Enhancing Drug-Target Interaction Prediction through Transfer Learning from Activity Cliff Prediction Tasks

TL;DR

This paper introduces a transfer learning approach from activity cliff prediction to drug-target interaction prediction, improving model accuracy in complex chemical regions by integrating AC-awareness into DTI models.

Contribution

It presents a novel unified framework that leverages AC prediction insights to enhance DTI prediction, addressing traditional model limitations and data scarcity issues.

Findings

Improved DTI prediction accuracy in challenging cases involving activity cliffs.

A universal AC prediction model capable of identifying activity cliffs across diverse targets.

Enhanced drug discovery models by integrating compound-specific and protein-contextual information.

Abstract

Recently, machine learning (ML) has gained popularity in the early stages of drug discovery. This trend is unsurprising given the increasing volume of relevant experimental data and the continuous improvement of ML algorithms. However, conventional models, which rely on the principle of molecular similarity, often fail to capture the complexities of chemical interactions, particularly those involving activity cliffs (ACs) - compounds that are structurally similar but exhibit evidently different activity behaviors. In this work, we address two distinct yet related tasks: (1) activity cliff (AC) prediction and (2) drug-target interaction (DTI) prediction. Leveraging insights gained from the AC prediction task, we aim to improve the performance of DTI prediction through transfer learning. A universal model was developed for AC prediction, capable of identifying activity cliffs across diverse targets. Insights from this model were then incorporated into DTI prediction, enabling better handling of challenging cases involving ACs while maintaining similar overall performance. This approach establishes a strong foundation for integrating AC awareness into predictive models for drug discovery. Scientific Contribution This study presents a novel approach that applies transfer learning from AC prediction to enhance DTI prediction, addressing limitations of traditional similarity-based models. By introducing AC-awareness, we improve DTI model performance in structurally complex regions, demonstrating the benefits of integrating compound-specific and protein-contextual information. Unlike previous studies, which treat AC and DTI predictions as separate problems, this work establishes a unified framework to address both data scarcity and prediction challenges in drug discovery.