AlphaGenome-50M

MedinaMemorySystems/AlphaGenome-50M

Model Description

AlphaGenome-50M is a state-of-the-art genomic sequence embedding and variant impact prediction model. Fine-tuned from the InstaDeepAI/nucleotide-transformer-v2-50m-multi-species base model, it is specifically designed for non-coding variant analysis and regulatory element classification.

The model leverages the Nucleotide Transformer architecture to capture complex genomic patterns. It uniquely provides Variant Impact Scores (AVI) and facilitates single-variant effect analysis across RNA-seq, DNASE, and ChIP assays. Furthermore, it supports tissue-type ontology resolution (UBERON/CL), saturation mutagenesis window scanning, and seamless extraction of GENCODE v46 coordinates.

Intended Uses

The primary use cases for AlphaGenome-50M include:

• Predicting the functional impact of genetic variants, particularly in non-coding regions.
• Classifying cis-regulatory elements (cCREs).
• Embedding genomic sequences for downstream biological machine learning tasks.
• Analyzing single-variant effects across multiple assay types (RNA-seq, DNASE, ChIP).

Genomic Sequence Representation

Sequences are represented using 6-mer tokenization with a BPE nucleotide vocabulary. The max context length is 1024 tokens. Input strings should be pure DNA sequences consisting of A, T, C, G characters.

Architecture Details

AlphaGenome-50M is based on the Nucleotide Transformer v2 architecture:

• Parameters: 50M
• Layers: 12
• Attention Heads: 12
• Hidden Dimension: 512
• Max Context Length: 1024 tokens
• Tokenization: 6-mer tokenization with a BPE nucleotide vocabulary

System Prompt / Prompting Template

While AlphaGenome-50M is a sequence feature extraction model rather than an instruction-tuned LLM, it requires specific input formatting. Do not use special control tokens like <s> or [CLS] manually unless bypassing the tokenizer. Pass the raw nucleotide string.

Sequence format: <DNA_STRING>
Example: ATGCGTACGTTAGCTAGCTAGCTAGCTAGCTAGC

Quantization & Inference Speed Table

Benchmark Results

AlphaGenome-50M was evaluated on several genomic benchmarks:

Python Usage Example (Transformers & Biopython)

You can use this model with the transformers library to encode DNA sequences and integrate with Biopython to parse FASTA files:

from transformers import AutoTokenizer, AutoModel
from Bio import SeqIO
import torch

# Load model and tokenizer
model_name = "MedinaMemorySystems/AlphaGenome-50M"
tokenizer = AutoTokenizer.from_pretrained(model_name)
model = AutoModel.from_pretrained(model_name)

# Parse a sequence using Biopython
record = next(SeqIO.parse("example.fasta", "fasta"))
dna_sequence = str(record.seq)

# Encode the DNA sequence
inputs = tokenizer(dna_sequence, return_tensors="pt", truncation=True, max_length=1024)

with torch.no_grad():
    outputs = model(**inputs)

# Extract sequence embeddings
embeddings = outputs.last_hidden_state
print(f"Embedding shape: {embeddings.shape}")

Ethics, Biosafety Note & Limitations

• Biosafety Note: This model provides variant impact predictions which are strictly for research purposes. It must not be used to make independent clinical decisions or guide human diagnostic processes without rigorous experimental validation and expert review.
• The model's predictions are specific to the GRCh38 human reference genome context.
• While it performs well on regulatory elements, performance on highly repetitive regions may be degraded due to 6-mer tokenization.

Citation

@misc{medinamemorysystems2026alphagenome,
  title={AlphaGenome-50M: Genomic Sequence Embedding and Variant Impact Prediction},
  author={MedinaMemorySystems},
  year={2026},
  publisher={Hugging Face}
}