biochatter 0.14.0

Backend library for conversational AI in biomedicine

BioChatter

License		Python
Package		Build status
Tests		Docker
Development		Contributions

Description

🤖 BioChatter is a community-driven Python library that connects biomedical applications to conversational AI, making it easy to leverage generative AI models in the biomedical domain.

🌟 Key Features

• Generic backend for biomedical AI applications
• Seamless integration with multiple LLM providers
• Native connection to BioCypher knowledge graphs
• Extensive testing and evaluation framework
• Living benchmark of specific biomedical applications

🚀 Demo Applications and Utilities

• BioChatter Light - Simple Python frontend (repo)

• BioChatter Next - Advanced Next.js frontend (repo)

• BioChatter Server - RESTful API server

📖 Learn more in our paper.

Installation

To use the package, install it from PyPI, for instance using pip (pip install biochatter) or Poetry (poetry add biochatter).

Extras

The package has some optional dependencies that can be installed using the following extras (e.g. pip install biochatter[xinference]):

• xinference: support for querying open-source LLMs through Xorbits Inference

• podcast: support for podcast text-to-speech (for the free Google TTS; the paid OpenAI TTS can be used without this extra)

• streamlit: support for streamlit UI functions (used in BioChatter Light)

Usage

Check out the documentation for examples, use cases, and more information. Many common functionalities covered by BioChatter can be seen in use in the BioChatter Light code base.

🤝 Getting involved

We are very happy about contributions from the community, large and small! If you would like to contribute to BioCypher development, please refer to our contribution guidelines and the developer docs. :)

If you want to ask informal questions, talk about dev things, or just chat, please join our community at https://biocypher.zulipchat.com!

Imposter syndrome disclaimer: We want your help. No, really. There may be a little voice inside your head that is telling you that you're not ready, that you aren't skilled enough to contribute. We assure you that the little voice in your head is wrong. Most importantly, there are many valuable ways to contribute besides writing code.

This disclaimer was adapted from the Pooch project.

Git LFS Configuration

This repository uses Git LFS for some large files. If you're a developer and don't need to work with these files, you have two options:

1. Disable Git LFS smudge globally (set once for all repositories):

git lfs install --skip-smudge
git clone https://github.com/biocypher/biochatter.git

2. Skip LFS files for a one-time clone:

GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/biocypher/biochatter.git

Both options will prevent Git LFS from downloading the large files while still allowing you to work with the repository normally.

More information about LLMs

Check out this repository for more info on computational biology usage of large language models.

Citation

If you use BioChatter in your work, please cite our paper.