README.md

---
license: mit
language:
- en
tags:
- genetics
- LLM
- embeddings
---

# Variant Foundation Embeddings
Here we present the variant level embeddings for large-scale genetic analyis as described in 'Incorporating LLM Embeddings for Variation Across the Human Genome,' based on curated annotations using high quality functional data from FAVOR, ClinVar, and GWAS Catalog. We currently present embeddings using either OpenAI's text-embedding-3-large (3072-dimensional) or Qwen's Qwen3-Embedding-0.6B (1024-dimensional) models. 

Genetic variants are identified with their chromosome, position (hg38 build), reference allele based on UKB coding, alternate allele based on UKB coding, and their respective LLM embeddings. 

Currently we release datasets at the following scales: 

  1. HapMap3 & MEGA (~1.5 million variants, OpenAI GPT-3.5)
  2. UKB Imputed (~90 million variants, OpenAI GPT-3.5)
  3. All FAVOR Variants (~9 billion variants, Qwen3-0.6B)

With more to come shortly. 

### Dataset Schema (OpenAI text-embedding-3-large)

| Field       | Type       | Description |
|-------------|------------|-------------|
| `chrom`     | string     | Chromosome (e.g., `"1"`, `"X"`) |
| `pos`       |string      | Base-pair position (hg38 coordinate system) |
| `ref_UKB`   | string     | Reference allele (A, C, G, T) |
| `alt_UKB`   | string     | Alternate allele (A, C, G, T) |
| `embedding` | list[float]| Embedding vector (dimension 3072, float) |

### Dataset Schema (Qwen qwen3-embedding-0.6B)

| Field       | Type       | Description |
|-------------|------------|-------------|
| `chrom`     | string     | Chromosome (e.g., `"1"`, `"X"`) |
| `pos`       |string      | Base-pair position (hg38 coordinate system) |
| `ref_UKB`   | string     | Reference allele (A, C, G, T) |
| `alt_UKB`   | string     | Alternate allele (A, C, G, T) |
| `embedding` | list[float]| Embedding vector (dimension 1024, float) |