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RFD4-Proteina-Diffusers

Diffusers
Safetensors
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RFD4ProteinaPipeline
biology
protein-design
biomolecular-design
structure-generation
flow-matching
annotated-cif
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1
kierandidi commited on
Commit
5db5138
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verified ·
1 Parent(s): 8c7b00d

Split the scheduler per modality, move recycle_depths to the pipeline config, rename feature-embedding keys

Browse files
Files changed (9) hide show
  1. bb_ca_scheduler/scheduler_config.json +12 -0
  2. local_latents_scheduler/scheduler_config.json +12 -0
  3. model_index.json +69 -3
  4. provenance.json +1 -1
  5. scheduler/scheduler_config.json +0 -132
  6. transformer/config.json +1 -1
  7. transformer/diffusion_pytorch_model.safetensors +2 -2
  8. vae/config.json +1 -1
  9. vae/diffusion_pytorch_model.safetensors +2 -2
bb_ca_scheduler/scheduler_config.json ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ {
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+ "_class_name": "RFD4ProteinaScheduler",
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+ "_diffusers_version": "0.42.0.dev0",
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+ "noise_mode": "1/t",
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+ "schedule_mode": "log",
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+ "t_lim_ode": 0.95,
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+ "t_lim_ode_below": 0.02,
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+ "tail_step_multiplier": 2,
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+ "tail_steps": 10,
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+ "tsr_k": 16.0,
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+ "tsr_sigma": 3.0
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+ }
local_latents_scheduler/scheduler_config.json ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ {
2
+ "_class_name": "RFD4ProteinaScheduler",
3
+ "_diffusers_version": "0.42.0.dev0",
4
+ "noise_mode": "tan",
5
+ "schedule_mode": "power",
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+ "t_lim_ode": 0.95,
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+ "t_lim_ode_below": 0.02,
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+ "tail_step_multiplier": 2,
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+ "tail_steps": 10,
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+ "tsr_k": 4.0,
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+ "tsr_sigma": 12.0
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+ }
model_index.json CHANGED
@@ -1,9 +1,75 @@
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  {
2
  "_class_name": "RFD4ProteinaPipeline",
3
- "_diffusers_version": "0.41.0.dev0",
4
- "scheduler": [
5
  "diffusers",
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- "RFD4ProductSpaceScheduler"
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  ],
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  "transformer": [
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  "diffusers",
 
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  {
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  "_class_name": "RFD4ProteinaPipeline",
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+ "_diffusers_version": "0.42.0.dev0",
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+ "bb_ca_scheduler": [
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  "diffusers",
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+ "RFD4ProteinaScheduler"
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+ ],
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+ "local_latents_scheduler": [
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+ "diffusers",
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+ "RFD4ProteinaScheduler"
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+ ],
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+ "recycle_depths": [
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  ],
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  "transformer": [
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  "diffusers",
provenance.json CHANGED
@@ -11,5 +11,5 @@
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  "token_type_vocabulary_size": 7,
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  "atom37_mask_sha256": "31670c6a6b5e89b97fcd0c09a24f074faa5460d9bc43deee6d59a9e1f22ef34e",
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  "path_length_search_cutoff": 64,
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- "converted_with": "diffusers 0.41.0.dev0, scripts/convert_rfd4_proteina_to_diffusers.py"
15
  }
 
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  "token_type_vocabulary_size": 7,
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  "atom37_mask_sha256": "31670c6a6b5e89b97fcd0c09a24f074faa5460d9bc43deee6d59a9e1f22ef34e",
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  "path_length_search_cutoff": 64,
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+ "converted_with": "diffusers 0.42.0.dev0, scripts/convert_rfd4_proteina_to_diffusers.py"
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  }
scheduler/scheduler_config.json DELETED
@@ -1,132 +0,0 @@
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- {
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- "_class_name": "RFD4ProductSpaceScheduler",
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- "_diffusers_version": "0.41.0.dev0",
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- "model_args": {
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- "bb_ca": {
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- "gt": {
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- "clamp_val": null,
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- "mode": "1/t",
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- "p": 1.0
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- "schedule": {
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- "mode": "log",
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- "p": 2.0,
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- "tail_step_multiplier": 2,
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- "tail_steps": 10
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- },
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- "simulation_step_params": {
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- "center_every_step": false,
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- "sampling_mode": "vf_tsr",
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- "sc_scale_noise": 1.0,
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- "t_lim_ode": 0.95,
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- "t_lim_ode_below": 0.02,
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- "tsr_k": 16.0,
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- "tsr_sigma": 3.0
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- }
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- },
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- "local_latents": {
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- "gt": {
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- "clamp_val": null,
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- "mode": "tan",
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- "p": 1.0
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- },
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- "schedule": {
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- "mode": "power",
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- "tail_step_multiplier": 2,
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- "tail_steps": 10
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- },
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- "simulation_step_params": {
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- "center_every_step": false,
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- "sampling_mode": "vf_tsr",
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- "sc_scale_noise": 1.0,
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- "t_lim_ode": 0.95,
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- "t_lim_ode_below": 0.02,
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- "tsr_k": 4.0,
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- "tsr_sigma": 12.0
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- }
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- }
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- },
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- "product_flowmatcher_config": {
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- "bb_ca": {
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- "dim": 3,
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- "guidance_enabled": true,
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- "stochastic_centering_group_keys": [
55
- "molecule_iid"
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- ],
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- "stochastic_centering_mode": "x_0",
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- "stochastic_centering_scale": 0.2,
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- "stochastic_centering_scope": "per_group",
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- "zero_com_noise": true
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- },
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- "local_latents": {
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- "dim": 32,
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- "guidance_enabled": true,
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- "stochastic_centering_mode": "none",
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- "stochastic_centering_scale": null,
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- "zero_com_noise": false
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- }
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- "recycle_depths": [
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transformer/config.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "_class_name": "RFD4ProteinaTransformer",
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- "_diffusers_version": "0.41.0.dev0",
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  "cath_emb_dim": 32,
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  "dim_cond": 256,
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  "feats_cond_seq": [
 
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  {
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  "_class_name": "RFD4ProteinaTransformer",
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+ "_diffusers_version": "0.42.0.dev0",
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  "cath_emb_dim": 32,
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  "dim_cond": 256,
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  "feats_cond_seq": [
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vae/config.json CHANGED
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  {
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  "_class_name": "RFD4ProteinaAutoencoder",
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- "_diffusers_version": "0.41.0.dev0",
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  "allowed_residue_types": [
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  [
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  {
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