BioChatter

License		Python
Package		Build status
Tests		Docker
Development		Contributions

Description

Generative AI models have shown tremendous usefulness in increasing accessibility and automation of a wide range of tasks. Yet, their application to the biomedical domain is still limited, in part due to the lack of a common framework for deploying, testing, and evaluating the diverse models and auxiliary technologies that are needed. This repository contains the biochatter Python package, a generic backend library for the connection of biomedical applications to conversational AI.

The library is described in this preprint and used in various demo applications for showcasing its use:

• a simple Python-based frontend called BioChatter Light, which we develop at https://github.com/biocypher/biochatter-light;

• an advanced Next.js-based frontend called BioChatter Next, which we develop at https://github.com/biocypher/biochatter-next;

• a RESTful API server for use by the Next frontend (and any other REST-based application) at https://github.com/biocypher/biochatter-server.

BioChatter is part of the BioCypher ecosystem, connecting natively to BioCypher knowledge graphs. The BioChatter paper is being written here.

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.

More information about LLMs

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

Troubleshooting

If you're on Apple Silicon, you may encounter issues with the grpcio dependency (grpc library, which is used in pymilvus). If so, try to install the binary from source after removing the installed package from the virtual environment from here:

pip uninstall grpcio
export GRPC_PYTHON_LDFLAGS=" -framework CoreFoundation"
pip install grpcio==1.53.0 --no-binary :all: