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config.py
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import os
import model_cnn
import model_mpnn
# ----- Global -----
N_ANNOTATIONS = 8943
MODEL_TYPE = model_cnn
MAX_GLOBAL_SEQ_LEN = 450
ADDED_TOKENS_PER_SEQ = 2
ALL_AAS = 'ACDEFGHIKLMNPQRSTUVWXY'
ADDITIONAL_TOKENS = ['<OTHER>', '<START>', '<END>', '<PAD>']
# ----- Pretraining -----
PRETRAINING_N = 10
PRETRAINING_SAVE_EVERY = 10
PRETRAINING_FIXED_SEED = True
PRETRAINING_RESUME_EPOCH = None
PRETRAINING_EPISODE_SETTINGS = [ (450, 32) ]
# ----- Fine-tuning -----
FINETUNING_MAX_EPOCHS = 80
FINETUNING_BATCH_SIZE = 8
FINETUNING_FAST_RUN = False
FINETUNING_DEBUG_MODE = False
FINETUNING_FAST_SAMPLE_RATIO = 0.03
FINETUNING_EARLY_STOPPING_PATIENCE = 4
FINETUNING_USE_PRETRAINED_WEIGHTS = True
FINETUNING_MAX_ALLOWED_INPUT_SEQ = MAX_GLOBAL_SEQ_LEN - 2
FINETUNING_BENCHMARKS = [
'signalP_binary.dataset',
# 'scop.dataset',
# 'remote_homology',
# 'secondary_structure',
# 'stability'
# 'phosphoserine.dataset',
# 'disorder_secondary_structure',
# 'PhosphositePTM.dataset',
# 'fluorescence',
]
if FINETUNING_FAST_RUN:
FINETUNING_MAX_EPOCHS = 1
FINETUNING_EARLY_STOPPING_PATIENCE = 2
FINETUNING_MAX_ALLOWED_INPUT_SEQ = 132
FINETUNING_BATCH_SIZE = FINETUNING_BATCH_SIZE // 2
# ----- Setup specific (path's, weights, etc..) -----
if os.path.exists('../data'):
# ----- Nadav's setup -----
BENCHMARKS_DIR = '../data'
H5_FILE_PATH = '/cs/phd/nadavb/cafa_project/data/dataset.h5'
PRETRAINING_BASE_WEIGHTS_DIR = '/cs/phd/nadavb/cafa_project/data/model_weights'
FINETUNING_PRETRAINED_MODEL_WEIGHTS_FILE_PATH = '' # TODO Fill me up
# ----- Nadav's setup -----
elif os.path.exists('/t/Dev/Yam'):
# ----- Yam's setup -----
BENCHMARKS_DIR = '/home/user/Desktop/slow_storage/protobert_new/data'
H5_FILE_PATH = '/home/user/Desktop/slow_storage/protobert_new/dataset.h5'
PRETRAINING_BASE_WEIGHTS_DIR = '/home/user/Desktop/slow_storage/protobert_new'
FINETUNING_PRETRAINED_MODEL_WEIGHTS_FILE_PATH = '/home/user/Desktop/slow_storage/protobert_new/models/epoch_28530_sample_91400000.pkl'
# ----- Yam's setup -----
else:
# ----- Dan's setup -----
BENCHMARKS_DIR = '' # TODO Fill me up
H5_FILE_PATH = '' # TODO Fill me up
PRETRAINING_BASE_WEIGHTS_DIR = '' # TODO Fill me up
FINETUNING_PRETRAINED_MODEL_WEIGHTS_FILE_PATH = '../models/fresh-paper/epoch_9840_sample_69400000.pkl'
# ----- Dan's setup -----