Update README.md

README.md

@@ -23,4 +23,50 @@ configs:
   - split: test
     path: "complex_traits_all/test.parquet"
 ---
-# TraitGym
+# TraitGym
+Benchmarking DNA Sequence Models for Causal Regulatory Variant Prediction in Human Genetics
+
+## Quick start
+- Load a dataset
+    ```python
+    from datasets import load_dataset
+    
+    dataset = load_dataset("songlab/TraitGym", "mendelian_traits", split="test")
+    ```
+- Example notebook to run variant effect prediction with a gLM, runs in 5 min on Google Colab: `TraitGym.ipynb` [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/songlab-cal/TraitGym/blob/main/TraitGym.ipynb)
+
+## Resources (https://huggingface.co/datasets/songlab/TraitGym)
+- Datasets: `{dataset}/test.parquet`
+- Subsets: `{dataset}/subset/{subset}.parquet`
+- Features: `{dataset}/features/{features}.parquet`
+- Predictions: `{dataset}/preds/{subset}/{model}.parquet`
+- Metrics: `{dataset}/{metric}/{subset}/{model}.csv`
+
+`dataset` examples (`load_dataset` config name):
+- `mendelian_traits_matched_9` (`mendelian_traits`)
+- `complex_traits_matched_9` (`complex_traits`)
+- `mendelian_traits_all` (`mendelian_traits_full`)
+- `complex_traits_all` (`complex_traits_full`)
+
+`subset` examples:
+- `all` (default)
+- `3_prime_UTR_variant`
+- `disease`
+- `BMI`
+
+`features` examples:
+- `GPN-MSA_LLR`
+- `GPN-MSA_InnerProducts`
+- `Borzoi_L2`
+
+`model` examples:
+-  `GPN-MSA_LLR.minus.score`
+-  `GPN-MSA.LogisticRegression.chrom`
+-  `CADD+GPN-MSA+Borzoi.LogisticRegression.chrom`
+
+`metric` examples:
+- `AUPRC_by_chrom_weighted_average` (main metric)
+- `AUPRC`
+
+## Code (https://github.com/songlab-cal/TraitGym)
+- Tries to follow [recommended Snakemake structure](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html)