Delete spurs

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spurs/.hydra/config.yaml +0 -105
spurs/.hydra/hydra.yaml +0 -219
spurs/.hydra/overrides.yaml +0 -21
spurs/checkpoints/best.ckpt +0 -3
spurs/config_tree.log +0 -109
spurs/domainome_pred_result.pt +0 -3
spurs/dtm_pred_scores.pt +0 -3
spurs/megascale_fig2d.pt +0 -3
spurs/pred_result.pt +0 -3
spurs/single_result_25.9.25.pt +0 -3
spurs/spurs_multi_single_25.9.25.pt +0 -3
spurs/srho_list_chain_list_pdb_chains_pf_mut_id_indices.pt +0 -3

spurs/.hydra/config.yaml DELETED Viewed

@@ -1,105 +0,0 @@
-datamodule:
-  _target_: megascale
-  batch_size: 1
-  num_workers: 8
-  pin_memory: true
-  alphabet:
-    name: esm
-    featurizer: megascale
-trainer:
-  _target_: pytorch_lightning.Trainer
-  gpus: auto
-  min_epochs: 1
-  max_epochs: 200
-  enable_progress_bar: true
-  log_every_n_steps: 10
-  resume_from_checkpoint: null
-  strategy: ddp_sharded_fbo
-  precision: 32
-  gradient_clip_val: 0.0
-  num_sanity_val_steps: 0
-  check_val_every_n_epoch: 1
-  reload_dataloaders_every_n_epochs: 100000
-  replace_sampler_ddp: false
-  max_steps: 200000
-name: megascale/spurs
-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: 4
-    output_dim: 21
-    dropout: 0.1
-  dropout: 0.5
-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: ${train.lr}
-    factor: 0.2
-    mode: min
-    monitor: val/rho_avg_mse
-train:
-  seed: 45
-  lr: 0.001
-  monitor: val/rho_avg_spearman
-  mode: max
-  patience: 30
-optimized_metric: val/rho_avg_spearman
-experiment: mpnn
-callbacks:
-  model_summary:
-    _target_: pytorch_lightning.callbacks.RichModelSummary
-    max_depth: -1
-  model_checkpoint:
-    _target_: spurs.utils.callbacks.ModelCheckpoint
-    monitor: ${train.monitor}
-    mode: ${train.mode}
-    save_top_k: 1
-    save_last: true
-    verbose: true
-    dirpath: checkpoints
-    filename: step_{global_step}-${train.monitor}_{${train.monitor}:.2f}
-    auto_insert_metric_name: false
-  early_stopping:
-    _target_: pytorch_lightning.callbacks.EarlyStopping
-    monitor: ${train.monitor}
-    mode: ${train.mode}
-    patience: ${train.patience}
-    min_delta: 0
-    check_on_train_epoch_end: false
-logger:
-  tensorboard:
-    _target_: pytorch_lightning.loggers.tensorboard.TensorBoardLogger
-    save_dir: tensorboard/
-    name: null
-    version: ${name}
-    log_graph: false
-    default_hp_metric: true
-    prefix: ''
-paths:
-  root_dir: ${oc.env:PROJECT_ROOT}
-  data_dir: ${paths.root_dir}/data/
-  log_dir: ${paths.root_dir}/logs/${name}
-  ckpt_dir: ${paths.log_dir}/checkpoints
-  psnetdata: ${paths.root_dir}/PSNet/data

spurs/.hydra/hydra.yaml DELETED Viewed

@@ -1,219 +0,0 @@
-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 DELETED Viewed

@@ -1,21 +0,0 @@
-- 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/checkpoints/best.ckpt DELETED Viewed

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spurs/config_tree.log DELETED Viewed

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-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 DELETED Viewed

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spurs/dtm_pred_scores.pt DELETED Viewed

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spurs/megascale_fig2d.pt DELETED Viewed

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spurs/srho_list_chain_list_pdb_chains_pf_mut_id_indices.pt DELETED Viewed

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