Custom Named Entity Recognition and Topic Classification for Global Health Publications

Abstract

How should natural language processing models be selected and adapted for global health literature in environments where annotated data and computational resources are limited? This thesis investigates these challenges through experiments on semantic tag discovery, named entity recognition (NER), and multi-label topic classification. First, skip-gram word2vec models trained on progressively larger specialized corpora are compared with BioWordVec to assess how corpus size and domain context influence tag discovery. Vocabulary coverage and qualitative evaluation indicate that broader coverage does not necessarily yield more useful domain-specific associations. The analysis then turns to entity extraction, comparing convolutional spaCy models with a RoBERTa-based transformer on 1,000 annotated sentences. Under a lenient scoring protocol, the transformer achieves 0.80 micro-F1 versus 0.65-0.69 for convolutional models, but takes 82 seconds rather than 5-6 seconds. This trade-off motivates fine-tuning convolutional models and integrating a disease recognizer that achieves 81.33% test F1 on the NCBI Disease Corpus. Combined with PDF preprocessing, entity filtering, and MeSH enrichment, the resulting pipeline supports document-level indexing. To complement entity extraction with thematic annotation, MiniLM-based few-shot classification is compared with BART-MNLI zero-shot inference across 50 topics and 1,000 handcrafted test sentences. BART-MNLI achieves 95.2% single-label accuracy versus 59%; reported multi-label accuracies are 88% and 32% under partly manual assessment. However, its higher inference cost limits practical integration. The results show where domain specialization and lightweight adaptation offer practical value, and where transformer accuracy justifies higher inference costs, providing an empirical basis for building knowledge systems under resource constraints.