autogen-builtsimple 0.1.0

AutoGen tools for Built-Simple research APIs (PubMed & ArXiv)

AutoGen Built-Simple Research Tools

GPU-accelerated research tools for Microsoft AutoGen agents.

Search millions of academic papers on PubMed (4.48M+ articles) and ArXiv (2.77M+ papers) with semantic understanding. Built on Built-Simple's high-performance research APIs.

🚀 Features

• 🔬 PubMed Search: Semantic + keyword hybrid search across 4.48M biomedical articles
• 📚 ArXiv Search: Fast search across 2.77M preprints (physics, math, CS, AI/ML)
• ⚡ GPU-Accelerated: Millisecond response times via Built-Simple APIs
• 📄 Full Text: Retrieve complete article text from PubMed Central
• 🤖 AutoGen Native: One-line registration with AutoGen agents

📦 Installation

pip install autogen-builtsimple

Or with AutoGen included:

pip install autogen-builtsimple[autogen]

🏃 Quick Start

import os
from autogen import ConversableAgent
from autogen_builtsimple import register_research_tools

# Create agents
assistant = ConversableAgent(
    name="ResearchAssistant",
    system_message="""You are a research assistant that helps find and analyze 
    scientific papers. Use the search tools to find relevant literature.""",
    llm_config={"config_list": [{"model": "gpt-4", "api_key": os.environ["OPENAI_API_KEY"]}]},
)

user_proxy = ConversableAgent(
    name="User",
    llm_config=False,
    is_termination_msg=lambda msg: "TERMINATE" in msg.get("content", ""),
    human_input_mode="NEVER",
)

# Register all research tools with one line!
register_research_tools(assistant, user_proxy)

# Start researching
chat_result = user_proxy.initiate_chat(
    assistant,
    message="Find 5 recent papers on CRISPR gene therapy for cancer treatment"
)

🔧 Available Tools

PubMed Tools

Tool	Description
search_pubmed	Hybrid semantic + keyword search across PubMed
get_pubmed_full_text	Retrieve full article text (PMC articles)
get_pubmed_metadata	Batch fetch metadata for multiple PMIDs

ArXiv Tools

Tool	Description
search_arxiv	Hybrid/vector/text search across ArXiv
get_arxiv_paper_url	Get PDF and abstract URLs for a paper

📖 Usage Examples

Search PubMed

from autogen_builtsimple import search_pubmed

# Semantic search for medical literature
results = search_pubmed(
    query="machine learning early cancer detection biomarkers",
    limit=10,
    min_year=2020
)
print(results)

Search ArXiv

from autogen_builtsimple import search_arxiv

# Search for AI papers
results = search_arxiv(
    query="large language models reasoning capabilities",
    limit=10,
    search_type="hybrid"  # or "vector" or "text"
)
print(results)

Get Full Text

from autogen_builtsimple import get_pubmed_full_text

# Get complete article text
full_text = get_pubmed_full_text(pmid="35421456")
print(full_text)

Selective Registration

from autogen_builtsimple import register_pubmed_tools, register_arxiv_tools

# Register only PubMed tools
register_pubmed_tools(assistant, user_proxy)

# Or only ArXiv tools
register_arxiv_tools(assistant, user_proxy)

🔑 API Keys (Optional)

The tools work without API keys using IP-based rate limiting. For higher limits, get a free API key:

• PubMed: https://pubmed.built-simple.ai
• ArXiv: https://arxiv.built-simple.ai

results = search_pubmed(
    query="diabetes treatment",
    limit=20,
    api_key="your-api-key"
)

🏗️ Architecture

┌─────────────────┐     ┌──────────────────┐     ┌─────────────────┐
│  AutoGen Agent  │────▶│  autogen-builtsimple │────▶│  Built-Simple   │
│   (Assistant)   │     │      Tools       │     │     APIs        │
└─────────────────┘     └──────────────────┘     └─────────────────┘
                                                        │
                                ┌───────────────────────┴───────────────────────┐
                                │                                               │
                        ┌───────▼───────┐                               ┌───────▼───────┐
                        │    PubMed     │                               │    ArXiv      │
                        │  GPU Search   │                               │  GPU Search   │
                        │  4.48M docs   │                               │  2.77M docs   │
                        └───────────────┘                               └───────────────┘

📊 Performance

Endpoint	Latency	Index Size
PubMed Hybrid Search	~100-150ms	4.48M articles
ArXiv Hybrid Search	~70-90ms	2.77M papers
PubMed Full Text	~50ms	PMC subset

🤝 Contributing

Contributions welcome! Please feel free to submit issues and pull requests.

📄 License

MIT License - see LICENSE for details.

🔗 Links

• Built-Simple: https://built-simple.ai
• PubMed API Docs: https://pubmed.built-simple.ai/docs
• ArXiv API Docs: https://arxiv.built-simple.ai/docs
• Microsoft AutoGen: https://microsoft.github.io/autogen/