# Biotech Agentic Analyst

An agentic workflow for analyzing scientific papers: extract figures from PDFs using Mistral OCR 4, then run CrewAI agentic flow to generate structured intelligence — key findings, biological significance, quantitative highlights, and knowledge-base tags — for each figure.

We use:

- [CrewAI](https://docs.crewai.com/) for multi-agent orchestration (Flow + Crew)
- [Mistral OCR 4](https://docs.mistral.ai/models/model-cards/ocr-4-0) for PDF conversion and figure extraction
- [Mistral](https://mistral.ai/) as the LLM provider
- [Streamlit](https://streamlit.io/) for an interactive UI

## How It Works

1. Upload a scientific PDF
2. Mistral OCR 4 runs with Document AI structured output to identify and extract all figures, axis labels, and captions in one pass
3. A CrewAI Flow with Analyst agent produces structured intelligence for each figure:
   - Chart type and key finding
   - Variables and conditions compared
   - Quantitative highlights
   - Biological significance
   - Knowledge-base tags
4. Results are displayed in the Streamlit UI with figure thumbnails

## Set Up

### Create .env File

Create a `.env` file in the root directory with the following content:

```env
MISTRAL_API_KEY=<your_mistral_api_key>
```

### Install Dependencies

```bash
uv sync
source .venv/bin/activate
```

On Windows (PowerShell):

```powershell
uv sync
.venv\Scripts\activate.ps1
```

## Run the Streamlit App

```bash
streamlit run app.py
```

Open the URL shown in the terminal (e.g. `http://localhost:8501`). Upload a scientific PDF in the sidebar and click **Run Analysis** to trigger the full workflow.

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## Contribution

Contributions are welcome! Feel free to fork this repository and submit pull requests with your improvements.