NDLI: DeepCCI: End-to-end Deep Learning for Chemical-Chemical Interaction Prediction

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DeepCCI: End-to-end Deep Learning for Chemical-Chemical Interaction Prediction

Content Provider	ACM Digital Library
Author	Kwon, Sunyoung Yoon, Sungroh
Abstract	Chemical-chemical interaction (CCI) plays a key role in predicting candidate drugs, toxicity, therapeutic effects, and biological functions. In various types of chemical analyses, computational approaches are often required due to the amount of data that needs to be handled. The recent remarkable growth and outstanding performance of deep learning have attracted considerable research attention. However, even in state-of-the-art drug analysis methods, deep learning continues to be used only as a classifier, although deep learning is capable of not only simple classification but also automated feature extraction. In this paper, we propose the first end- to-end learning method for CCI, named DeepCCI. Hidden features are derived from a simplified molecular input line entry system (SMILES), which is a string notation representing the chemical structure, instead of learning from crafted features. To discover hidden representations for the SMILES strings, we use convolutional neural networks (CNNs). To guarantee the commutative property for homogeneous interaction, we apply model sharing and hidden representation merging techniques. The performance of DeepCCI was compared with a plain deep classifier and conventional machine learning methods. The proposed DeepCCI showed the best performance in all seven evaluation metrics used. In addition, the commutative property was experimentally validated. The automatically extracted features through end-to-end SMILES learning alleviates the significant efforts required for manual feature engineering. It is expected to improve prediction performance in drug analyses.
Starting Page	203
Ending Page	212
Page Count	10
File Format	PDF
ISBN	9781450347228
DOI	10.1145/3107411.3107451
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2017-08-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Deep learning Cnn Chemical-chemical interaction Neural network Commutative property
Content Type	Text
Resource Type	Article

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