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Add Nucleotide Transformer notebooks and restructure notebook list #24669

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Jul 5, 2023
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Add Nucleotide Transformer notebooks and restructure notebook list #24669

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Add Nucleotide Transformer notebooks and restructure lists
Rocketknight1 Jul 5, 2023
385bb69
Add missing linebreak!
Rocketknight1 Jul 5, 2023
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12 changes: 10 additions & 2 deletions notebooks/README.md
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Expand Up @@ -80,12 +80,20 @@ You can open any page of the documentation as a notebook in Colab (there is a bu
| [How to fine-tune a speech recognition model in any language](https://github.com/huggingface/notebooks/blob/main/examples/multi_lingual_speech_recognition.ipynb)| Show how to preprocess the data and fine-tune a multi-lingually pretrained speech model on Common Voice | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/multi_lingual_speech_recognition.ipynb)| [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/multi_lingual_speech_recognition.ipynb)|
| [How to fine-tune a model on audio classification](https://github.com/huggingface/notebooks/blob/main/examples/audio_classification.ipynb)| Show how to preprocess the data and fine-tune a pretrained Speech model on Keyword Spotting | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/audio_classification.ipynb)| [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/audio_classification.ipynb)|

#### Other modalities[[pytorch-other]]
#### Biological Sequences[[pytorch-bio]]

| Notebook | Description | | |
|:----------|:----------------------------------------------------------------------------------------|:-------------|------:|
| [How to fine-tune a pre-trained protein model](https://github.com/huggingface/notebooks/blob/main/examples/protein_language_modeling.ipynb) | See how to tokenize proteins and fine-tune a large pre-trained protein "language" model | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/protein_language_modeling.ipynb) | [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/protein_language_modeling.ipynb) |
| [How to generate protein folds](https://github.com/huggingface/notebooks/blob/main/examples/protein_folding.ipynb) | See how to go from protein sequence to a full protein model and PDB file | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/protein_folding.ipynb) | [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/protein_folding.ipynb) |
| [How to fine-tune a Nucleotide Transformer model](https://github.com/huggingface/notebooks/blob/main/examples/nucleotide_transformer_dna_sequence_modelling.ipynb) | See how to tokenize DNA and fine-tune a large pre-trained DNA "language" model | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/nucleotide_transformer_dna_sequence_modelling.ipynb) | [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/nucleotide_transformer_dna_sequence_modelling.ipynb) |
| [Fine-tune a Nucleotide Transformer model with LoRA](https://github.com/huggingface/notebooks/blob/main/examples/nucleotide_transformer_dna_sequence_modelling_with_peft.ipynb) | Train even larger DNA models in a memory-efficient way | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/nucleotide_transformer_dna_sequence_modelling_with_peft.ipynb) | [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/nucleotide_transformer_dna_sequence_modelling_with_peft.ipynb) |


#### Other modalities[[pytorch-other]]

| Notebook | Description | | |
|:----------|:----------------------------------------------------------------------------------------|:-------------|------:|
| [Probabilistic Time Series Forecasting](https://github.com/huggingface/notebooks/blob/main/examples/time-series-transformers.ipynb) | See how to train Time Series Transformer on a custom dataset | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/time-series-transformers.ipynb) | [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/time-series-transformers.ipynb) |

#### Utility notebooks[[pytorch-utility]]
Expand Down Expand Up @@ -118,7 +126,7 @@ You can open any page of the documentation as a notebook in Colab (there is a bu
| [How to fine-tune a model on image classification](https://github.com/huggingface/notebooks/blob/main/examples/image_classification-tf.ipynb) | Show how to preprocess the data and fine-tune any pretrained Vision model on Image Classification | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/image_classification-tf.ipynb)| [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/image_classification-tf.ipynb)|
| [How to fine-tune a SegFormer model on semantic segmentation](https://github.com/huggingface/notebooks/blob/main/examples/semantic_segmentation-tf.ipynb) | Show how to preprocess the data and fine-tune a pretrained SegFormer model on Semantic Segmentation | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/semantic_segmentation-tf.ipynb)| [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/semantic_segmentation-tf.ipynb)|

#### Other modalities[[tensorflow-other]]
#### Biological Sequences[[tensorflow-bio]]

| Notebook | Description | | |
|:----------|:-------------|:-------------|------:|
Expand Down