README.md

🧬 Biological Network Analyzer

An intelligent assistant for analyzing biological networks from text or image input. This app can extract reaction networks from uploaded diagrams using Gemini Vision API, parse them into graph structures, and generate:

• 📈 ODEs (Ordinary Differential Equations)
• 🧮 Jacobian matrices
• 🔄 Cyclic dependency checks
• 📊 Graph stats (edges, variables)

All via a Gradio-based conversational interface.

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🚀 Features

• 🔤 Text input (e.g. A + B -> C, C <-> D)
• 🖼️ Image input (upload scanned or digital diagrams)
• 🧠 Google Gemini API integration to extract text-based reactions from images
• 🧪 ODE system generation using mass-action kinetics
• 🧠 Jacobian matrix computation via symbolic algebra (SymPy)
• 🔁 Cycle detection and variable/edge counting
• 🤖 LLM-based fallback Q&A via flan-t5-base
• 🎨 Customizable Gradio theme (e.g. Soft, Glass, etc.)

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🧰 Tech Stack

Component	Technology
Frontend UI	Gradio
LLM Query	Flan-T5
Image-to-Text	Gemini API (Vision multimodal API)
Graph Parsing	NetworkX
Symbolic Math	SymPy

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🖥️ Running the App on your device

✅ Prerequisites

• Python ≥ 3.8
• Install dependencies:

pip install gradio transformers networkx sympy google-generativeai python-dotenv pillow

• Set your Gemini API key in a .env file:

GEMINI_API=your_api_key_here

▶️ Run

python your_script.py

Or use inside a Google Colab notebook for instant testing.

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📷 Example Inputs

Text:

A + B -> C, C <-> D, D -> E

Image:

• Upload PNG or JPG of a biological reaction network
• Gemini will parse it automatically

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📌 Future Additions

• Export ODEs/Jacobian as LaTeX/PDF
• Stoichiometry & reaction rate customization

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🧑‍🔬 Author

Built by [Devansh] for a project on LLM-based Equation Discovery from Biological Networks.

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📝 License

MIT License

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title: Network Analyzer emoji: 🦀 colorFrom: green colorTo: green sdk: gradio sdk_version: 5.35.0 app_file: app.py pinned: false

Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference