Update SPURS checkpoints

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spurs/.hydra/config.yaml +1 -1
spurs/.hydra/hydra.yaml +219 -0
spurs/.hydra/overrides.yaml +21 -0
spurs/config_tree.log +109 -0
spurs/domainome_pred_result.pt +3 -0
spurs/dtm_pred_scores.pt +3 -0
spurs/megascale_fig2d.pt +3 -0
spurs/pred_result.pt +3 -0
spurs/single_result_25.9.25.pt +3 -0
spurs/spurs_multi_single_25.9.25.pt +3 -0
spurs/srho_list_chain_list_pdb_chains_pf_mut_id_indices.pt +3 -0

spurs/.hydra/config.yaml CHANGED Viewed

@@ -37,7 +37,7 @@ model:
     flat_dim: 128
     input_dim: 256
     hidden_dim: 1024
-    num_layers: 2
     output_dim: 21
     dropout: 0.1
   dropout: 0.5

     flat_dim: 128
     input_dim: 256
     hidden_dim: 1024
+    num_layers: 4
     output_dim: 21
     dropout: 0.1
   dropout: 0.5

spurs/.hydra/hydra.yaml ADDED Viewed

	@@ -0,0 +1,219 @@

+hydra:
+  run:
+    dir: outputs/${now:%Y-%m-%d}/${now:%H-%M-%S}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    sampler:
+      _target_: optuna.samplers.TPESampler
+      seed: 100
+      consider_prior: true
+      prior_weight: 1.0
+      consider_magic_clip: true
+      consider_endpoints: false
+      n_startup_trials: 1
+      n_ei_candidates: 24
+      multivariate: false
+      warn_independent_sampling: true
+    _target_: hydra_plugins.hydra_optuna_sweeper.optuna_sweeper.OptunaSweeper
+    direction: maximize
+    storage: null
+    study_name: mpnn_esm_cat
+    n_trials: 50
+    n_jobs: 1
+    search_space: null
+    params:
+      task.optimizer.lr: choice(0.0001, 0.001, 0.01, 0.1, 5e-5)
+      task.optimizer.weight_decay: choice(0.0001, 5e-4,0.001, 5e-3)
+      task.lr_scheduler.factor: range(0.1,0.9,step=0.1)
+      model.encoder.use_input_decoding_order: choice(True, False)
+      model.encoder.tune: choice(True, False)
+      trainer.precision: choice(16, 32)
+      train.seed: choice(42, 43, 44, 45, 46, 47, 48, 49, 50)
+      model.dropout: range(0,0.7,step=0.1)
+      model.mlp.flat_dim: choice(-1,128,258,512,1024)
+      model.mlp.hidden_dim: choice(512, 1024,256,768, 2048)
+      model.mlp.input_dim: choice(128, 256, 384,512)
+      model.mlp.dropout: range(0,0.7,step=0.1)
+      model.mlp.num_layers: choice(2, 3, 4, 5)
+      model.use_ssm: choice(True, False)
+      model.ssm.d_state: choice(16, 32, 64, 128)
+      model.ssm.d_conv: choice(4, 8, 16, 32)
+      model.ssm.expand: choice(6, 4, 8)
+      model.ssm.num_layer: choice(2, 3,4,8)
+      model.ssm.dropout: range(0,0.7,step=0.1)
+      model.ssm.layernorm: choice(True, False)
+      model.adapter_layer_indices: choice([-1,-2], [-1], [-2], [-3], [-3,-2], [-3,-2,-1],[-4,-3,-2,-1])
+    custom_search_space: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+      Use --hydra-help to view Hydra specific help
+      '
+    template: '${hydra.help.header}
+      == Configuration groups ==
+      Compose your configuration from those groups (group=option)
+      $APP_CONFIG_GROUPS
+      == Config ==
+      Override anything in the config (foo.bar=value)
+      $CONFIG
+      ${hydra.help.footer}
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+      See https://hydra.cc for more info.
+      == Flags ==
+      $FLAGS_HELP
+      == Configuration groups ==
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+      $HYDRA_CONFIG_GROUPS
+      Use ''--cfg hydra'' to Show the Hydra config.
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: MULTIRUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=MULTIRUN
+    task:
+    - task.optimizer.lr=0.0001
+    - task.optimizer.weight_decay=0.001
+    - task.lr_scheduler.factor=0.2
+    - model.encoder.use_input_decoding_order=True
+    - model.encoder.tune=True
+    - trainer.precision=32
+    - train.seed=45
+    - model.dropout=0.5
+    - model.mlp.flat_dim=128
+    - model.mlp.hidden_dim=1024
+    - model.mlp.input_dim=256
+    - model.mlp.dropout=0.1
+    - model.mlp.num_layers=2
+    - model.use_ssm=False
+    - model.ssm.d_state=32
+    - model.ssm.d_conv=16
+    - model.ssm.expand=4
+    - model.ssm.num_layer=3
+    - model.ssm.dropout=0.6000000000000001
+    - model.ssm.layernorm=True
+    - model.adapter_layer_indices=[-3]
+  job:
+    name: search
+    chdir: null
+    override_dirname: model.adapter_layer_indices=[-3],model.dropout=0.5,model.encoder.tune=True,model.encoder.use_input_decoding_order=True,model.mlp.dropout=0.1,model.mlp.flat_dim=128,model.mlp.hidden_dim=1024,model.mlp.input_dim=256,model.mlp.num_layers=2,model.ssm.d_conv=16,model.ssm.d_state=32,model.ssm.dropout=0.6000000000000001,model.ssm.expand=4,model.ssm.layernorm=True,model.ssm.num_layer=3,model.use_ssm=False,task.lr_scheduler.factor=0.2,task.optimizer.lr=0.0001,task.optimizer.weight_decay=0.001,train.seed=45,trainer.precision=32
+    id: '23'
+    num: 23
+    config_name: mpnn_esm.yaml
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.1'
+    cwd: /work/ziang/PSNet
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /work/ziang/PSNet/configs
+      schema: file
+      provider: main
+    - path: hydra_plugins.hydra_colorlog.conf
+      schema: pkg
+      provider: hydra-colorlog
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /work/ziang/PSNet/multirun/2024-03-21/15-39-31/23
+    choices:
+      trainer: ddp_fp16
+      datamodule: megascale
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: optuna
+      hydra/sweeper/sampler: tpe
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false

spurs/.hydra/overrides.yaml ADDED Viewed

	@@ -0,0 +1,21 @@

+- task.optimizer.lr=0.0001
+- task.optimizer.weight_decay=0.001
+- task.lr_scheduler.factor=0.2
+- model.encoder.use_input_decoding_order=True
+- model.encoder.tune=True
+- trainer.precision=32
+- train.seed=45
+- model.dropout=0.5
+- model.mlp.flat_dim=128
+- model.mlp.hidden_dim=1024
+- model.mlp.input_dim=256
+- model.mlp.dropout=0.1
+- model.mlp.num_layers=2
+- model.use_ssm=False
+- model.ssm.d_state=32
+- model.ssm.d_conv=16
+- model.ssm.expand=4
+- model.ssm.num_layer=3
+- model.ssm.dropout=0.6000000000000001
+- model.ssm.layernorm=True
+- model.adapter_layer_indices=[-3]

spurs/config_tree.log ADDED Viewed

	@@ -0,0 +1,109 @@

+CONFIG
+├── datamodule
+│   └── _target_: megascale
+│       batch_size: 1
+│       num_workers: 8
+│       pin_memory: true
+│       alphabet:
+│         name: esm
+│         featurizer: megascale
+│
+├── task
+│   └── _target_: stability/megascale
+│       criterion:
+│         _target_: spurs.modules.mseloss.MSELoss
+│       optimizer:
+│         type: adamw
+│         _partial_: true
+│         lr: 0.0001
+│         betas:
+│         - 0.9
+│         - 0.98
+│         weight_decay: 0.001
+│       lr_scheduler:
+│         type: plateau
+│         lr: 0.001
+│         factor: 0.2
+│         mode: min
+│         monitor: val/rho_avg_mse
+│
+├── model
+│   └── _target_: spurs
+│       encoder:
+│         d_model: 128
+│         n_enc_layers: 3
+│         n_dec_layers: 3
+│         tune: true
+│         use_input_decoding_order: true
+│       adapter_layer_indices:
+│       - -3
+│       mlp:
+│         flat_dim: 128
+│         input_dim: 256
+│         hidden_dim: 1024
+│         num_layers: 2
+│         output_dim: 21
+│         dropout: 0.1
+│       dropout: 0.5
+│
+├── callbacks
+│   └── model_summary:
+│         _target_: pytorch_lightning.callbacks.RichModelSummary
+│         max_depth: -1
+│       model_checkpoint:
+│         _target_: spurs.utils.callbacks.ModelCheckpoint
+│         monitor: val/rho_avg_spearman
+│         mode: max
+│         save_top_k: 1
+│         save_last: true
+│         verbose: true
+│         dirpath: checkpoints
+│         filename: step_{global_step}-val/rho_avg_spearman_{val/rho_avg_spearman:.2f}
+│         auto_insert_metric_name: false
+│       early_stopping:
+│         _target_: pytorch_lightning.callbacks.EarlyStopping
+│         monitor: val/rho_avg_spearman
+│         mode: max
+│         patience: 30
+│         min_delta: 0
+│         check_on_train_epoch_end: false
+│
+├── trainer
+│   └── _target_: pytorch_lightning.Trainer
+│       gpus: auto
+│       min_epochs: 1
+│       max_epochs: 10
+│       enable_progress_bar: true
+│       log_every_n_steps: 10
+│       resume_from_checkpoint: null
+│
+├── experiment_path
+│   └── /nethome/zli3161/DATA-nash/SPURS/data/checkpoints/spurs
+├── ckpt_path
+│   └── best.ckpt
+├── data_split
+│   └── test
+├── mode
+│   └── predict
+├── name
+│   └── megascale/spurs
+├── train
+│   └── seed: 45
+│       lr: 0.001
+│       monitor: val/rho_avg_spearman
+│       mode: max
+│       patience: 30
+│
+├── print_config
+│   └── True
+├── ignore_warnings
+│   └── True
+├── seed
+│   └── 42
+└── paths
+    └── root_dir: /work/ziang/SPURS
+        data_dir: /work/ziang/SPURS/data/
+        log_dir: /nethome/zli3161/DATA-nash/SPURS/data/checkpoints/spurs
+        ckpt_dir: /nethome/zli3161/DATA-nash/SPURS/data/checkpoints/spurs/checkpoints
+        psnetdata: /work/ziang/SPURS/PSNet/data

spurs/domainome_pred_result.pt ADDED Viewed

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spurs/dtm_pred_scores.pt ADDED Viewed

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spurs/srho_list_chain_list_pdb_chains_pf_mut_id_indices.pt ADDED Viewed

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