Acyclic Subgraph based Descriptor Spaces for Chemical Compound Retrieval and Classification

In recent years the development of computational techniques that build models to correctly assign chemical compounds to various classes or to retrieve potential drug-like compounds has been an active area of research. These techniques are used extensively at various phases during the drug development process. Many of the best-performing techniques for these tasks, utilize a descriptor-based representation of the compound that captures various aspects of the underlying molecular graph’s topology. In this paper we introduce and describe algorithms for efficiently generating a new set of descriptors that are derived from all connected acyclic fragments present in the molecular graphs. In addition, we introduce an extension to existing vector-based kernel functions to take into account the length of the fragments present in the descriptors. We experimentally evaluate the performance of the new descriptors in the context of SVM-based classification and ranked-retrieval on 28 classification and retrieval problems derived from 17 datasets. Our experiments show that for both the classification and retrieval tasks, these new descriptors consistently and statistically outperform previously developed schemes based on the widely used fingerprintand Maccs keys-based descriptors, as well as recently introduced descriptors obtained by mining and analyzing the structure of the molecular graphs.