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README.md

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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.