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config.ini

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+output_dir = /home/ljw/sdc1/CRISPR_results
+seed = 63036
+# device = cpu # cpu, cuda, if not specified, use cuda if available
+log = WARNING
+
+[dataset]
+owner = ljw20180420
+data_name = SX_spcas9 # SX_spcas9, SX_spymac, SX_ispymac
+test_ratio = 0.05
+validation_ratio = 0.05
+
+[data loader]
+batch_size = 100
+
+[optimizer]
+optimizer = adamw_torch # adamw_hf, adamw_torch, adamw_torch_fused, adamw_apex_fused, adamw_anyprecision, adafactor
+learning_rate = 0.001
+
+[scheduler]
+scheduler = linear # linear, cosine, cosine_with_restarts, polynomial, constant, constant_with_warmup, inverse_sqrt, reduce_lr_on_plateau, cosine_with_min_lr, warmup_stable_decay
+num_epochs = 30.0
+warmup_ratio = 0.05
+
+[CRISPR transformer]
+hidden_size = 256 # model embedding dimension
+num_hidden_layers = 3 # number of EncoderLayer
+num_attention_heads = 4 # number of attention heads
+intermediate_size = 1024 # FeedForward intermediate dimension size
+hidden_dropout_prob = 0.1 # The dropout probability for all fully connected layers in the embeddings, encoder, and pooler
+attention_probs_dropout_prob = 0.1 # The dropout ratio for the attention probabilities
+
+[CRISPR diffuser]
+max_micro_homology = 7
+MCMC_corrector_factor = [0., 0., 1.]
+unet_channels = [32, 64, 96, 64, 32]
+noise_scheduler = exp # linear, cosine, exp, uniform
+noise_timesteps = 20
+cosine_factor = 0.008
+exp_scale = 5.0
+exp_base = 5.0
+uniform_scale = 1.0
+display_scale_factor = 0.1
+
+[inDelphi]
+DELLEN_LIMIT = 60
+
+[Lindel]
+Lindel_dlen = 30
+Lindel_mh_len = 4
+Lindel_reg_const = 0.01
+Lindel_reg_mode = l2
+
+[FOREcasT]
+FOREcasT_MAX_DEL_SIZE = 30
+FOREcasT_reg_const = 0.01
+FOREcasT_i1_reg_const =0.01
+
+[inference]
+ref1len = 127
+ref2len = 127