Overview

Biotrainer is an open-source framework that simplifies machine learning model development for protein analysis. It is the main backbone of the functionality provided in the biocentral ecosystem.

It provides the following modules:

• Training: Easy to use training and inference pipelines for protein feature prediction
• Embedding: Built-in support for protein language models (ProtT5, ESM-2, ESM-C, ...) and baselines (blosum62, one_hot_encoding, ...)
• BioEngineer: Zero-shot predictions and mutation generation of protein sequences
• AutoEval: Automated evaluation of protein language models on curated downstream tasks

Installation

Install from pypi using pip:

pip install biotrainer