Probing the Hypothesis of SAR Continuity Restoration by the Removal of Activity Cliffs Generators in QSAR

• Type: Another Publication in an International Scientific Journal
• Date: 2016

Authors

Cruz Monteagudo, M (Author) Other; Medina Franco, JL (Author) Other; Perera Sardina, Y (Author) Other; Fernanda Borges (Author) FCUP; Tejera, E (Author) Other; Paz y Mino, C (Author) Other; Perez Castillo, Y (Author) Other; Sanchez Rodriguez, A (Author) Other; Contreras Posada, Z (Author) Other; Natalia N D S Cordeiro (Author) FCUP

Journal

Title: Current Pharmaceutical Design

Vol. 22

Pages: 5043-5056

ISSN: 1381-6128

Publisher: Bentham

Indexing

ISI Web of Knowledge - 7 Citations

Scopus - 8 Citations

Other information

Authenticus ID: P-00M-90P

DOI: 10.2174/1381612822666160509124337

Abstract (EN): In this work we report the first attempt to study the effect of activity cliffs over the generalization ability of machine learning (ML) based QSAR classifiers, using as study case a previously reported diverse and noisy dataset focused on drug induced liver injury (DILI) and more than 40 ML classification algorithms. Here, the hypothesis of structure-activity relationship (SAR) continuity restoration by activity cliffs removal is tested as a potential solution to overcome such limitation. Previously, a parallelism was established between activity cliffs generators (ACGs) and instances that should be misclassified (ISMs), a related concept from the field of machine learning. Based on this concept we comparatively studied the classification performance of multiple machine learning classifiers as well as the consensus classifier derived from predictive classifiers obtained from training sets including or excluding ACGs. The influence of the removal of ACGs from the training set over the virtual screening performance was also studied for the respective consensus classifiers algorithms. In general terms, the removal of the ACGs from the training process slightly decreased the overall accuracy of the ML classifiers and multi-classifiers, improving their sensitivity (the weakest feature of ML classifiers trained with ACGs) but decreasing their specificity. Although these results do not support a positive effect of the removal of ACGs over the classification performance of ML classifiers, the "balancing effect" of ACG removal demonstrated to positively influence the virtual screening performance of multi-classifiers based on valid base ML classifiers. Specially, the early recognition ability was significantly favored after ACGs removal. The results presented and discussed in this work represent the first step towards the application of a remedial solution to the activity cliffs problem in QSAR studies.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 14