title: Evaluation of hierarchical structured representations for QSPR studies of small molecules and polymers by recursive neural networks.
abstract: This paper reports some recent results from the empirical evaluation of different types of structured molecular representations used in QSPR analysis through a recursive neural network (RNN) model, which allows for their direct use without the need for measuring or computing molecular descriptors. This RNN methodology has been applied to the prediction of the properties of small molecules and polymers. In particular, three different descriptions of cyclic moieties, namely group, template and cyclebreak have been proposed. The effectiveness of the proposed method in dealing with different representations of chemical structures, either specifically designed or of more general use, has been demonstrated by its application to data sets encompassing various types of cyclic structures. For each class of experiments a test set with data that were not used for the development of the model was used for validation, and the comparisons have been based on the test results. The reported results highlight the flexibility of the RNN in directly treating different classes of structured input data without using input descriptors.
authors.affiliation: Department of Chemistry and Industrial Chemistry, University of Pisa, via Risorgimento 35, 56126 Pisa, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Bertinetto
authors.forename: Celia
authors.initials: C
authors.lastname: Duce
authors.forename: Alessio
authors.initials: A
authors.lastname: Micheli
authors.forename: Roberto
authors.initials: R
authors.lastname: Solaro
authors.forename: Antonina
authors.initials: A
authors.lastname: Starita
authors.forename: Maria Rosaria
authors.initials: MR
authors.lastname: Tiné
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D015394:Molecular Structure; D016571:Neural Networks, Computer; D011108:Polymers / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D021281:Quantitative Structure-Activity Relationship; D015203:Reproducibility of Results; D044366:Transition Temperature
chemical_list: D011108:Polymers; D011506:Proteins