Datasets:
Lal Claude Opus 4.6 commited on
Commit ·
886ffff
1
Parent(s): 9b86426
Add split distributions and fix loading code
Browse files- Add human split distribution (train/valid/test counts)
- Add mouse split distribution (train/valid/test counts)
- Fix repo_type="dataset" missing from hf_hub_download
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
README.md
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# enformer-data
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## Dataset Summary
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This dataset contains the specific genomic intervals used for training, validating, and testing the Enformer model, a deep learning architecture for predicting functional genomic tracks from DNA sequence. The intervals are provided for both human and mouse genomes. As done in the publication, we modified the Basenji2 dataset by extending the input sequence to 196,608
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- **Source Publication:** [Avsec, Ž., et al. "Effective gene expression prediction from sequence by integrating long-range interactions." Nat Methods 18, 1196–1203 (2021).](https://www.nature.com/articles/s41592-021-01252-x)
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- **Genome Builds:**
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| `human_intervals.tsv` | 38,171 | hg38 |
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| `mouse_intervals.tsv` | 33,521 | mm10 |
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## Usage
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```python
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from huggingface_hub import hf_hub_download
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import pandas as pd
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file_path = hf_hub_download(
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df_human = pd.read_csv(file_path, sep='\t')
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file_path = hf_hub_download(
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df_mouse = pd.read_csv(file_path, sep='\t')
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```
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# enformer-data
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## Dataset Summary
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This dataset contains the specific genomic intervals used for training, validating, and testing the Enformer model, a deep learning architecture for predicting functional genomic tracks from DNA sequence. The intervals are provided for both human and mouse genomes. As done in the publication, we modified the Basenji2 dataset by extending the input sequence to 196,608 bp from the original 131,072 bp using the hg38 reference genome.
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- **Source Publication:** [Avsec, Ž., et al. "Effective gene expression prediction from sequence by integrating long-range interactions." Nat Methods 18, 1196–1203 (2021).](https://www.nature.com/articles/s41592-021-01252-x)
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- **Genome Builds:**
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| `human_intervals.tsv` | 38,171 | hg38 |
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| `mouse_intervals.tsv` | 33,521 | mm10 |
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### Data Splits
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**Human (hg38)**
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| Split | Count |
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|-------|-------|
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| train | 34,021 |
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| valid | 2,213 |
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| test | 1,937 |
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**Mouse (mm10)**
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| Split | Count |
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|-------|-------|
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| train | 29,295 |
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| valid | 2,209 |
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| test | 2,017 |
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## Usage
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```python
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from huggingface_hub import hf_hub_download
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import pandas as pd
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file_path = hf_hub_download(
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repo_id="Genentech/enformer-data",
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filename="human_intervals.tsv",
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repo_type="dataset"
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)
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df_human = pd.read_csv(file_path, sep='\t')
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file_path = hf_hub_download(
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repo_id="Genentech/enformer-data",
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filename="mouse_intervals.tsv",
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repo_type="dataset"
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)
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df_mouse = pd.read_csv(file_path, sep='\t')
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```
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