Datasets:
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README.md
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- split: test
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path: "complex_traits_all/test.parquet"
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---
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# TraitGym
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Benchmarking DNA Sequence Models for Causal Regulatory Variant Prediction in Human Genetics
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🏆 Leaderboard: https://huggingface.co/spaces/songlab/TraitGym-leaderboard
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## Quick start
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- Load a dataset
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```python
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from datasets import load_dataset
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```
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- Example notebook to run variant effect prediction with a gLM, runs in 5 min on Google Colab: `TraitGym.ipynb` [](https://colab.research.google.com/github/songlab-cal/TraitGym/blob/main/TraitGym.ipynb)
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## Resources (https://huggingface.co/datasets/songlab/TraitGym)
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- Datasets: `{dataset}/test.parquet`
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- Subsets: `{dataset}/subset/{subset}.parquet`
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- Features: `{dataset}/features/{features}.parquet`
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- `AUPRC_by_chrom_weighted_average` (main metric)
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- `AUPRC`
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## Code (https://github.com/songlab-cal/TraitGym)
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- Tries to follow [recommended Snakemake structure](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html)
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- GPN-Promoter code is in [the main GPN repo](https://github.com/songlab-cal/gpn)
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- split: test
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path: "complex_traits_all/test.parquet"
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---
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# 🧬 TraitGym
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Benchmarking DNA Sequence Models for Causal Regulatory Variant Prediction in Human Genetics
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🏆 Leaderboard: https://huggingface.co/spaces/songlab/TraitGym-leaderboard
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## ⚡️ Quick start
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- Load a dataset
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```python
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from datasets import load_dataset
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```
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- Example notebook to run variant effect prediction with a gLM, runs in 5 min on Google Colab: `TraitGym.ipynb` [](https://colab.research.google.com/github/songlab-cal/TraitGym/blob/main/TraitGym.ipynb)
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## 🤗 Resources (https://huggingface.co/datasets/songlab/TraitGym)
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- Datasets: `{dataset}/test.parquet`
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- Subsets: `{dataset}/subset/{subset}.parquet`
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- Features: `{dataset}/features/{features}.parquet`
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- `AUPRC_by_chrom_weighted_average` (main metric)
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- `AUPRC`
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## 💻 Code (https://github.com/songlab-cal/TraitGym)
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- Tries to follow [recommended Snakemake structure](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html)
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- GPN-Promoter code is in [the main GPN repo](https://github.com/songlab-cal/gpn)
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