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initial upload

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  1. model.ckpt +3 -0
  2. splice_site_prediction.yaml +218 -0
model.ckpt ADDED
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:76bfefcc651b4e71e3272a0f343d7c48d7ee67a42ac8f7f521d4290fb35ffc9b
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+ size 114338496
splice_site_prediction.yaml ADDED
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+ # lightning.pytorch==2.4.0
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+ seed_everything: 42
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+ trainer:
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+ accelerator: auto
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+ strategy:
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+ 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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+ 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:
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+ class_path: genbio_finetune.tasks.SequenceClassification
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+ init_args:
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+ backbone:
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+ 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:
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+ - 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:
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+ 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
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+ - 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:
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+ class_path: genbio_finetune.data.SpliceSitePrediction
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+ init_args:
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+ path: genbio-ai/rna-downstream-tasks
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+ config_name: splice_site_acceptor
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+ 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