Uncertainty

configs/exps/catalyst/gflownet.yaml

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+job:
+  mem: 32GB
+  cpus: 4
+  gres: gpu:1
+  partition: long
+  time: 15:00:00
+
+default:
+  wandb_project: ocp-deup  # ocp-alvaro
+  wandb_tags: gflownet-model, depfaenet
+  test_ri: True
+  mode: train
+  # graph_rewiring: remove-tag-0
+  graph_rewiring: ""
+  frame_averaging: 2D
+  fa_method: se3-random
+  cp_data_to_tmpdir: True
+  is_disconnected: true
+  model:
+    mp_type: updownscale_base
+    phys_embeds: True
+    tag_hidden_channels: 0
+    pg_hidden_channels: 96
+    energy_head: weighted-av-final-embeds
+    complex_mp: True
+    graph_norm: True
+    hidden_channels: 352
+    num_filters: 288
+    num_gaussians: 68
+    num_interactions: 5
+    second_layer_MLP: False
+    skip_co: concat
+    cutoff: 4.0
+  optim:
+    batch_size: 256
+    eval_batch_size: 256
+    lr_initial: 0.002
+    scheduler: LinearWarmupCosineAnnealingLR
+    max_epochs: 9
+    eval_every: 0.4
+
+runs:
+
+  # - config: faenet-is2re-all
+  #   note: baseline faenet
+
+  # - config: depfaenet-is2re-all
+  #   note: depfaenet baseline
+
+  # - config: depfaenet-is2re-all
+  #   note: depfaenet per-adsorbate
+  #   adsorbates: {'*O', '*OH', '*OH2', '*H'}
+
+  # - config: depfaenet-is2re-all
+  #   note: depfaenet per-adsorbate long string
+  #   adsorbates: '*O, *OH, *OH2, *H'
+
+  # - config: depfaenet-is2re-all
+  #   note: depfaenet per-adsorbate string of a list
+  #   adsorbates: "*O, *OH, *OH2, *H"
+
+  # - config: depfaenet-is2re-all
+  #   note: Trained on selected adsorbate more epochs
+  #   adsorbates: "*O, *OH, *OH2, *H"
+  #   optim:
+  #     max_epochs: 10
+
+  # - config: depfaenet-is2re-all
+  #   note: depfaenet full data
+
+  # - config: depfaenet-is2re-all
+  #   note: To be used for continue from dir
+
+  # - config: depfaenet-is2re-all
+  #   note: Fine-tune on per-ads-dataset 4 epoch
+  #   continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4023244
+  #   adsorbates: "*O, *OH, *OH2, *H"
+  #   optim:
+  #     max_epochs: 4
+  #     lr_initial: 0.00015
+
+  # - config: depfaenet-is2re-all
+  #   note: Fine-tune on per-ads-dataset 10 epoch
+  #   continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4023244
+  #   adsorbates: "*O, *OH, *OH2, *H"
+  #   optim:
+  #     max_epochs: 10
+  #     lr_initial: 0.00015
+
+  # - config: depfaenet-is2re-all
+  #   note: Fine-tune on per-ads-dataset 10 epoch
+  #   continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4023244
+  #   adsorbates: "*O, *OH, *OH2, *H"
+  #   optim:
+  #     max_epochs: 20
+  #     lr_initial: 0.0001
+
+  # - config: depfaenet-is2re-all
+  #   note: Fine-tune on per-ads-dataset 20 epoch
+  #   continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4023244
+  #   adsorbates: "*O, *OH, *OH2, *H"
+  #   optim:
+  #     max_epochs: 20
+  #     lr_initial: 0.00015
+
+  - config: depfaenet-is2re-all
+    note: Depfaenet per-ads-dataset
+    continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4023244
+    adsorbates: "*O, *OH, *OH2, *H"
+    optim:
+      max_epochs: 12
+      lr_initial: 0.0002
+
+  - config: depfaenet-is2re-all
+    note: Depfaenet per-ads-dataset
+    continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4023244
+    adsorbates: "*O, *OH, *OH2, *H"
+    optim:
+      max_epochs: 10
+      lr_initial: 0.0001
+
+  # - config: depfaenet-is2re-all
+  #   note: Fine-tune on per-ads-dataset starting from fine-tuned model
+  #   continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4071859
+  #   adsorbates: "*O, *OH, *OH2, *H"
+  #   optim:
+  #     max_epochs: 10
+  #     lr_initial: 0.0001
+
+  # - config: depfaenet-is2re-all
+  #   note: Trained on selected adsorbate
+  #   adsorbates: "*O, *OH, *OH2, *H"
+  #   optim:
+  #     max_epochs: 25
+  #     lr_initial: 0.0001
+
+  # - config: depfaenet-is2re-all
+  #   note: Trained on selected adsorbate
+  #   adsorbates: "*O, *OH, *OH2, *H"
+  #   optim:
+  #     max_epochs: 25

configs/exps/catalyst/reproduce-configs.yaml

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+job:
+  mem: 32GB
+  cpus: 4
+  gres: gpu:rtx8000:1
+  partition: long
+  time: 15:00:00
+
+default:
+  # wandb_name: alvaro-carbonero-math
+  wandb_project: ocp-alvaro
+  wandb_tags: "reproduce-best-config"
+  test_ri: True
+  mode: train
+  graph_rewiring: remove-tag-0
+  note: "repoduce-top-run"
+  frame_averaging: 2D
+  fa_method: se3-random
+  cp_data_to_tmpdir: True
+  is_disconnected: true
+  model:
+    edge_embed_type: all_rij
+    mp_type: updownscale_base
+    phys_embeds: True
+    tag_hidden_channels: 32
+    pg_hidden_channels: 96
+    energy_head: weighted-av-final-embeds
+    complex_mp: True
+    graph_norm: True
+    hidden_channels: 352
+    num_filters: 288
+    num_gaussians: 68
+    num_interactions: 5
+    second_layer_MLP: False
+    skip_co: concat
+    cutoff: 4.0
+  optim:
+    batch_size: 256
+    eval_batch_size: 256
+    lr_initial: 0.002
+    scheduler: LinearWarmupCosineAnnealingLR
+    max_epochs: 9
+    eval_every: 0.4
+
+runs:
+
+  - config: faenet-is2re-all
+    note: baseline faenet
+
+  - config: indfaenet-is2re-all
+    note: baseline with top configs 
+
+  - config: indfaenet-is2re-all
+    note: baseline with runs' configs 
+    model: 
+      tag_hidden_channels: 32
+      pg_hidden_channels: 96
+      energy_head: weighted-av-final-embeds
+      complex_mp: True
+      graph_norm: True
+      hidden_channels: 528
+      num_filters: 672
+      num_gaussians: 148
+      num_interactions: 5
+      second_layer_MLP: False
+      skip_co: concat
+
+  - config: depfaenet-is2re-all
+    note: baseline with top configs
+
+  - config: indfaenet-is2re-all
+    note: so that ads get old dimensions
+    model:
+      hidden_channels: 704 
+      num_gaussians: 200
+      num_filters: 896

configs/exps/deup/datasets/data-with-depfaenet.yaml

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+job:
+  mem: 32GB
+  cpus: 4
+  gres: gpu:1
+  partition: long
+
+default:
+  config: depfaenet-is2re-all
+  wandb_project: ocp-deup
+  wandb_tags: depfaenet, MC-D,4621042
+  test_ri: True
+  mode: train
+  checkpoint: /network/scratch/a/alexandre.duval/ocp/runs/4621042/checkpoints/best_checkpoint.pt
+  restart_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4621042/
+  model:
+    dropout_lowest_layer: output
+    first_trainable_layer: dropout
+    dropout_lin: 0.3
+  cp_data_to_tmpdir: true
+  inference_time_loops: 1
+  deup_dataset:
+    create: after # "before" -> created before training (for deup) "after" -> created after training (for is2re) "" - not created
+    dataset_strs: ["train", "val_id", "val_ood_cat", "val_ood_ads"]
+    n_samples: 7
+
+runs:
+  - optim:
+      max_epochs: 12

configs/exps/deup/datasets/mc-faenet.yaml

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+job:
+  mem: 32GB
+  cpus: 4
+  gres: gpu:1
+  partition: long
+
+default:
+  config: faenet-is2re-all
+  wandb_project: ocp-deup
+  wandb_tags: base-model, MC-D, 4616500
+  test_ri: True
+  mode: train
+  checkpoint: /network/scratch/a/alexandre.duval/ocp/runs/4616500/checkpoints/best_checkpoint.pt
+  restart_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4616500/
+  model:
+    dropout_lowest_layer: output
+    first_trainable_layer: dropout
+    dropout_lin: 0.7
+  cp_data_to_tmpdir: true
+  inference_time_loops: 1
+  deup_dataset:
+    create: after # "before" -> created before training (for deup) "after" -> created after training (for is2re) "" - not created
+    dataset_strs: ["train", "val_id", "val_ood_cat", "val_ood_ads"]
+    n_samples: 7
+
+runs:
+  - optim:
+      max_epochs: 12

configs/exps/deup/gnn/depfaenet-finetune.yaml

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+job:
+  mem: 32GB
+  cpus: 4
+  gres: gpu:1
+  partition: long
+  time: 15:00:00
+
+default:
+  wandb_project: ocp-deup
+  wandb_tags: depfaenet, no-concat, with-tag0, dropout
+  test_ri: True
+  mode: train
+  graph_rewiring: ""
+  frame_averaging: 2D
+  fa_method: se3-random
+  is_disconnected: true
+
+runs:
+
+  - config: depfaenet-is2re-all
+    note: Depfaenet per-ads-dataset
+    continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4647488  #4647466 #4023244
+    adsorbates: "*O, *OH, *OH2, *H"
+    optim:
+      max_epochs: 10
+      lr_initial: 0.0002
+
+  - config: depfaenet-is2re-all
+    note: Depfaenet per-ads-dataset
+    continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4647488 #4647466  # 4023244
+    adsorbates: "*O, *OH, *OH2, *H"
+    optim:
+      max_epochs: 12
+      lr_initial: 0.0001
+
+- config: depfaenet-is2re-all
+  note: Depfaenet per-ads-dataset
+  continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4647466 # 4023244
+  adsorbates: "*O, *OH, *OH2, *H"
+  graph_rewiring: ""
+  frame_averaging: 2D
+  fa_method: se3-random
+  cp_data_to_tmpdir: True
+  is_disconnected: true
+  model:
+    mp_type: updownscale_base
+    phys_embeds: True
+    tag_hidden_channels: 0
+    pg_hidden_channels: 96
+    energy_head: weighted-av-final-embeds
+    complex_mp: True
+    graph_norm: True
+    hidden_channels: 352
+    num_filters: 288
+    num_gaussians: 68
+    num_interactions: 5
+    second_layer_MLP: False
+    skip_co: False
+    cutoff: 4.0
+    dropout_lin: 0.3
+  optim:
+    batch_size: 256
+    eval_batch_size: 256
+    lr_initial: 0.002
+    scheduler: LinearWarmupCosineAnnealingLR
+    eval_every: 0.4
+    max_epochs: 12

configs/exps/deup/gnn/faenet-finetune.yaml

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+job:
+  mem: 32GB
+  cpus: 4
+  gres: gpu:1
+  partition: long
+  time: 18:00:00
+
+default:
+  test_ri: True
+  mode: train
+  wandb_tags: faenet, no-concat, with-tag0, dropout, fine-tuned
+  wandb_project: ocp-deup
+  graph_rewiring: ""
+  optim:
+    batch_size: 232
+    eval_batch_size: 232
+  cp_data_to_tmpdir: True
+
+runs:
+  - config: faenet-is2re-all
+    note: "fine-tuned faenet"
+    continue_from_dir: /network/scratch/a/alexandre.duval/ocp/runs/4647489
+    adsorbates: "*O, *OH, *OH2, *H"
+    frame_averaging: 2D
+    fa_method: se3-random
+    model:
+      mp_type: updownscale_base
+      phys_embeds: True
+      tag_hidden_channels: 32
+      pg_hidden_channels: 96
+      energy_head: weighted-av-final-embeds
+      complex_mp: True
+      graph_norm: True
+      hidden_channels: 384
+      num_filters: 480
+      num_gaussians: 104
+      num_interactions: 5
+      second_layer_MLP: False
+      skip_co: False
+      cutoff: 6.0
+      dropout_lin: 0.3
+      dropout_lowest_layer: output
+    optim:
+      lr_initial: 0.002
+      scheduler: LinearWarmupCosineAnnealingLR
+      max_epochs: 14
+      eval_every: 0.25