Datasets:
File size: 3,166 Bytes
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license: cc-by-4.0
task_categories:
- other
tags:
- genomics
- dna
- embeddings
- alphagenome
- hg38
- grch38
pretty_name: ALPHAGenome hg38 Embeddings
size_categories:
- 10K<n<100K
---
# ALPHAGenome hg38 Embeddings
Pre-computed **ALPHAGenome** DNA foundation model embeddings for the entire human genome (hg38 / GRCh38).
The human genome is divided into **~22,000 non-overlapping 131 KB bins**. Each bin's DNA sequence is embedded into a **3,072-dimensional latent space** using the ALPHAGenome foundation model.
## Companion project
These embeddings power the **ALPHAGenome UMAP Explorer** — an interactive browser visualization of latent relationships between genomic regions:
**→ [GitHub: DNAEmbeddings](https://github.com/lagosproject/DNAEmbeddings)**
**→ [Live Demo](https://lagosproject.github.io/DNAEmbeddings/)**
Scripts to download this dataset and re-run the UMAP pipeline are included in that repo.
## Dataset structure
```
data/
chr1_embeddings.npy # float32 array, shape (N, 3072)
chr1_metadata.csv # columns: chrom, start, end
chr2_embeddings.npy
chr2_metadata.csv
... # one pair per chromosome (chr1–22, chrX, chrY)
```
Each `.npy` file and its paired `.csv` share the same row order — row `i` in the embeddings corresponds to row `i` in the metadata.
## Quick usage
```python
from huggingface_hub import hf_hub_download
import numpy as np
import pandas as pd
# Download a single chromosome
emb_path = hf_hub_download("lagosproject/ALPHAGenome-Embeddings", "data/chr1_embeddings.npy", repo_type="dataset")
meta_path = hf_hub_download("lagosproject/ALPHAGenome-Embeddings", "data/chr1_metadata.csv", repo_type="dataset")
embeddings = np.load(emb_path) # (1750, 3072)
metadata = pd.read_csv(meta_path) # chrom | start | end
```
Or download everything at once (≈312 MB):
```python
from huggingface_hub import snapshot_download
snapshot_download("lagosproject/ALPHAGenome-Embeddings", repo_type="dataset", local_dir="res/")
```
## Statistics
| Chromosome | Windows | Embedding shape |
|---|---|---|
| chr1 | 1,750 | (1750, 3072) |
| chr2 | 1,829 | (1829, 3072) |
| chr3 | 1,509 | (1509, 3072) |
| chr4 | 1,439 | (1439, 3072) |
| chr5 | 1,379 | (1379, 3072) |
| chr6 | 1,294 | (1294, 3072) |
| chr7 | 1,206 | (1206, 3072) |
| chr8 | 1,100 | (1100, 3072) |
| chr9 | 915 | (915, 3072) |
| chr10 | 1,013 | (1013, 3072) |
| chr11 | 1,022 | (1022, 3072) |
| chr12 | 1,012 | (1012, 3072) |
| chr13 | 743 | (743, 3072) |
| chr14 | 687 | (687, 3072) |
| chr15 | 640 | (640, 3072) |
| chr16 | 619 | (619, 3072) |
| chr17 | 627 | (627, 3072) |
| chr18 | 609 | (609, 3072) |
| chr19 | 444 | (444, 3072) |
| chr20 | 482 | (482, 3072) |
| chr21 | 288 | (288, 3072) |
| chr22 | 285 | (285, 3072) |
| chrX | 1,170 | (1170, 3072) |
| chrY | 191 | (191, 3072) |
| **Total** | **22,253** | **3,072-dim** |
## Data sources
| Source | Usage |
|--------|-------|
| **ALPHAGenome** | DNA sequence embeddings (3,072-dim per 131 KB bin) |
| **UCSC hg38** | Reference genome coordinates |
## License
CC BY 4.0 — free to use for research and educational purposes with attribution.
|