NDLI: Comparison of descriptor spaces for chemical compound retrieval and classification

Content Provider	Springer Nature Link
Author	Wale, Nikil Watson, Ian A. Karypis, George
Copyright Year	2007
Abstract	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. 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 compare five different set of descriptors that are currently used for chemical compound classification. We also introduce four different descriptors derived from all connected fragments present in the molecular graphs primarily for the purpose of comparing them to the currently used descriptor spaces and analyzing what properties of descriptor spaces are helpful in providing effective representation for 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 previously introduced and the new descriptors in the context of SVM-based classification and ranked-retrieval on 28 classification and retrieval problems derived from 18 datasets. Our experiments show that for both of these tasks, two of the four descriptors introduced in this paper along with the extended connectivity fingerprint based descriptors consistently and statistically outperform previously developed schemes based on the widely used fingerprint- and Maccs keys-based descriptors, as well as recently introduced descriptors obtained by mining and analyzing the structure of the molecular graphs.
Starting Page	347
Ending Page	375
Page Count	29
File Format	PDF
ISSN	02191377
Journal	Knowledge and Information Systems
Volume Number	14
Issue Number	3
e-ISSN	02193116
Language	English
Publisher	Springer-Verlag
Publisher Date	2007-08-23
Publisher Place	London
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	SVM Classification Retreival Descriptor space Kernel Business Information Systems Information Systems and Communication Service
Content Type	Text
Resource Type	Article
Subject	Artificial Intelligence Information Systems Human-Computer Interaction Hardware and Architecture Software

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