Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments

Abstract

This paper proposes algorithms for inferring a chemical structure from a feature vector based on frequency of labeled paths and small fragments, where this inference problem has a potential application to drug design. In this paper, chemical structures are modeled as trees or tree-like structures. It is shown that the inference problems for these kinds of structures can be solved in polynomial time using dynamic programming-based algorithms. Since these algorithms are not practical, a branchand-bound type algorithm is also proposed. The result of computational experiment suggests that the algorithm can solve the inference problem in a few or few-tens of seconds for moderate size chemical compounds.