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seed_everything: 42 |
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trainer: |
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accelerator: auto |
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strategy: |
|
class_path: lightning.pytorch.strategies.DDPStrategy |
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init_args: |
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accelerator: null |
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parallel_devices: null |
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cluster_environment: null |
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checkpoint_io: null |
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precision_plugin: null |
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ddp_comm_state: null |
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ddp_comm_hook: null |
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ddp_comm_wrapper: null |
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model_averaging_period: null |
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process_group_backend: null |
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timeout: 0:30:00 |
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start_method: popen |
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output_device: null |
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dim: 0 |
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broadcast_buffers: true |
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process_group: null |
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bucket_cap_mb: 25 |
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find_unused_parameters: false |
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check_reduction: false |
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gradient_as_bucket_view: false |
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static_graph: false |
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delay_all_reduce_named_params: null |
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param_to_hook_all_reduce: null |
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mixed_precision: null |
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device_mesh: null |
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devices: auto |
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num_nodes: 1 |
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precision: 32 |
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logger: |
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class_path: lightning.pytorch.loggers.WandbLogger |
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init_args: |
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name: csp_acceptor_rnafm_1.6B |
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save_dir: genbio_finetune/logs |
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version: null |
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offline: false |
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dir: null |
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id: null |
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anonymous: null |
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project: rna_tasks |
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log_model: false |
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experiment: null |
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prefix: '' |
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checkpoint_name: null |
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job_type: null |
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config: null |
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entity: null |
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reinit: null |
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tags: null |
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group: null |
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notes: null |
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magic: null |
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config_exclude_keys: null |
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config_include_keys: null |
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mode: null |
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allow_val_change: null |
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resume: null |
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force: null |
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tensorboard: null |
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sync_tensorboard: null |
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monitor_gym: null |
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save_code: true |
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settings: null |
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callbacks: |
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- class_path: lightning.pytorch.callbacks.LearningRateMonitor |
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init_args: |
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logging_interval: step |
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log_momentum: false |
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log_weight_decay: false |
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- class_path: lightning.pytorch.callbacks.ModelCheckpoint |
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init_args: |
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dirpath: genbio_finetune/logs/rna_tasks/csp_acceptor_rnafm_1.6B |
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filename: best_val:{epoch}-{val_f1:.3f} |
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monitor: val_f1 |
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verbose: false |
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save_last: null |
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save_top_k: 1 |
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save_weights_only: false |
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mode: max |
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auto_insert_metric_name: true |
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every_n_train_steps: null |
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train_time_interval: null |
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every_n_epochs: 1 |
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save_on_train_epoch_end: null |
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enable_version_counter: true |
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fast_dev_run: false |
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max_epochs: 10 |
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min_epochs: null |
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max_steps: -1 |
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min_steps: null |
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max_time: null |
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limit_train_batches: null |
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limit_val_batches: null |
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limit_test_batches: null |
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limit_predict_batches: null |
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overfit_batches: 0.0 |
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val_check_interval: null |
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check_val_every_n_epoch: 1 |
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num_sanity_val_steps: null |
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log_every_n_steps: 50 |
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enable_checkpointing: null |
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enable_progress_bar: null |
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enable_model_summary: null |
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accumulate_grad_batches: 1 |
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gradient_clip_val: 1 |
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gradient_clip_algorithm: null |
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deterministic: null |
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benchmark: null |
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inference_mode: true |
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use_distributed_sampler: true |
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profiler: |
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class_path: lightning.pytorch.profilers.PyTorchProfiler |
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init_args: |
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dirpath: null |
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filename: null |
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group_by_input_shapes: false |
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emit_nvtx: false |
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export_to_chrome: true |
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row_limit: 20 |
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sort_by_key: null |
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record_module_names: true |
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table_kwargs: null |
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record_shapes: false |
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dict_kwargs: |
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profile_memory: true |
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detect_anomaly: false |
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barebones: false |
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plugins: null |
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sync_batchnorm: false |
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reload_dataloaders_every_n_epochs: 0 |
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default_root_dir: genbio_finetune/logs |
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model: |
|
class_path: genbio_finetune.tasks.SequenceClassification |
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init_args: |
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backbone: |
|
class_path: genbio_finetune.models.rnafm |
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init_args: |
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from_scratch: false |
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max_length: 1024 |
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use_peft: true |
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save_peft_only: true |
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lora_r: 32 |
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lora_alpha: 64 |
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lora_dropout: 0.1 |
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lora_target_modules: |
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- query |
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- value |
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config_overwrites: |
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hidden_dropout_prob: 0.1 |
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attention_probs_dropout_prob: 0.1 |
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model_init_args: null |
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adapter: |
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class_path: genbio_finetune.models.MLPPoolAdapter |
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init_args: |
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pooling: cls_pooling |
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hidden_sizes: |
|
- 512 |
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- 128 |
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bias: true |
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dropout: 0.1 |
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dropout_in_middle: false |
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n_classes: 2 |
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multilabel: false |
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optimizer: |
|
class_path: torch.optim.AdamW |
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init_args: |
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lr: 0.00025 |
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betas: |
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- 0.9 |
|
- 0.999 |
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eps: 1.0e-08 |
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weight_decay: 0.01 |
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amsgrad: false |
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maximize: false |
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foreach: null |
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capturable: false |
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differentiable: false |
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fused: null |
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lr_scheduler: |
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class_path: genbio_finetune.lr_schedulers.LinearWithWarmup |
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init_args: |
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warmup_ratio: 0.01 |
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num_warmup_steps: null |
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last_epoch: -1 |
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verbose: deprecated |
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use_legacy_adapter: false |
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strict_loading: true |
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reset_optimizer_states: false |
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data: |
|
class_path: genbio_finetune.data.SpliceSitePrediction |
|
init_args: |
|
path: genbio-ai/rna-downstream-tasks |
|
config_name: splice_site_acceptor |
|
test_split_name: test_danio |
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class_filter: null |
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train_split_files: null |
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test_split_files: null |
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valid_split_files: null |
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test_split_size: 0 |
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valid_split_size: 0 |
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random_seed: 42 |
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batch_size: 16 |
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shuffle: true |
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sampler: null |
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num_workers: 0 |
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pin_memory: true |
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persistent_workers: false |
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cv_num_folds: 1 |
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cv_test_fold_id: 0 |
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cv_enable_val_fold: true |
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cv_fold_id_col: null |
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ckpt_path: null |
|
|
