create config file (#1)
Browse files- create config file (4f247a7e70cccf28d32bd861ae2956b3c6d87209)
Co-authored-by: Ryan Keivanfar <[email protected]>
- configs/config.yaml +57 -0
configs/config.yaml
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# ----------------------------------------------------
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# Full Dataset Run Config
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# ----------------------------------------------------
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experiment_name: 'MorganFP_full_dataset_run'
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data:
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regions_csv_path: "data/Enformer_genomic_regions_TSSCenteredGenes_FixedOverlapRemoval_subset500_priorityCustom_parquetFiltered.csv" # Ensure this is correct
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regions_gene_col: 'gene_name'
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regions_chr_col: 'seqnames'
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regions_start_col: 'starts'
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regions_end_col: 'ends'
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pbulk_parquet_path: "/home/ubuntu/pseudoBulk_celllineXdrug_8Cellline_27Drugs_1Dosage_includeZero.parquet" # Ensure this is correct
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pbulk_gene_col: 'gene_id'
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pbulk_drug_col: 'drug_id'
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pbulk_dose_col: 'drug_dose'
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pbulk_expr_col: 'expression'
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pbulk_cell_line_col: 'cell_line'
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drug_meta_csv_path: "data/drug_metadata.csv"
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drug_meta_id_col: 'drug'
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fasta_file_path: "/home/ubuntu/data/hg38.fa" # Ensure this is correct for your full run
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enformer_input_seq_length: 49152
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morgan_fp_radius: 2
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morgan_fp_nbits: 2048
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model:
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enformer_model_name: 'EleutherAI/enformer-official-rough'
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morgan_fingerprint_dim: 2048
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learning_rate: 5.0e-6
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weight_decay: 0.01
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training:
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batch_size: 16 # Increased for full run
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max_epochs: 100 # Increased for full run
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precision: 'bf16-mixed'
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deterministic: True
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seed: 42
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gradient_clip_val: 0.05
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accumulate_grad_batches: 1
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gpus: -1 # Use all available GPUs
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strategy: 'ddp_find_unused_parameters_true' # Suitable for multi-GPU
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logging:
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wandb_project: 'tahoeformer' # Specific project for these tests
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# wandb_entity: 'your_wandb_username_or_team'
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save_dir: 'outputs/morgan_full_dataset_runs' # Updated save directory
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# checkpoint_monitor_metric: 'validation_pearson_epoch' # default
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# checkpoint_monitor_mode: 'max' # default
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# early_stopping_metric: 'validation_pearson_epoch' # default
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# early_stopping_mode: 'max' # default
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early_stopping_patience: 30 # Increased patience
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use_wandb: True
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validate_before_train: True
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delete_checkpoint_after_run: False
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# check_val_every_n_epoch: 1 # default
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