Upload 4aa_config.yaml
Browse files- 4aa_config.yaml +88 -0
4aa_config.yaml
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dataset: 4AA-big2
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model_config:
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model_type: custom_attention_transformer_nvp
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transformer_cvae_config: null
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transformer_nvp_config: null
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custom_transformer_nvp_config:
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atom_embedding_dim: 128
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latent_mlp_hidden_dims:
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- 2048
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num_coupling_layers: 16
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num_transformer_layers: 16
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encoder_layer_config:
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d_model: 128
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dim_feedforward: 2048
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dropout: 0.0
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num_heads: 6
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attention_type: kernel
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lengthscales:
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- 0.1
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- 0.2
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- 0.5
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- 0.7
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- 1.0
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- 1.2
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max_radius: null
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normalise_kernel_values: true
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cheb_order: null
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force_asymptotic_zero: null
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position_layer_index_mod_2: 0
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conditional_flow_density:
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scale_requires_grad: true
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ignore_conditional_velocity: true
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use_displacement_as_target: true
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equivariant_nvp_config: null
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gaussian_density_transformer_config: null
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graphormer_nvp_config: null
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step_width: 100000
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batch_size: 64
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num_epochs: 100000000
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patience: 100
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data_augmentation: true
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measure_equivariance_discrepancy: false
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use_aml_logging: false
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loss:
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nll: null
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nll_and_energy: null
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nll_and_acceptance:
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openmm_provider:
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pdb_dirs: /mnt/simulated-data/trajectory-data/4AA
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device: cpu
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cache_size: 8
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random_velocs: true
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beta: 0.0
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clamp: false
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num_samples: 1
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weights:
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- 0.9
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- 0.1
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pre_softmax_weights: null
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loss_schedule: null
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run_prefix: ''
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optimizer: Lamb
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learning_rate: 1.0e-05
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warmup_steps: 1000
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weight_decay: 0.0
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clip_grad_norm: 100.0
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seed: 0
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randomise_seed: true
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data_dir: /mnt/lmdb-simulated-data/trajectory-data/4AA-big2/step_width_100000
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dataset_cache_dir: .data
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dataset_use_lmdb: true
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pdb_dir: /mnt/simulated-data/trajectory-data/4AA
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output_folder: /mnt/output/projects/timewarp/amlt-results/7327065479.65140-4ac81810-81dc-4bba-bb5b-03a44edc313b
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enable_profiler: false
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saved_model_path: /mnt/default/projects/timewarp/amlt-results/7328526925.13393-e5d91ef8-97b8-4566-a61d-447608055d22
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valid_batch_size: 512
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min_check_point_iters: 1000
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random_velocities: true
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warm_start: false
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num_pdbs_per_local_batch: 4
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equal_data_spacing: false
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run_valid_first: false
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lr_scheduler:
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type: plateau
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factor: 0.5
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iteration_patience: 10000
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logging_period: 100
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alpha: 0.1
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