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uspto50k_forward/config.yaml

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+name: vaedifm_uspto50k_forward
+version: vaedifm_uspto50k_forward
+chem:
+  reaction_data_dir: ./data/uspto50k
+  reaction_file_tag: data
+  file_type: pickle
+data:
+  train_transforms:
+  - type: random_permute
+    attr_name: elements
+model:
+  name: vaedifm_uniform
+  flow:
+    kappa:
+      type: linear
+    sigma:
+      type: sqrtsquare
+  mol_encoder:
+    nlayer: 6
+    dim: 256
+    ntoken: 192
+    nhead: 8
+    dropout: 0.1
+  merge_encoder:
+    nlayer: 6
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+  vae_decoder:
+    nlayer: 12
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+    out_logits: 4
+    pred_diff: false
+  decoder_only: true
+schedule_sampler:
+  name: continuous-uniform
+train:
+  mode: forward
+  loss_weights:
+    bond: 1.0
+    aroma: 1.0
+    charge: 1.0
+    element: 0.0
+  max_iters: 400000
+  val_freq: 1000
+  max_grad_norm: 5.0
+  optimizer:
+    type: adamw
+    lr: 0.0001
+    weight_decay: 0
+    beta1: 0.9
+    beta2: 0.999
+  scheduler:
+    type: cosine
+    T_max: ${train.max_iters}
+    eta_min: 1.0e-06
+    warmup_steps: 2000
+  seed: 42
+  batch_size: 128
+  num_workers: 8
+  devices: 2
+  num_nodes: 1
+  num_sanity_val_steps: 1
+  log_dir: ./logs
+  resume: null
+  wandb_project: null
+  sample_num: 1
+  sample_steps: 100

uspto50k_forward/epoch=313-step=98000.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:a775b48013c2831683e26a8590b11eb551d0e9389a02e27aa590e99f5c8c86d2
+size 181049243

uspto50k_mix/config.yaml

@@ -0,0 +1,70 @@
+name: vaedifm_uspto50k_mix
+version: vaedifm_uspto50k_mix
+chem:
+  reaction_data_dir: ./data/uspto50k
+  reaction_file_tag: data
+  file_type: pickle
+data:
+  train_transforms:
+  - type: random_permute
+    attr_name: elements
+model:
+  name: vaedifm_uniform
+  flow:
+    kappa:
+      type: linear
+    sigma:
+      type: sqrtsquare
+  mol_encoder:
+    nlayer: 6
+    dim: 256
+    ntoken: 192
+    nhead: 8
+    dropout: 0.1
+  merge_encoder:
+    nlayer: 1
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+  vae_decoder:
+    nlayer: 12
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+    out_logits: 4
+    pred_diff: false
+  decoder_only: true
+schedule_sampler:
+  name: continuous-uniform
+train:
+  mode: mix
+  loss_weights:
+    bond: 1.0
+    aroma: 1.0
+    charge: 1.0
+    element: 1.0
+  max_iters: 600000
+  val_freq: 1000
+  max_grad_norm: 5.0
+  optimizer:
+    type: adamw
+    lr: 0.0001
+    weight_decay: 0
+    beta1: 0.9
+    beta2: 0.999
+  scheduler:
+    type: cosine
+    T_max: ${train.max_iters}
+    eta_min: 1.0e-06
+    warmup_steps: 2000
+  seed: 42
+  batch_size: 512
+  num_workers: 8
+  devices: 2
+  num_nodes: 1
+  num_sanity_val_steps: 1
+  log_dir: ./logs
+  resume: null
+  wandb_project: null
+  sample_num: 1
+  sample_steps: 100

uspto50k_mix/epoch=721-step=57000.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:ea050db8765371e1a0dd121d7bab213519a71df27bb1986ef439e5da0c9b6c60
+size 190700321

uspto50k_retro/config.yaml

@@ -0,0 +1,70 @@
+name: vaedifm_uspto50k_retro
+version: vaedifm_uspto50k_retro
+chem:
+  reaction_data_dir: ./data/uspto50k
+  reaction_file_tag: data
+  file_type: pickle
+data:
+  train_transforms:
+  - type: random_permute
+    attr_name: elements
+model:
+  name: vaedifm_uniform
+  flow:
+    kappa:
+      type: linear
+    sigma:
+      type: sqrtsquare
+  mol_encoder:
+    nlayer: 6
+    dim: 256
+    ntoken: 192
+    nhead: 8
+    dropout: 0.1
+  merge_encoder:
+    nlayer: 6
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+  vae_decoder:
+    nlayer: 12
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+    out_logits: 4
+    pred_diff: false
+  decoder_only: true
+schedule_sampler:
+  name: continuous-uniform
+train:
+  mode: retro
+  loss_weights:
+    bond: 1.0
+    aroma: 1.0
+    charge: 1.0
+    element: 1.0
+  max_iters: 400000
+  val_freq: 1000
+  max_grad_norm: 5.0
+  optimizer:
+    type: adamw
+    lr: 0.0001
+    weight_decay: 0
+    beta1: 0.9
+    beta2: 0.999
+  scheduler:
+    type: cosine
+    T_max: ${train.max_iters}
+    eta_min: 1.0e-06
+    warmup_steps: 2000
+  seed: 42
+  batch_size: 128
+  num_workers: 8
+  devices: 2
+  num_nodes: 1
+  num_sanity_val_steps: 1
+  log_dir: ./logs
+  resume: null
+  wandb_project: null
+  sample_num: 1
+  sample_steps: 100

uspto50k_retro/epoch=341-step=107000.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:e67477f613772a7511328847c7be10f9df679bac3e91c71681ebc5fd9a4f498e
+size 181200917

usptomit_forward/config.yaml

@@ -0,0 +1,70 @@
+name: vaedifm_uspto50k_forward
+version: vaedifm_uspto50k_forward
+chem:
+  reaction_data_dir: ./data/uspto50k
+  reaction_file_tag: data
+  file_type: pickle
+data:
+  train_transforms:
+  - type: random_permute
+    attr_name: elements
+model:
+  name: vaedifm_uniform
+  flow:
+    kappa:
+      type: linear
+    sigma:
+      type: sqrtsquare
+  mol_encoder:
+    nlayer: 6
+    dim: 256
+    ntoken: 192
+    nhead: 8
+    dropout: 0.1
+  merge_encoder:
+    nlayer: 6
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+  vae_decoder:
+    nlayer: 12
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+    out_logits: 4
+    pred_diff: false
+  decoder_only: true
+schedule_sampler:
+  name: continuous-uniform
+train:
+  mode: forward
+  loss_weights:
+    bond: 1.0
+    aroma: 1.0
+    charge: 1.0
+    element: 0.0
+  max_iters: 400000
+  val_freq: 1000
+  max_grad_norm: 5.0
+  optimizer:
+    type: adamw
+    lr: 0.0001
+    weight_decay: 0
+    beta1: 0.9
+    beta2: 0.999
+  scheduler:
+    type: cosine
+    T_max: ${train.max_iters}
+    eta_min: 1.0e-06
+    warmup_steps: 2000
+  seed: 42
+  batch_size: 128
+  num_workers: 8
+  devices: 2
+  num_nodes: 1
+  num_sanity_val_steps: 1
+  log_dir: ./logs
+  resume: null
+  wandb_project: null
+  sample_num: 1
+  sample_steps: 100

usptomit_forward/epoch=576-step=230000.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:1360d0a13782bdafc7c3cdeeff95159b52eb3b9737331854da1fbd0cbd844890
+size 181049307

usptomit_mix/config.yaml

@@ -0,0 +1,71 @@
+name: vaedifm_usptomit_uniform
+version: vaedifm_usptomit_uniform
+chem:
+  reaction_data_dir: ./data/usptomit
+  reaction_file_tag: data
+  file_type: pickle
+data:
+  train_transforms:
+  - type: random_permute
+    attr_name: elements
+model:
+  name: vaedifm_uniform
+  flow:
+    kappa:
+      type: linear
+    sigma:
+      type: sqrtsquare
+  mol_encoder:
+    nlayer: 12
+    dim: 256
+    ntoken: 192
+    nhead: 8
+    dropout: 0.1
+  merge_encoder:
+    nlayer: 12
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+    ntoken: 192
+  vae_decoder:
+    nlayer: 12
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+    out_logits: 4
+    pred_diff: false
+  decoder_only: true
+schedule_sampler:
+  name: continuous-uniform
+train:
+  mode: mix
+  loss_weights:
+    bond: 1.0
+    aroma: 1.0
+    charge: 1.0
+    element: 1.0
+  max_iters: 600000
+  val_freq: 1000
+  max_grad_norm: 5.0
+  optimizer:
+    type: adamw
+    lr: 0.0001
+    weight_decay: 0
+    beta1: 0.9
+    beta2: 0.999
+  scheduler:
+    type: cosine
+    T_max: ${train.max_iters}
+    eta_min: 1.0e-06
+    warmup_steps: 2000
+  seed: 42
+  batch_size: 1024
+  num_workers: 8
+  devices: 4
+  num_nodes: 1
+  num_sanity_val_steps: 1
+  log_dir: ./logs
+  resume: null
+  wandb_project: null
+  sample_num: 1
+  sample_steps: 100

usptomit_mix/epoch=561-step=224000.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:a1da00dfa8dbf16f71146995b6c4eaae9a3f8af7c2f671e4019e7d228b4e49ca
+size 362400073

usptomit_retro/config.yaml

@@ -0,0 +1,70 @@
+name: difm_retro_usptomit_uniform
+version: synflow_dfm_bsz1024_ldec12_400epo
+chem:
+  reaction_data_dir: ./data/usptomit
+  reaction_file_tag: data
+  file_type: pickle
+data:
+  train_transforms:
+  - type: random_permute
+    attr_name: elements
+model:
+  name: vaedifm_uniform
+  flow:
+    kappa:
+      type: linear
+    sigma:
+      type: sqrtsquare
+  mol_encoder:
+    nlayer: 12
+    dim: 256
+    ntoken: 192
+    nhead: 8
+    dropout: 0.1
+  merge_encoder:
+    nlayer: 6
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+  vae_decoder:
+    nlayer: 12
+    dim: 256
+    nhead: 8
+    dropout: 0.1
+    out_logits: 4
+    pred_diff: false
+  decoder_only: true
+schedule_sampler:
+  name: continuous-uniform
+train:
+  mode: retro
+  loss_weights:
+    bond: 1.0
+    aroma: 1.0
+    charge: 1.0
+    element: 1.0
+  max_iters: 4000000
+  val_freq: 1000
+  max_grad_norm: 5.0
+  optimizer:
+    type: adamw
+    lr: 0.0001
+    weight_decay: 0
+    beta1: 0.9
+    beta2: 0.999
+  scheduler:
+    type: cosine
+    T_max: ${train.max_iters}
+    eta_min: 1.0e-06
+    warmup_steps: 2000
+  seed: 42
+  batch_size: 1024
+  num_workers: 8
+  devices: 4
+  num_nodes: 1
+  num_sanity_val_steps: 10
+  log_dir: ./logs
+  resume: null
+  wandb_project: difm_retro
+  sample_num: 1
+  sample_steps: 100

usptomit_retro/epoch=1802-step=719000.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:783969f851ee91cd6db216230e57de3af0f90c84db8794fbacce80bc985a03d5
+size 247907789