RFD4-Proteina / config.json
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Update root model bundle config to the 2026-10-19 release
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{
"model_type": "rfd4_proteina",
"format_version": 1,
"weights_sha256": "5b549dd61adb2f6c6b5cb95bda13f40f5e31556b4e6c755edc0ca6f011c68fb0",
"config": {
"nn": {
"name": "local_latents_transformer",
"output_parameterization": {
"bb_ca": "v",
"local_latents": "v"
},
"sequence_readout": {
"enabled": true,
"detach": true,
"num_classes": 147
},
"nlayers": 14,
"token_dim": 768,
"nheads": 12,
"parallel_mha_transition": false,
"token_type_emb_dim": 32,
"cath_emb_dim": 32,
"strict_feats": false,
"noise_align_chirality": true,
"noise_align_internal_coords": false,
"noise_align_chirality_translate": false,
"noise_align_internal_coords_translate": false,
"use_atom37_factory": true,
"feats_seq": [
"xt_bb_ca",
"xt_local_latents",
"token_type",
"sequence_probabilities",
"cond_a37coors_nm",
"cond_a37coors_internal_nm",
"rasa_binned",
"secondary_structure",
"hbond_modernized",
"pistack",
"pication",
"saltbridge",
"hydrophobic",
"metal_coord",
"na_ss_state",
"hotspot",
"atom_charge",
"atomic_element",
"coord_group_seq",
"chirality",
"chain_centroid_xyz"
],
"feats_cond_seq": [
"time_emb_bb_ca",
"time_emb_local_latents",
"cath_code",
"recycle_remaining"
],
"dim_cond": 256,
"idx_emb_dim": 256,
"t_emb_dim": 256,
"feats_pair_repr": [
"xt_bb_ca_pair_dists",
"bond_mask",
"bond_order",
"is_aromatic",
"index_group_pair",
"molecule_idx_pair",
"molecule_entity_pair",
"token_bond_path_length",
"canonical_polymer_ordering",
"na_ss_pair"
],
"feats_pair_cond": [
"time_emb_bb_ca",
"time_emb_local_latents"
],
"xt_pair_dist_dim": 30,
"xt_pair_dist_min": 0.1,
"xt_pair_dist_max": 3,
"seq_sep_dim": 64,
"pair_repr_dim": 384,
"update_pair_repr": true,
"update_pair_repr_every_n": 2,
"use_tri_mult": true,
"tri_mult_c": 256,
"tri_mult_bias": false,
"tri_mult_backend": "cuequivariance",
"recycle": {
"enabled": true,
"grad": "last",
"training_max_recycles": 9,
"condition_probability": 0.5
},
"checkpointing": "none",
"pair_write": "hadamard",
"use_qkln": true,
"attention_type": "torch",
"use_torch_compile": false,
"norm_type": "rmsnorm_torch_fused"
},
"product_flowmatcher": {
"bb_ca": {
"zero_com_noise": true,
"guidance_enabled": true,
"dim": 3,
"stochastic_centering_mode": "x_0",
"stochastic_centering_scale": 0.2,
"stochastic_centering_scope": "per_group",
"stochastic_centering_group_keys": [
"molecule_iid"
]
},
"local_latents": {
"zero_com_noise": false,
"guidance_enabled": true,
"dim": 32,
"stochastic_centering_mode": "none",
"stochastic_centering_scale": null
}
},
"loss": {
"signed_volume_weight": 2.5,
"sequence_prediction": {
"enabled": true,
"t_min": 0.0,
"t_max": 1.0
},
"t_distribution": {
"bb_ca": {
"name": "mix_unif_beta",
"p1": 1.9,
"p2": 1.0,
"p3": 0.02
},
"local_latents": {
"name": "mix_unif_beta",
"p1": 1.0,
"p2": 1.5,
"p3": 0.2
},
"shared_groups": null
}
},
"training": {
"exploration_k": 4,
"exploration_losses": [
"bb_ca",
"local_latents"
],
"n_recycle_max": 9,
"n_recycle_sampler": "poisson",
"n_recycle_lambda": 3.0,
"n_recycle_sync": true,
"n_recycle_val_loss": 3,
"motif_conditioning": false
},
"opt": {
"lr": 5e-05,
"muon_warmup_steps": 0,
"adam_warmup_steps": 10000,
"gradient_clip_val": 1.0,
"max_epochs": 10000000,
"accumulate_grad_batches": 2,
"dist_strategy": "ddp",
"steps_per_epoch": 1000,
"val_every_n_epochs": 5,
"val_start_epoch": 0,
"compute_val_loss": false,
"foldseek_timeout_minutes": 25,
"muon_exclude_param_patterns": [
"_factory\\.",
"^nn\\.(local_latents_linear|ca_linear|insertion_q_proj|insertion_k_proj)\\.",
"^nn\\.sequence_readout\\."
],
"muon_adjust_lr_fn": "match_rms_adamw",
"muon_grouped": true,
"num_sanity_val_steps": 2,
"coordinate_descent_tuning": false
},
"autoencoder_config": {
"nn_ae": {
"name": "transformer_ae_aa_rna_dna_glycan_ncaa",
"latent_z_dim": 32,
"allow_oxt": true,
"use_torch_compile": false,
"torch_compile_fullgraph": false,
"n_residue_types": 147,
"encoder": {
"nlayers": 12,
"token_dim": 768,
"nheads": 12,
"parallel_mha_transition": false,
"token_type_emb_dim": 32,
"strict_feats": false,
"feats_seq": [
"token_type",
"x1_a37coors_nm",
"x1_a37coors_nm_rel",
"chain_idx_seq",
"incident_bond_type_counts",
"atom37_element_charge_embedding"
],
"feats_cond_seq": null,
"dim_cond": 128,
"idx_emb_dim": 128,
"feats_pair_repr": [
"token_bond_path_length",
"canonical_polymer_ordering",
"molecule_idx_pair",
"x1_bb_pair_dists_nm"
],
"seq_sep_dim": 64,
"pair_repr_dim": 256,
"update_pair_repr": false,
"update_pair_repr_every_n": 3,
"use_tri_mult": false,
"use_attn_pair_bias": false,
"use_qkln": true,
"normalize_latent": false,
"latent_z_dim": 32,
"n_residue_types": 147,
"charge_emb_dim": 16
},
"decoder": {
"nlayers": 12,
"token_dim": 768,
"abs_coors": false,
"nheads": 12,
"token_type_emb_dim": 32,
"parallel_mha_transition": false,
"strict_feats": false,
"feats_seq": [
"ca_coors_nm",
"z_latent_seq",
"token_type",
"cond_residue_type"
],
"feats_cond_seq": null,
"dim_cond": 128,
"idx_emb_dim": 128,
"feats_pair_repr": [
"token_bond_path_length",
"canonical_polymer_ordering",
"molecule_idx_pair",
"ca_coors_nm_pair_dists"
],
"seq_sep_dim": 64,
"pair_repr_dim": 256,
"update_pair_repr": false,
"update_pair_repr_every_n": 3,
"use_tri_mult": false,
"use_attn_pair_bias": false,
"use_qkln": true,
"latent_z_dim": 32,
"n_residue_types": 147
}
}
},
"path_length_search_cutoffs": [
64
]
}
}