Title:Identifying Protein Subcellular Location with Embedding Features Learned from Networks
Volume: 18
Issue: 5
Author(s): Hongwei Liu, Bin Hu, Lei Chen*Lin Lu
Affiliation:
- College of Information Engineering, Shanghai Maritime University, Shanghai,China
Keywords:
Protein subcellular location prediction, network embedding algorithm, deepWalk, Node2vec, mashup, machine
learning algorithm, support vector machine, random forest.
Abstract:
Background: Identification of protein subcellular location is an important problem because
the subcellular location is highly related to protein function. It is fundamental to determine
the locations with biology experiments. However, these experiments are of high costs and time-consuming.
The alternative way to address such a problem is to design effective computational methods.
Objective: To date, several computational methods have been proposed in this regard. However, these
methods mainly adopted the features derived from the proteins themselves. On the other hand,
with the development of the network technique, several embedding algorithms have been proposed,
which can encode nodes in the network into feature vectors. Such algorithms connected the
network and traditional classification algorithms. Thus, they provided a new way to construct models
for the prediction of protein subcellular location.
Methods: In this study, we analyzed features produced by three network embedding algorithms
(DeepWalk, Node2vec and Mashup) that were applied on one or multiple protein networks. Obtained
features were learned by one machine learning algorithm (support vector machine or random
forest) to construct the model. The cross-validation method was adopted to evaluate all constructed
models.
Results: After evaluating models with the cross-validation method, embedding features yielded by
Mashup on multiple networks were quite informative for predicting protein subcellular location.
The model based on these features were superior to some classic models.
Conclusion: Embedding features yielded by a proper and powerful network embedding algorithm
were effective for building the model for prediction of protein subcellular location, providing new
pipelines to build more efficient models.
