iMPT-FRAKEL: A Simple Multi-label Web-server that Only Uses Fingerprints to Identify which Metabolic Pathway Types Compounds can Participate In

Yanjuan Jia1
, Lei Chen1, 2, *
, Jian-Peng Zhou1
, Min Liu1

1 College of Information Engineering, Shanghai Maritime University, Shanghai, China
2 Shanghai Key Laboratory of PMMP, East China Normal University, Shanghai, China

© 2020 Jia et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the College of Information Engineering, Shanghai Maritime University, People’s Republic of China; Shanghai, China; Tel: 0086-21-38282825; Fax: 0086-21-38282800; E-mail:



Metabolic pathway is one of the most basic biological pathways in living organisms. It consists of a series of chemical reactions and provides the necessary molecules and energies for organisms. To date, lots of metabolic pathways have been detected. However, there still exist hidden participants (compounds and enzymes) for some metabolic pathways due to the complexity and diversity of metabolic pathways. It is necessary to develop quick, reliable, and non-animal-involved prediction model to recognize metabolic pathways for any compound.


In this study, a multi-label classifier, namely iMPT-FRAKEL, was developed for identifying which metabolic pathway types that compounds can participate in. Compounds and 12 metabolic pathway types were retrieved from KEGG. Each compound was represented by its fingerprints, which was the most widely used form for representing compounds and can be extracted from its SMILES format. A popular multi-label classification scheme, Random k-Labelsets (RAKEL) algorithm, was adopted to build the classifier. Classic machine learning algorithm, Support Vector Machine (SVM) with RBF kernel, was selected as the basic classification algorithm. Ten-fold cross-validation was used to evaluate the performance of the iMPT-FRAKEL. In addition, a web-server version of such classifier was set up, which can be assessed at


iMPT-FRAKEL yielded the accuracy of 0.804, exact match of 0.745 and hamming loss of 0.039. Comparison results indicated that such classifier was superior to other models, including models with Binary Relevance (BR) or other classification algorithms.


The proposed classifier employed limited prior knowledge of compounds but gives satisfying performance for recognizing metabolic pathways of compounds.

Keywords: Metabolic pathway, Fingerprint, RAKEL, Support vector machine, Meka, Web-server, Classic machine learning algorithm.