This paper studies automatic type qualifier inference for pluggable type systems, which extend the type system of a programming language to incorporate programmer-defined semantic properties. Specifically, we present a method for automatically inferring type qualifiers using machine learning, enabling easy application of pluggable type systems to legacy codebases. To achieve this, we propose a novel representation, NaP-AST, and evaluate various model architectures, including a Graph Transformer Network (GTN), a Graph Convolutional Network, and a Large Language Model. We validate the performance of our models by applying them to 12 open-source programs used in the previous evaluation of the NullAway pluggable type checker, with GTN demonstrating the best performance. Furthermore, we conduct research to estimate the number of Java classes required for a trained model to perform well.