme_reaction: f1
fold: f1
localization_deeploc: macro_f1
secondary_structure: accuracy
optimizer:
name: adam
lr: 5e-5
weight_decouple: True
weight_decay: 1e-2
eps: 1e-16
beta_1: 0.9
beta_2: 0.999
use_8bit_adam: False
grad_clip_norm: 1
decay:
warmup: 256
min_lr: 1e-6
gamma: 0.2
num_restarts: 1
tasks:
phosphorylation: False
localization: False
localization_deeploc: False
fold: False
enzyme_reaction: False
human_ppi: False
structure_similarity: False
protein_protein_interface: False # decoder max length: 210
protein_ligand_affinity: False
fluorescence: False
stability: True
amino_to_fold_seek: False # decoder max length: max input length + 1
secondary_structure: False # decoder max length: max input length + 1
gene_ontology: False # decoder max length: 625
enzyme_commission: False # decoder max length: 47
auxiliary: False
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