Update README.md
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README.md
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@@ -7,7 +7,7 @@ AIDO.RNA 650M is an RNA foundation model trained on 42 million non-coding RNA se
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#### Embedding
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```python
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from genbio_finetune.tasks import Embed
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model = Embed.from_config({"model.backbone": "
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collated_batch = model.collate({"sequences": ["ACGT", "AGCT"]})
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embedding = model(collated_batch)
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print(embedding.shape)
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@@ -17,7 +17,7 @@ print(embedding)
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```python
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import torch
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from genbio_finetune.tasks import SequenceClassification
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model = SequenceClassification.from_config({"model.backbone": "
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collated_batch = model.collate({"sequences": ["ACGT", "AGCT"]})
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logits = model(collated_batch)
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print(logits)
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@@ -27,7 +27,7 @@ print(torch.argmax(logits, dim=-1))
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```python
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import torch
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from genbio_finetune.tasks import TokenClassification
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model = TokenClassification.from_config({"model.backbone": "
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collated_batch = model.collate({"sequences": ["ACGT", "AGCT"]})
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logits = model(collated_batch)
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print(logits)
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#### Regression
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```python
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from genbio_finetune.tasks import SequenceRegression
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model = SequenceRegression.from_config({"model.backbone": "
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collated_batch = model.collate({"sequences": ["ACGT", "AGCT"]})
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logits = model(collated_batch)
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print(logits)
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```
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#### Or use our one-liner CLI to finetune or evaluate any of the above!
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```
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gbft fit --model SequenceClassification --model.backbone
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gbft test --model SequenceClassification --model.backbone
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```
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For more information, visit: [Model Generator](https://github.com/genbio-ai/modelgenerator)
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#### Embedding
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```python
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from genbio_finetune.tasks import Embed
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model = Embed.from_config({"model.backbone": "rnafm_650m"}).eval()
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collated_batch = model.collate({"sequences": ["ACGT", "AGCT"]})
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embedding = model(collated_batch)
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print(embedding.shape)
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```python
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import torch
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from genbio_finetune.tasks import SequenceClassification
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model = SequenceClassification.from_config({"model.backbone": "rnafm_650m", "model.n_classes": 2}).eval()
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collated_batch = model.collate({"sequences": ["ACGT", "AGCT"]})
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logits = model(collated_batch)
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print(logits)
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```python
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import torch
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from genbio_finetune.tasks import TokenClassification
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model = TokenClassification.from_config({"model.backbone": "rnafm_650m", "model.n_classes": 3}).eval()
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collated_batch = model.collate({"sequences": ["ACGT", "AGCT"]})
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logits = model(collated_batch)
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print(logits)
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#### Regression
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```python
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from genbio_finetune.tasks import SequenceRegression
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model = SequenceRegression.from_config({"model.backbone": "rnafm_650m"}).eval()
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collated_batch = model.collate({"sequences": ["ACGT", "AGCT"]})
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logits = model(collated_batch)
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print(logits)
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```
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#### Or use our one-liner CLI to finetune or evaluate any of the above!
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```
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gbft fit --model SequenceClassification --model.backbone rnafm_650m --data SequenceClassification --data.path <hf_or_local_path_to_your_dataset>
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gbft test --model SequenceClassification --model.backbone rnafm_650m --data SequenceClassification --data.path <hf_or_local_path_to_your_dataset>
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```
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For more information, visit: [Model Generator](https://github.com/genbio-ai/modelgenerator)
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