tumorimagingbench 0.1.0

A package for tumor imaging feature extraction and benchmarking.

TumorImagingBench

A comprehensive framework for evaluating and comparing foundation model feature extractors for radiomics in medical imaging.

📋 Overview

TumorImagingBench is a robust platform that enables researchers and practitioners to:

• Extract meaningful features from medical images using state-of-the-art foundation models
• Compare performance metrics across diverse radiomics datasets
• Systematically evaluate model stability, robustness, and interpretability
• Benchmark novel foundation models against established approaches

This framework bridges the gap between advancing foundation models and their practical application in medical imaging analysis.

🔍 Key Features

• Unified Interface: Common API for all foundation model extractors
• Comprehensive Evaluation: Standardized metrics across multiple datasets
• Interpretability Tools: Generation of saliency maps and attribution analysis
• Extensible Architecture: Easily integrate new models and datasets

📂 Repository Structure

FM-extractors-radiomics/
├── models/              # Foundation model implementations
├── notebooks/           
│   ├── modelling/       # Dataset-specific modeling notebooks
│   └── analysis/        # Performance, robustness, and stability analysis
├── scripts/             # Utility scripts for batch processing
├── data/                # Dataset directory (not tracked in git)
├── utils/               # Utility functions for data processing
└── evaluation/          # Evaluation metrics and protocols

🧠 Supported Foundation Models

Model	Description
FMCIB	Foundation Model for Cancer Image Biomarkers
CT-FM	CT Foundation Model
CT-CLIP-ViT	CT-specific CLIP Vision Transformer
PASTA	Pathology and Radiology Image Analysis Model
VISTA3D	3D Vision Transformer for Medical Imaging
Voco	Volumetric Contrastive Learning Model
SUPREM	Supervised Pretraining for Medical Imaging
Merlin	Multi-modal Embedding for Radiology and Learning
MedImageInsight	Medical Image Understanding Framework
ModelsGen	Generative Foundation Models for Medical Imaging

📊 Supported Datasets

• LUNA16: Lung Nodule Analysis
• DLCS: Duke Lung Cancer Dataset
• NSCLC Radiomics: Non-Small Cell Lung Cancer
• NSCLC Radiogenomics: Radiogenomic Analysis of NSCLC
• C4KC-KiTs: Clear Cell Renal Cell Carcinoma Kidney Tumor Segmentation
• Colorectal Liver Metastases: Liver Metastases Dataset

💻 Installation

# Clone the repository
git clone https://github.com/AIM-Harvard/TumorImagingBench.git
cd TumorImagingBench

# Install dependencies
pip install -r requirements.txt

🚀 Usage

Feature Extraction

from models import CTClipVitExtractor, FMCIBExtractor

# Initialize a model
model = FMCIBExtractor()
model.load()

# Extract features from a sample
features = model.extract(sample_path)

For systematic feature extraction across datasets, we provide dedicated scripts in the evaluation/ directory. These scripts offer a standardized approach that can be extended to new datasets through our base feature extractor class.

Model Evaluation

For examples of model evaluation on different datasets, explore the notebooks in the notebooks/modelling/ directory. These notebooks demonstrate:

• Feature extraction workflows
• Model training and validation
• Performance analysis and comparison
• Visualization of results

📈 Analysis Tools

Our repository includes specialized analysis notebooks:

Notebook	Purpose
stability_analysis.ipynb	Evaluate model stability with various perturbations
robustness_analysis.ipynb	Assess model robustness to noise and transformations
saliency_analysis.ipynb	Visualize and analyze model activation maps
overall_analysis.ipynb	Compare aggregate performance across models and datasets

🤝 Contributing

We welcome contributions to improve this framework! Here's how you can contribute:

1. Fork the repository
2. Create your feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add some amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request

Development Guidelines

• Follow the existing code style and documentation patterns
• Add tests for new functionality
• Update documentation to reflect changes
• Ensure backward compatibility where possible

📚 Citation

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

@article{TumorImagingBench,
  title={Foundation model embeddings for quantitative tumor imaging biomarkers},
  author={}, 
  journal={},
  year={},
  volume={},
  pages={},
  publisher={}
}

📄 License

This project is licensed under the [LICENSE NAME] - see the LICENSE file for details.