TWIX: a Two-Stage Approach for End-To-End Named Entity Recognition and Relation Extraction

Abstract

The exponential growth of scientific publications calls for automatic Information Extraction (IE) systems to support knowledge discovery. In this context, the GutBrainIE benchmark evaluates Named Entity Recognition (NER), Named Entity Recognition and Disambiguation (NERD), and Relation Extraction (RE) systems in the gut-brain axis domain. We propose Two-stage Workflow for Information eXtraction (TWIX), an end-to-end IE pipeline featuring three interconnected modules, each leveraging a two-stage framework to solve all four GutBrainIE subtasks. Evaluation on the development and test sets shows that our method substantially outperforms the baseline by a wide margin, while also ranking first among all participant submissions across all subtasks. These results indicate that the proposed two-stage pipeline effectively improves both precision and recall in practical settings.