# NuroMind

NuroMind is under the ADAM project by UMass Chan at Microbiology & Microbiome Dynamics AI HUB, Haran Research Group, and Bucci Lab. NuroMind is a comprehensive Python library for neuroscience research with a focus on Alzheimer's disease and microbiome-brain interactions. Developed at UMass Chan Medical School's Microbiology & Microbiome Dynamics AI HUB.

Note: This library is still under development, and we are actively conducting extensive testing on this package. The code may not behave as expected at the moment.

[![PyPI version](https://badge.fury.io/py/nuromind.svg)](https://badge.fury.io/py/nuromind)
[![Python Version](https://img.shields.io/pypi/pyversions/nuromind.svg)](https://pypi.org/project/nuromind/)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

## Project Structure

```
nuromind/
│
├── src/
│   └── nuromind/
│       ├── __init__.py
│       ├── core.py
│       ├── config.py
│       ├── utils.py
│       ├── imaging/
│       │   ├── __init__.py
│       │   ├── preprocessing.py
│       │   ├── segmentation.py
│       │   └── visualization.py
│       ├── models/
│       │   ├── __init__.py
│       │   ├── base.py
│       │   ├── alzheimer.py
│       │   └── predictors.py
│       ├── microbiome/
│       │   ├── __init__.py
│       │   ├── analysis.py
│       │   ├── diversity.py
│       │   └── visualization.py
│       └── llm/
│           ├── __init__.py
│           ├── assistant.py
│           ├── prompts.py
│           └── literature.py
│
├── tests/
│   ├── __init__.py
│   ├── conftest.py
│   ├── test_core.py
│   ├── test_imaging/
│   ├── test_models/
│   ├── test_microbiome/
│   └── test_llm/
│
├── examples/
│   ├── __init__.py
│   ├── basic_usage.py
│   ├── alzheimer_analysis.py
│   └── microbiome_integration.py
│
├── docs/
│   ├── index.md
│   ├── installation.md
│   ├── quickstart.md
│   └── api/
│
├── pyproject.toml
├── README.md
├── LICENSE
├── CHANGELOG.md
├── CONTRIBUTING.md
├── .gitignore
├── .github/
│   └── workflows/
│       ├── tests.yml
│       └── publish.yml
└── requirements/
    ├── base.txt
    ├── dev.txt
    └── docs.txt
```

## Description

Nuromind is a structured Python package tailored for analyzing neurological data, specifically targeting Alzheimer's disease. The project integrates imaging preprocessing, microbiome analysis, specialized Alzheimer's models, and large language model (LLM) functionalities.

## Key Directories

* **src/nuromind/**: Core modules and functionalities.

  * **core.py**: Main functionalities and utilities.
  * **imaging/**: Preprocessing tools for imaging data.
  * **models/**: Specialized models for Alzheimer's disease research.
  * **microbiome/**: Analysis tools for microbiome datasets.
  * **llm/**: Integration with large language models.

* **tests/**: Unit and integration tests to ensure the reliability of the package.

## Installation

```bash
# Basic installation
pip install nuromind

# With all optional dependencies
pip install nuromind[dev,viz,bio,microbiome]
```

## Quick Start

```python
import nuromind as nm

# Check available dependencies
deps = nm.check_dependencies()
print(f"Available components: {deps}")

# Initialize configuration
config = nm.NuroMindConfig(device="cuda")

# Load and analyze data (placeholder functionality)
from nuromind.imaging import load_mri, preprocess
from nuromind.models import AlzheimerClassifier

# Load brain scan
scan = load_mri("path/to/scan.nii")
processed = preprocess(scan)

# Analyze with model
classifier = AlzheimerClassifier()
results = classifier.predict(processed)
print(f"AD probability: {results['ad_probability']}")
```

## Features (In Development)

- **Alzheimer's Disease Research**: Biomarker analysis, neuroimaging pipelines
- **Microbiome Integration**: Gut-brain axis analysis, dysbiosis detection
- **LLM Research Assistant**: Automated literature reviews, hypothesis generation
- **Medical Imaging**: MRI/PET preprocessing, brain segmentation
- **Multi-Omics**: Integrated analysis of microbiome, imaging, and clinical data

## Development

```bash
# Clone the repository
git clone https://github.com/melhzy/nuromind.git
cd nuromind

# Install in development mode
pip install -e .[dev]

# Run tests
pytest

# Format code
black src/nuromind tests/
```

## Author

**Ziyuan Huang**  
UMass Chan Medical School  
Microbiology & Microbiome Dynamics AI HUB, Haran Research Group, & Bucci Lab  
Email: ziyuan.huang2@umassmed.edu

## License

MIT License - see [LICENSE](LICENSE) file for details.

## Citation

```bibtex
@software{nuromind2025,
  author = {Huang, Ziyuan},
  title = {},
  year = {2025},
  organization = {UMass Chan Medical School},
  url = {}
}
```
```

### LICENSE
```
MIT License

Copyright (c) 2024 Ziyuan Huang, UMass Chan Medical School

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
```
