Caleb Ellington
commited on
Commit
·
beaed13
1
Parent(s):
49d76bc
update with major refactor
Browse files- README.md +2 -2
- config.yaml +6 -6
README.md
CHANGED
@@ -20,12 +20,12 @@ snapshot_download(repo_id=model_name, local_dir=genbio_models_path)
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### Load model for inference
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```python
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import torch
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-
from
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ckpt_path = genbio_models_path.joinpath('model.ckpt')
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model = TokenClassification.load_from_checkpoint(ckpt_path, strict_loading=False).eval()
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-
collated_batch = model.
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logits = model(collated_batch)
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print(logits)
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print(torch.argmax(logits, dim=-1))
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### Load model for inference
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```python
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import torch
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+
from modelgenerator.tasks import TokenClassification
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ckpt_path = genbio_models_path.joinpath('model.ckpt')
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model = TokenClassification.load_from_checkpoint(ckpt_path, strict_loading=False).eval()
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+
collated_batch = model.transform({"sequences": ["ACGT", "AGCT"]})
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logits = model(collated_batch)
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print(logits)
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print(torch.argmax(logits, dim=-1))
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config.yaml
CHANGED
@@ -77,7 +77,7 @@ 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:
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filename: best_val:{epoch}-{val_accuracy:.3f}
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monitor: val_accuracy
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verbose: false
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@@ -138,10 +138,10 @@ trainer:
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reload_dataloaders_every_n_epochs: 0
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default_root_dir: null
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model:
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-
class_path:
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init_args:
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adapter:
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-
class_path:
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init_args:
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hidden_sizes:
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- 128
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@@ -149,7 +149,7 @@ model:
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dropout: 0.1
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dropout_in_middle: true
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backbone:
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class_path:
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init_args:
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from_scratch: false
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max_length: 512
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@@ -187,7 +187,7 @@ model:
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differentiable: false
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fused: null
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lr_scheduler:
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class_path:
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init_args:
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warmup_ratio: 0.05
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num_warmup_steps: null
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@@ -197,7 +197,7 @@ model:
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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:
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init_args:
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path: biomap-research/ssp_q3
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batch_size: 1
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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/xtrimo_benchmark_gbft_reproduction/ssp_proteinmoe_16B
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filename: best_val:{epoch}-{val_accuracy:.3f}
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monitor: val_accuracy
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verbose: false
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reload_dataloaders_every_n_epochs: 0
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default_root_dir: null
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model:
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class_path: modelgenerator.tasks.TokenClassification
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init_args:
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adapter:
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class_path: modelgenerator.adapters.MLPAdapter
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init_args:
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hidden_sizes:
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- 128
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dropout: 0.1
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dropout_in_middle: true
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backbone:
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class_path: modelgenerator.backbones.proteinfm
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init_args:
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from_scratch: false
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max_length: 512
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differentiable: false
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fused: null
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lr_scheduler:
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class_path: modelgenerator.lr_schedulers.CosineWithWarmup
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init_args:
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warmup_ratio: 0.05
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num_warmup_steps: null
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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: modelgenerator.data.SspQ3
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init_args:
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path: biomap-research/ssp_q3
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batch_size: 1
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