Maximum margin classifier working in a set of strings

TL;DR

This paper introduces a novel maximum margin classifier designed to operate directly on string data, avoiding information loss from vectorization, and provides theoretical analysis of its generalization error.

Contribution

It develops a classifier that works directly on strings and extends probability theory for strings to evaluate its asymptotic optimality.

Findings

The classifier operates directly on string data without vectorization.

Theoretical proof of asymptotic optimality of the classifier.

Application to protein interaction prediction demonstrates practical usefulness.

Abstract

Numbers and numerical vectors account for a large portion of data. However, recently the amount of string data generated has increased dramatically. Consequently, classifying string data is a common problem in many fields. The most widely used approach to this problem is to convert strings into numerical vectors using string kernels and subsequently apply a support vector machine that works in a numerical vector space. However, this non-one-to-one conversion involves a loss of information and makes it impossible to evaluate, using probability theory, the generalization error of a learning machine, considering that the given data to train and test the machine are strings generated according to probability laws. In this study, we approach this classification problem by constructing a classifier that works in a set of strings. To evaluate the generalization error of such a classifier theoretically, probability theory for strings is required. Therefore, we first extend a limit theorem on the asymptotic behavior of a consensus sequence of strings, which is the counterpart of the mean of numerical vectors, as demonstrated in the probability theory on a metric space of strings developed by one of the authors and his colleague in a previous study [18]. Using the obtained result, we then demonstrate that our learning machine classifies strings in an asymptotically optimal manner. Furthermore, we demonstrate the usefulness of our machine in practical data analysis by applying it to predicting protein--protein interactions using amino acid sequences.