Reply to ‘Inflated performance measures in enhancer–promoter interaction-prediction methods’

Background:The identification of drug-target interactions is a crucial issue in drug discovery. In recent years, researchers have made great efforts on the drug-target interaction predictions, and developed databases, software and computational methods.Results:In the paper, we review the recent advances in machine learning-based drug-target interaction prediction. First, we briefly introduce the datasets and data, and summarize features for drugs and targets which can be extracted from different data. Since drug-drug similarity and target-target similarity are important for many machine learning prediction models, we introduce how to calculate similarities based on data or features. Different machine learningbased drug-target interaction prediction methods can be proposed by using different features or information. Thus, we summarize, analyze and compare different machine learning-based prediction methods.Conclusion:This study provides the guide to the development of computational methods for the drug-target interaction prediction.

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MLRDA: A Multi-Task Semi-Supervised Learning Framework for Drug-Drug Interaction Prediction

Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence ◽

10.24963/ijcai.2019/628 ◽

2019 ◽

Author(s):

Xu Chu ◽

Yang Lin ◽

Yasha Wang ◽

Leye Wang ◽

Jiangtao Wang ◽

...

Keyword(s):

Supervised Learning ◽

State Of The Art ◽

Multiple Drug ◽

Prediction Methods ◽

Learning Models ◽

Preventable Hospitalizations ◽

Interaction Prediction ◽

Learning Framework ◽

Task Learning ◽

Real World Datasets

Drug-drug interactions (DDIs) are a major cause of preventable hospitalizations and deaths. Recently, researchers in the AI community try to improve DDI prediction in two directions, incorporating multiple drug features to better model the pharmacodynamics and adopting multi-task learning to exploit associations among DDI types. However, these two directions are challenging to reconcile due to the sparse nature of the DDI labels which inflates the risk of overfitting of multi-task learning models when incorporating multiple drug features. In this paper, we propose a multi-task semi-supervised learning framework MLRDA for DDI prediction. MLRDA effectively exploits information that is beneficial for DDI prediction in unlabeled drug data by leveraging a novel unsupervised disentangling loss CuXCov. The CuXCov loss cooperates with the classification loss to disentangle the DDI prediction relevant part from the irrelevant part in a representation learnt by an autoencoder, which helps to ease the difficulty in mining useful information for DDI prediction in both labeled and unlabeled drug data. Moreover, MLRDA adopts a multi-task learning framework to exploit associations among DDI types. Experimental results on real-world datasets demonstrate that MLRDA significantly outperforms state-of-the-art DDI prediction methods by up to 10.3% in AUPR.

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