experiments/sciplex_hparam/config_sciplex_finetuning_hparam.yaml

# Config for fine-tuning CCPA on Trapnell from LINCS pre-training with identical gene sets 
# This lead direclt to part 1 and 3 of `finetuning_num_genes`
seml:
  executable: chemCPA/seml_sweep_icb.py
  name: ft_sciplex_hparam
  output_dir: sweeps/logs
  conda_environment: chemical_CPA
  project_root_dir: ../..

slurm:
  max_simultaneous_jobs: 17
  experiments_per_job: 2
  sbatch_options_template: GPU
  sbatch_options:
    gres: gpu:1       # num GPUs
    mem: 32G          # memory
    cpus-per-task: 6  # num cores
    # speeds is roughly 3 epochs / minute
    time: 1-00:01     # max time, D-HH:MM
###### BEGIN PARAMETER CONFIGURATION ######

fixed:
  profiling.run_profiler: False
  profiling.outdir: "./"

  training.checkpoint_freq: 15 # checkpoint frequency to run evaluate, and maybe save checkpoint
  training.num_epochs: 1500 # maximum epochs for training. One epoch updates either autoencoder, or adversary, depending on adversary_steps.
  training.max_minutes: 1200 # maximum computation time
  training.full_eval_during_train: False
  training.run_eval_disentangle: True # whether to calc the disentanglement loss when running the full eval
  training.save_checkpoints: True # checkpoints tend to be ~250MB large for LINCS.
  training.save_dir: /storage/groups/ml01/projects/2021_chemicalCPA_leon.hetzel/sweeps/checkpoints
  
  dataset.dataset_type: trapnell
  dataset.data_params.dataset_path: /storage/groups/ml01/projects/2021_chemicalCPA_leon.hetzel/datasets/trapnell_cpa_lincs_genes.h5ad # full path to the anndata dataset
  dataset.data_params.perturbation_key: condition # stores name of the drug
  dataset.data_params.pert_category: cov_drug_dose_name # stores celltype_drugname_drugdose
  dataset.data_params.dose_key: dose # stores drug dose as a float
  dataset.data_params.covariate_keys: cell_type # necessary field for cell types. Fill it with a dummy variable if no celltypes present.
  dataset.data_params.smiles_key: SMILES
  dataset.data_params.degs_key: lincs_DEGs # `uns` column name denoting the DEGs for each perturbation
  dataset.data_params.split_key: split_ho_pathway # necessary field for train, test, ood splits.
  dataset.data_params.use_drugs_idx: True # If false, will use One-hot encoding instead

  # model.load_pretrained: True
  model.pretrained_model_path: /storage/groups/ml01/projects/2021_chemicalCPA_leon.hetzel/sweeps/checkpoints
  model.pretrained_model_hashes: # seml config_hashes for the pretrained models for each embedding. Used for loading model checkpoints. Hashes taken from `analyze_lincs_all_embeddings_hparam.ipynb`
      grover_base: ff420aea264fca7668ecb147f60762a1
      MPNN: ff9629a1b216372be8b205556cabc6fb
      rdkit: 4f061dbfc7af05cf84f06a724b0c8563
      weave: 1244d8b476696a7e1c01fd05d73d7450
      jtvae: a7060ac4e2c6154e64a13acd414cbba2
      seq2seq: e31119adc782888d5b75c57f8c803ee0
      GCN: aedb25c686fb856e574a951f749b8dcf
      vanilla: ba3569d1f5898a6bb964b7fafbed2641 # Vanilla CPA, new embedding will be trained.
  model.additional_params.patience: 4 # patience for early stopping. Effective epochs: patience * checkpoint_freq.
  model.additional_params.decoder_activation: linear # last layer of the decoder
  model.additional_params.doser_type: amortized # non-linearity for doser function
  model.embedding.directory: null # null will load the path from paths.py

  model.additional_params.seed: 1337

  # these were picked in the `lincs_rdkit_hparam` experiment
  model.hparams.dim: 32
  model.hparams.dropout: 0.262378
  model.hparams.autoencoder_width: 256
  model.hparams.autoencoder_depth: 4

random: 
  samples: 10
  seed: 42
  model.hparams.batch_size:
    type: choice
    options:
      - 32
      - 64
      - 128
  model.hparams.autoencoder_lr:
    type: loguniform
    min: 1e-4
    max: 1e-2
  model.hparams.autoencoder_wd:
    type: loguniform
    min: 1e-8
    max: 1e-5
  model.hparams.adversary_width:
    type: choice
    options:
      - 64
      - 128
      - 256
  model.hparams.adversary_depth:
    type: choice
    options:
      - 2
      - 3
      - 4
  model.hparams.adversary_lr:
    type: loguniform
    min: 5e-5
    max: 1e-2
  model.hparams.adversary_wd:
    type: loguniform
    min: 1e-8
    max: 1e-3
  model.hparams.adversary_steps: # every X steps, update the adversary INSTEAD OF the autoencoder.
    type: choice
    options:
      - 2
      - 3
  model.hparams.reg_adversary:
    type: loguniform
    min: 5
    max: 100
  model.hparams.penalty_adversary:
    type: loguniform
    min: 1
    max: 10
  model.hparams.dosers_lr:
    type: loguniform
    min: 1e-4
    max: 1e-2
  model.hparams.dosers_wd:
    type: loguniform
    min: 1e-8
    max: 1e-5

grid:
  model.load_pretrained:
    type: choice
    options:
      - True
      - False
rdkit:
  fixed:
    model.embedding.model: rdkit
    model.hparams.dosers_width: 64
    model.hparams.dosers_depth: 3
    # Params for corresponding hash - left in for reference
    # model.hparams.dosers_lr: 0.001121
    # model.hparams.dosers_wd: 3.752056e-7
    model.hparams.step_size_lr: 50 # this applies to all optimizers (AE, ADV, DRUG)
    model.hparams.embedding_encoder_width: 128
    model.hparams.embedding_encoder_depth: 4

grover_base:
  fixed:
    model.embedding.model: grover_base
    model.hparams.dosers_width: 512
    model.hparams.dosers_depth: 2
    # Params for corresponding hash - left in for reference
    # model.hparams.dosers_lr: 0.000561
    # model.hparams.dosers_wd: 1.329292e-07 
    model.hparams.step_size_lr: 50 # this applies to all optimizers (AE, ADV, DRUG)
    model.hparams.embedding_encoder_width: 512
    model.hparams.embedding_encoder_depth: 3

jtvae:
  fixed:
    model.embedding.model: jtvae
    model.hparams.dosers_width: 64
    model.hparams.dosers_depth: 2
    # Params for corresponding hash - left in for reference
    # model.hparams.dosers_lr: 0.000205
    # model.hparams.dosers_wd: 2.937538e-08 
    model.hparams.step_size_lr: 50 # this applies to all optimizers (AE, ADV, DRUG)
    model.hparams.embedding_encoder_width: 256
    model.hparams.embedding_encoder_depth: 4

MPNN:
  fixed:
    model.embedding.model: MPNN
    model.hparams.dosers_width: 64
    model.hparams.dosers_depth: 2
    # Params for corresponding hash - left in for reference
    # model.hparams.dosers_lr: 0.001575
    # model.hparams.dosers_wd: 6.251374e-07
    model.hparams.step_size_lr: 50 # this applies to all optimizers (AE, ADV, DRUG)
    model.hparams.embedding_encoder_width: 128
    model.hparams.embedding_encoder_depth: 4

seq2seq:
  fixed:
    model.embedding.model: seq2seq
    model.hparams.dosers_width: 256
    model.hparams.dosers_depth: 3
    # Params for corresponding hash - left in for reference
    # model.hparams.dosers_lr: 0.005399
    # model.hparams.dosers_wd: 3.967605e-06
    model.hparams.step_size_lr: 50 # this applies to all optimizers (AE, ADV, DRUG)
    model.hparams.embedding_encoder_width: 256
    model.hparams.embedding_encoder_depth: 4

vanilla:
  fixed:
    model.embedding.model: vanilla
    model.hparams.dosers_width: 512
    model.hparams.dosers_depth: 2
    # Params for corresponding hash - left in for reference
    # model.hparams.dosers_lr: 0.000233
    # model.hparams.dosers_wd: 3.549879e-08
    model.hparams.step_size_lr: 50 # this applies to all optimizers (AE, ADV, DRUG)
    model.hparams.embedding_encoder_width: 128
    model.hparams.embedding_encoder_depth: 2