OncoScope Cancer Genomics Analysis Model

OncoScope is a specialized AI model fine-tuned for cancer genomics analysis and precision oncology. Built on Google's Gemma 3n architecture, this model provides expert-level analysis of cancer mutations, risk assessments, and therapeutic recommendations while maintaining complete privacy through on-device inference.

Model Details

Base Model: Google Gemma 3n 2B E4B Chat IT
Parameters: 6.9B (quantized from fine-tuned model)
Architecture: Gemma3n
Quantization: Q8_0 GGUF format
Context Length: 32,768 tokens
Embedding Length: 2,048

Key Features

Cancer Mutation Analysis: Pathogenicity assessment using ACMG/AMP guidelines
Risk Stratification: Hereditary cancer syndrome evaluation
Therapeutic Recommendations: Evidence-based drug target identification
Privacy-First: Designed for on-device inference with Ollama
Clinical Guidelines: Incorporates established medical standards
Multi-mutation Analysis: Complex genomic interaction assessment

Training Data

The model was fine-tuned on a curated dataset of 5,998 cancer genomics examples from:

ClinVar: Clinical variant database
COSMIC Top 50: Cancer mutation signatures
Expert-curated: Clinical oncology cases

Usage

With Ollama

Download the model files:
- oncoscope-gemma-3n-merged.Q8_0.gguf (6.8GB)
- Modelfile
Create the model:
```
ollama create oncoscope -f Modelfile
```

Run inference:

ollama run oncoscope "Analyze the clinical significance of BRCA1 c.5266dupC mutation"

Example Usage

ollama run oncoscope "Patient: 45-year-old female with family history of breast cancer. 
Mutation: BRCA1 c.68_69delAG (p.Glu23ValfsTer17). 
Please provide pathogenicity assessment and recommendations."

Example Response:

{
  "mutation_analysis": {
    "gene": "BRCA1",
    "variant": "c.68_69delAG",
    "protein_change": "p.Glu23ValfsTer17",
    "pathogenicity": "Pathogenic",
    "confidence_score": 0.95,
    "acmg_classification": "PVS1, PM2, PP3"
  },
  "clinical_significance": {
    "cancer_risk": "High",
    "associated_cancers": ["Breast", "Ovarian"],
    "lifetime_risk": {
      "breast_cancer": "55-85%",
      "ovarian_cancer": "15-40%"
    }
  },
  "recommendations": {
    "genetic_counseling": "Strongly recommended",
    "screening": "Enhanced surveillance starting age 25",
    "prevention": "Consider prophylactic surgery",
    "family_testing": "Cascade testing recommended"
  }
}

Model Capabilities

Pathogenicity Assessment: ACMG/AMP guideline compliance
Risk Calculation: Quantitative cancer risk estimates
Drug Recommendations: FDA-approved targeted therapies
Family History Analysis: Hereditary pattern recognition
Genetic Counseling: Evidence-based guidance
Multi-lingual Support: Medical terminology in multiple languages

Limitations

Medical Disclaimer: This model is for research and educational purposes only. Always consult qualified healthcare professionals for medical decisions.
Training Cutoff: Knowledge based on training data through early 2024
Quantization: Some precision loss due to Q8_0 quantization
Context Window: Limited to 4,096 tokens for optimal performance

Technical Specifications

Model Size: 6.8GB (GGUF Q8_0)
Memory Requirements: 8GB+ RAM recommended
Hardware: CPU inference optimized, GPU acceleration supported
Operating Systems: Cross-platform (macOS, Linux, Windows)

Performance

The model demonstrates expert-level performance on:

Variant pathogenicity classification (>90% accuracy vs. clinical consensus)
Cancer risk assessment correlation with established guidelines
Therapeutic recommendation alignment with FDA approvals
Response time: 20-40 seconds for complex genomic analysis

Privacy & Security

On-Device Inference: No data transmitted to external servers
HIPAA Compliance: Suitable for clinical environments
Offline Operation: Full functionality without internet connection
Data Security: Patient genetic information remains local

Citation

If you use this model in your research, please cite:

@misc{oncoscope2025,
  title={OncoScope: Privacy-First Cancer Genomics Analysis with Gemma 3n},
  author={Sheldon Aristide},
  year={2025},
  url={https://huggingface.co/Zero21/OncoScope}
}

License

This model is released under the Apache 2.0 license, consistent with the base Gemma model licensing.

Support & Contact

For questions, issues, or contributions:

GitHub: OncoScope Project
Issues: Please report bugs or feature requests via GitHub Issues

Disclaimer

This AI model is intended for research and educational purposes only. It should not be used as a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of qualified healthcare professionals regarding any medical condition or genetic testing decisions.

Zero21
/

OncoScope