KnoxAI - A Framework for Combinatorial Design Prediction

knoxAI is a modular deep learning framework for graph-based and rule-based machine learning, built with FastAPI. It supports regression, classification, and ranking tasks on graph-structured data, and provides a REST API for model training, evaluation, and prediction. Runs are saved and managed through MLflow.

Quickstart

Installation

1. Clone this repository
2. Install dependencies pip install -r requirements.txt
3. Run uvicorn app.main:api --reload --host 0.0.0.0 --port 8000 in the root directory of this repo
4. For MLflow user-interface run mlflow ui --port 5000 --workers 1 in the root directory of this repo

Use with Knox or Standalone

Manuscripts

Nicholas Roehner, James Roberts, Andrei Lapets, Dany Gould, Vidya Akavoor, Lucy Qin, D. Benjamin Gordon, Christopher Voigt, and Douglas Densmore. GOLDBAR: A Framework for Combinatorial Biological Design. ACS Synthetic Biology Article ASAP (2024). DOI: https://pubs.acs.org/doi/full/10.1021/acssynbio.4c00296

Webpage

https://www.cidarlab.org/knox