Medical document coding is the process of assigning labels from a structured label space (ontology – e.g., ICD-9) to medical documents. This process is laborious, costly, and error-prone. In recent years, efforts have been made to automate this process with neural models. The label spaces are large (in the order of thousands of labels) and follow a big-head long-tail label distribution, giving rise to few-shot and zero-shot scenarios. Previous efforts tried to address these scenarios within the model, leading to improvements on rare labels, but worse results on frequent ones. We propose data augmentation and synthesis techniques in order to address these scenarios. We further introduce an analysis technique for this setting inspired by confusion matrices. This analysis technique points to the positive impact of data augmentation and synthesis, but also highlights more general issues of confusion within families of codes, and underprediction.

Large-Scale Multi-Label Text Classification (LMTC) includes tasks with hierarchical label spaces, such as automatic assignment of ICD-9 codes to discharge summaries. Performance of models in prior art is evaluated with standard precision, recall, and F1 measures without regard for the rich hierarchical structure. In this work we argue for hierarchical evaluation of the predictions of neural LMTC models. With the example of the ICD-9 ontology we describe a structural issue in the representation of the structured label space in prior art, and propose an alternative representation based on the depth of the ontology. We propose a set of metrics for hierarchical evaluation using the depth-based representation. We compare the evaluation scores from the proposed metrics with previously used metrics on prior art LMTC models for ICD-9 coding in MIMIC-III. We also propose further avenues of research involving the proposed ontological representation.

We propose a novel attention network for document annotation with user-generated tags. The network is designed according to the human reading and annotation behaviour. Usually, users try to digest the title and obtain a rough idea about the topic first, and then read the content of the document. Present research shows that the title metadata could largely affect the social annotation. To better utilise this information, we design a framework that separates the title from the content of a document and apply a title-guided attention mechanism over each sentence in the content. We also propose two semantic-based loss regularisers that enforce the output of the network to conform to label semantics, i.e. similarity and subsumption. We analyse each part of the proposed system with two real-world open datasets on publication and question annotation. The integrated approach, Joint Multi-label Attention Network (JMAN), significantly outperformed the Bidirectional Gated Recurrent Unit (Bi-GRU) by around 13%-26% and the Hierarchical Attention Network (HAN) by around 4%-12% on both datasets, with around 10%-30% reduction of training time.