Using Jupyter Notebooks for re-training machine learning models

Abstract

Abstract Machine learning (ML) models require an extensive, user-driven selection of molecular descriptors in order to learn from chemical structures to predict actives and inactives with a high reliability. In addition, privacy concerns often restrict the access to sufficient data, leading to models with a narrow chemical space. Therefore, we propose a framework of re-trainable models that can be transferred from one local instance to another, and further allow a less extensive descriptor selection. The models are shared via a Jupyter Notebook, allowing the evaluation and implementation of a broader chemical space by keeping most of the tunable parameters pre-defined. This enables the models to be updated in a decentralized, facile, and fast manner. Herein, the method was evaluated with six transporter datasets (BCRP, BSEP, OATP1B1, OATP1B3, MRP3, P-gp), which revealed the general applicability of this approach.

Keywords

• Classification models
• Transporter proteins
• Decentralization
• Re-training
• Jupyter Notebook