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--- |
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task_categories: |
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- text-generation |
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language: |
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- en |
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tags: |
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- proteins |
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- biology |
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- uniprot |
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size_categories: |
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- 100K<n<1M |
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--- |
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# Dataset Card for PAIR |
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This dataset contains all the text annotations we collected and parsed from UniProt Swiss-Prot February 2023 and used to train PAIR -- a simple framework to finetune protein language models using text annotations. You can read more details about PAIR here: https://www.biorxiv.org/content/10.1101/2024.07.22.604688v2.abstract |
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## Dataset Details |
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### Dataset Description |
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<!-- Provide a longer summary of what this dataset is. --> |
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### Dataset Sources |
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- **Repository:** (coming soon!) |
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- **Paper:** https://www.biorxiv.org/content/10.1101/2024.07.22.604688v2.abstract |
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- **Model checkpoints:** https://huggingface.co/h4duan |
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## Uses |
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<!-- Address questions around how the dataset is intended to be used. --> |
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### Example usage |
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``` |
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from datasets import load_dataset |
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``` |
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### Out-of-Scope Use |
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<!-- This section addresses misuse, malicious use, and uses that the dataset will not work well for. --> |
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This dataset contains text annotations from Swiss-Prot February 2023; our models were trained on all of them. Please be mindful about potential data leakage from time splits/identical protein sequences on any downstream tasks in your setup. |
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## Dataset Structure |
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<!-- This section provides a description of the dataset fields, and additional information about the dataset structure such as criteria used to create the splits, relationships between data points, etc. --> |
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[More Information Needed] |
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## Dataset Creation |
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### Source Data |
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This data was collected from the Swiss-Prot checkpoint from February 2023, found here: XXX |
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#### Data Collection and Processing |
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<!-- This section describes the data collection and processing process such as data selection criteria, filtering and normalization methods, tools and libraries used, etc. --> |
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[More Information Needed] |
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#### Who are the source data producers? |
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<!-- This section describes the people or systems who originally created the data. It should also include self-reported demographic or identity information for the source data creators if this information is available. --> |
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[More Information Needed] |
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### Annotations |
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I don't think we did any annotations for parsing only for loading (double check) |
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#### Personal and Sensitive Information |
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To our knowledge, this dataset does not contain any private information. |
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## Bias, Risks, and Limitations |
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In general, the dataset is highly imbalanced in terms of how many and what protein sequences in Swiss-Prot have an annotation for a given annotation type. This dataset is sparse |
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## Citation |
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**BibTeX:** |
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``` |
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@article{duan2024boosting, |
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title={Boosting the Predictive Power of Protein Representations with a Corpus of Text Annotations}, |
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author={Duan, Haonan and Skreta, Marta and Cotta, Leonardo and Rajaonson, Ella Miray and Dhawan, Nikita and Aspuru-Guzik, Alán and Maddison, Chris J}, |
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journal={bioRxiv}, |
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pages={2024--07}, |
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year={2024}, |
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publisher={Cold Spring Harbor Laboratory} |
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} |
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``` |
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## Dataset Card Authors |
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[More Information Needed] |
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## Dataset Card Contact |
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For any issues with this dataset, please contact `[email protected]` or `[email protected]` |
