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SCIENTIA SINICA Informationis, Volume 47, Issue 10: 1349-1368(2017) https://doi.org/10.1360/N112017-00009

Predicting irrelevant functions of proteins based on dimensionality reduction

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  • ReceivedJan 10, 2017
  • AcceptedMar 16, 2017
  • PublishedAug 31, 2017

Abstract

Proteins are the foundation for many life processes and accurately annotating their biological functions can significantly boost the development of life sciences. Current function prediction models focus on employing the knowledge that proteins perform specific functions (positive examples), but ignore the knowledge that some functions are irrelevant for a protein (negative examples). Recent research indicates that incorporating negative examples can reduce the complexity and improve the accuracy of protein function prediction. In this paper, we propose an approach for predicting irrelevant functions of proteins based on dimensionality reduction (IFDR). Initially, IFDR performs random walks through matrices in a protein-protein interactions (PPI) network, as well as the corresponding protein-function association matrices, in order to explore the underlying relationships between proteins and model the missing functional annotations of proteins. Next, IFDR uses single value decomposition to project these matrices into low-dimensional numerical matrices. Finally, IFDR uses semi-supervised regression to predict negative examples of proteins. Experiments on S. cerevisiae, H. sapiens, and A. thaliana data demonstrate that IFDR can more accurately predict negative examples when compared to related methods. Dimensionality reduction in the network space and label space can both improve the accuracy of negative example prediction.


Funded by

中央高校基本科研业务费(2362015X- K07)

国家自然科学基金(61532014)

重庆市研究生科研创新项目(CYS16070)

国家自然科学基金(61402378)

重庆市基础与前沿研究计划项目(cstc2014jcyjA40031)

国家自然科学基金(61671189)

重庆市基础与前沿研究计划项目(cstc2016jcyjA0351)

国家自然科学基金(61571163)


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  • Figure 1

    (Color online) Influence of the size of target dimensionality on H.sapiens. $d$ and $c$ represent the target dimensionality of PPI network and function label space, respectively. (a) BP; (b) CC; (c) MF

  • Figure 2

    (Color online) Statistics of runtime cost of four comparing methods on different datasets. (a) H.sapiens; protectłinebreak (b) S.cerevisiae; (c) A.thaliana

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