RNA_model / MASTER_config.json
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{
"data": {
"seed": 42,
"profile": "t4x2",
"train_max_len": 256,
"eval_max_len": 850,
"min_len": 24,
"train_targets": 1000000000,
"calibration_fraction": 0.15,
"cluster_jaccard": 0.62,
"cluster_len_ratio": 0.72,
"msa_max_sequences": 96,
"template_bank_size": 420,
"kmer": 3,
"d_node": 80,
"d_pair": 48,
"n_node_layers": 3,
"n_pair_blocks": 4,
"dropout": 0.1,
"batch_size": 2,
"val_batch_size": 1,
"ablation_epochs": 4,
"geometry_epochs": 10,
"geometry_lr": 0.0002,
"weight_decay": 0.01,
"grad_clip": 1.0,
"patience": 3,
"num_workers": 2,
"use_amp": true,
"epoch_val_structures": 32,
"contact_cutoff": 12.0,
"bp_distance_cutoff": 15.0,
"stacking_cutoff": 8.0,
"w_dist": 1.0,
"w_contact": 0.15,
"w_bp": 0.2,
"w_orient": 0.1,
"w_stack": 0.08,
"w_router_entropy": 0.002,
"local_pair_boost": 1.25,
"p_drop_msa": 0.15,
"p_drop_template": 0.25,
"p_drop_bp": 0.15,
"p_sequence_only": 0.08,
"flow_d_hidden": 80,
"flow_layers": 4,
"flow_epochs": 6,
"flow_batch_size": 4,
"flow_lr": 0.0001,
"flow_patience": 2,
"flow_distance_weight": 0.1,
"flow_template_drop": 0.5,
"flow_noise_scale": 16.0,
"flow_steps": 14,
"calib_candidates_aware": 5,
"calib_candidates_denovo": 5,
"final_candidates_aware": 8,
"final_candidates_denovo": 8,
"candidate_micro_batch": 4,
"refine_steps": 8,
"refine_lr": 0.03,
"selector_epochs": 120,
"selector_lr": 0.002,
"selector_mc_dropout": 8,
"uncertainty_lambda": 0.1,
"diversity_lambda": 0.15,
"n_top": 5,
"hard_infer_len": 850,
"out_dir": "/kaggle/working/EVIRNA_NOVA_CONTINUE_V12"
},
"nova": {
"profile": "t4",
"seed": 42,
"d_node": 160,
"d_pair": 96,
"d_msa": 64,
"n_node_heads": 8,
"n_pair_blocks": 8,
"pair_transition_mult": 4,
"triangle_rank": 24,
"dropout": 0.1,
"use_axial_attention": true,
"axial_heads": 4,
"axial_every": 3,
"triangle_chunk": 32,
"recycle_iters": 2,
"gradient_checkpointing": true,
"n_sources": 5,
"router_hidden": 192,
"router_temperature": 0.85,
"evidential_router": true,
"router_dropout": 0.1,
"relpos_buckets": 64,
"relpos_max": 1024,
"n_dist_bins": 64,
"dist_min": 2.0,
"dist_max": 42.0,
"contact_cutoff": 12.0,
"stack_cutoff": 8.0,
"flow_node_dim": 160,
"flow_pair_dim": 64,
"flow_blocks": 6,
"flow_rbf_bins": 32,
"flow_time_dim": 64,
"flow_noise_scale": 18.0,
"flow_train_template_prob": 0.5,
"flow_template_noise": 3.0,
"flow_steps_train": 1,
"flow_steps_infer": 48,
"flow_heun": true,
"dynamic_flow_trust": true,
"flow_coord_clip": 5.0,
"n_conformers": 5,
"p_drop_foundation": 0.08,
"p_drop_msa": 0.15,
"p_drop_template": 0.25,
"p_drop_ss": 0.12,
"w_distogram": 0.4,
"w_distance": 0.3,
"w_contact": 0.12,
"w_bp": 0.2,
"w_stack": 0.08,
"w_orientation": 0.06,
"w_pair_conf": 0.05,
"w_flow": 1.0,
"w_flow_distance": 0.15,
"w_router_entropy": 0.002,
"w_router_smooth": 0.002,
"w_router_balance": 0.001,
"w_uncertainty_calibration": 0.03,
"w_teacher_distill": 0.1,
"lr": 0.00015,
"weight_decay": 0.05,
"warmup_steps": 2000,
"grad_clip": 1.0
},
"args": {
"profile": "t4",
"data_profile": "t4x2",
"epochs": 0,
"batch_size": 2,
"grad_accum": 8,
"val_batch_size": 1,
"val_batches": 24,
"train_targets": 0,
"train_max_len": 256,
"eval_max_len": 850,
"crop_len": 256,
"crop_stride": 192,
"max_windows_per_target": 2,
"rnet_extract_len": 192,
"conformers": 5,
"flow_steps": 48,
"diversity_lambda": 0.1,
"seed": 42,
"workers": 2,
"rnet_cache": null,
"rnet_checkpoint": null,
"rnet_single_dim": 128,
"rnet_pair_dim": 16,
"no_rnet_auto_download": false,
"allow_internal_rna_proxy": false,
"bp_cache": null,
"resume": true,
"resume_from": "/kaggle/input/datasets/leminhhung0101/arn3d-agent/EVIRNA_NOVA_CONTINUE",
"resume_history": "/kaggle/input/datasets/leminhhung0101/arn3d-agent/EVIRNA_NOVA_CONTINUE/NOVA_history.csv",
"skip_test": false,
"single_gpu": false,
"disable_gradient_checkpointing": false,
"self_test": false,
"eval_only": false,
"out_dir": "/kaggle/working/EVIRNA_NOVA_CONTINUE_V12"
}
}