Open Access Highly Accessed Research article

Integrative relational machine-learning for understanding drug side-effect profiles

Emmanuel Bresso123*, Renaud Grisoni2, Gino Marchetti24, Arnaud Sinan Karaboga3, Michel Souchet3, Marie-Dominique Devignes24 and Malika Smaïl-Tabbone12*

Author Affiliations

1 Université de Lorraine, LORIA, UMR 7503, Vandoeuvre-lès-Nancy, 54506, France

2 INRIA, Villers-lès-Nancy, 54600, France

3 Harmonic Pharma, Espace Transfert INRIA NGE, Villers-lès-Nancy, 54600, France

4 CNRS, LORIA, UMR 7503, Vandoeuvre-lès-Nancy, 54506, France

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BMC Bioinformatics 2013, 14:207  doi:10.1186/1471-2105-14-207

Published: 26 June 2013



Drug side effects represent a common reason for stopping drug development during clinical trials. Improving our ability to understand drug side effects is necessary to reduce attrition rates during drug development as well as the risk of discovering novel side effects in available drugs. Today, most investigations deal with isolated side effects and overlook possible redundancy and their frequent co-occurrence.


In this work, drug annotations are collected from SIDER and DrugBank databases. Terms describing individual side effects reported in SIDER are clustered with a semantic similarity measure into term clusters (TCs). Maximal frequent itemsets are extracted from the resulting drug x TC binary table, leading to the identification of what we call side-effect profiles (SEPs). A SEP is defined as the longest combination of TCs which are shared by a significant number of drugs. Frequent SEPs are explored on the basis of integrated drug and target descriptors using two machine learning methods: decision-trees and inductive-logic programming. Although both methods yield explicit models, inductive-logic programming method performs relational learning and is able to exploit not only drug properties but also background knowledge. Learning efficiency is evaluated by cross-validation and direct testing with new molecules. Comparison of the two machine-learning methods shows that the inductive-logic-programming method displays a greater sensitivity than decision trees and successfully exploit background knowledge such as functional annotations and pathways of drug targets, thereby producing rich and expressive rules. All models and theories are available on a dedicated web site.


Side effect profiles covering significant number of drugs have been extracted from a drug ×side-effect association table. Integration of background knowledge concerning both chemical and biological spaces has been combined with a relational learning method for discovering rules which explicitly characterize drug-SEP associations. These rules are successfully used for predicting SEPs associated with new drugs.

Relational machine learning; Data integration; Drug discovery; Data mining; Drug side-effects