Caleb Ellington commited on
Commit
8b87d57
1 Parent(s): b7a40ba

Update paths

Browse files
Files changed (2) hide show
  1. README.md +2 -2
  2. config.yaml +5 -5
README.md CHANGED
@@ -2,7 +2,7 @@
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  datasets:
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  - genbio-ai/rna-downstream-tasks
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  base_model:
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- - genbio-ai/rnafm-1.6b
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  ---
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  LoRA fine-tuned checkpoint for splice site prediction.
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@@ -12,7 +12,7 @@ LoRA fine-tuned checkpoint for splice site prediction.
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  from huggingface_hub import snapshot_download
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  from pathlib import Path
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- model_name = "genbio-ai/rnafm-1.6b-csp-acceptor-ckpt"
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  genbio_models_path = Path.home().joinpath('genbio_models', model_name)
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  genbio_models_path.mkdir(parents=True, exist_ok=True)
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  snapshot_download(repo_id=model_name, local_dir=genbio_models_path)
 
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  datasets:
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  - genbio-ai/rna-downstream-tasks
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  base_model:
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+ - genbio-ai/AIDO.RNA-1.6B
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  ---
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  LoRA fine-tuned checkpoint for splice site prediction.
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  from huggingface_hub import snapshot_download
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  from pathlib import Path
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+ model_name = "genbio-ai/AIDO.RNA-1.6B-csp-acceptor"
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  genbio_models_path = Path.home().joinpath('genbio_models', model_name)
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  genbio_models_path.mkdir(parents=True, exist_ok=True)
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  snapshot_download(repo_id=model_name, local_dir=genbio_models_path)
config.yaml CHANGED
@@ -36,8 +36,8 @@ trainer:
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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: modelgenerator/logs
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  version: null
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  offline: false
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  dir: null
@@ -75,7 +75,7 @@ trainer:
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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: modelgenerator/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
@@ -134,12 +134,12 @@ trainer:
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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: modelgenerator/logs
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  model:
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  class_path: modelgenerator.tasks.SequenceClassification
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  init_args:
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  backbone:
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- class_path: modelgenerator.backbones.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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  logger:
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  class_path: lightning.pytorch.loggers.WandbLogger
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  init_args:
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+ name: csp_acceptor_AIDO.RNA-1.6B
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+ save_dir: logs
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  version: null
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  offline: false
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  dir: null
 
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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: logs/rna_tasks/csp_acceptor_AIDO.RNA-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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  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: logs
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  model:
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  class_path: modelgenerator.tasks.SequenceClassification
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  init_args:
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  backbone:
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+ class_path: modelgenerator.backbones.aido_rna_1b600m
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  init_args:
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  from_scratch: false
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  max_length: 1024