mlDEEPre: Multi-functional enzyme function prediction with hierarchical multi-label deep learning

Zou，Zhenzhen1; Tian，Shuye2; Gao，Xin1; Li，Yu1

2019

10.3389/fgene.2018.00714

Frontiers in Genetics   影响因子和分区

1664-8021

1664-8021

As a great challenge in bioinformatics, enzyme function prediction is a significant step toward designing novel enzymes and diagnosing enzyme-related diseases. Existing studies mainly focus on the mono-functional enzyme function prediction. However, the number of multifunctional enzymes is growing rapidly, which requires novel computational methods to be developed. In this paper, following our previous work, DEEPre, which uses deep learning to annotate mono-functional enzyme's function, we propose a novel method, mlDEEPre, which is designed specifically for predicting the functionalities of multifunctional enzymes. By adopting a novel loss function, associated with the relationship between different labels, and a self-adapted label assigning threshold, mlDEEPre can accurately and efficiently perform multi-functional enzyme prediction. Extensive experiments also show that mlDEEPre can outperform the other methods in predicting whether an enzyme is a mono-functional or a multi-functional enzyme (mono-functional vs. multi-functional), as well as the main class prediction across different criteria. Furthermore, due to the flexibility of mlDEEPre and DEEPre, mlDEEPre can be incorporated into DEEPre seamlessly, which enables the updated DEEPre to handle both mono-functional and multi-functional predictions without human intervention.

Deep learning EC number Function prediction Hierarchical classification Multi-functional enzyme Multi-label learning

SCI

英语

其他

WOS:000456233600001

2-s2.0-85064190168

Scopus

1.ComputerElectrical and Mathematical Sciences and Engineering (CEMSE) DivisionComputational Bioscience Research Center (CBRC)King Abdullah University of Science and Technology (KAUST),Thuwal,Saudi Arabia
2.Department of BiologySouthern University of Science and Technology (SUSTC),Shenzhen,China

Zou，Zhenzhen,Tian，Shuye,Gao，Xin,et al. mlDEEPre: Multi-functional enzyme function prediction with hierarchical multi-label deep learning[J]. Frontiers in Genetics,2019,10(JAN).

Zou，Zhenzhen,Tian，Shuye,Gao，Xin,&Li，Yu.(2019).mlDEEPre: Multi-functional enzyme function prediction with hierarchical multi-label deep learning.Frontiers in Genetics,10(JAN).

Zou，Zhenzhen,et al."mlDEEPre: Multi-functional enzyme function prediction with hierarchical multi-label deep learning".Frontiers in Genetics 10.JAN(2019).