Entity extraction, animal disease-related event recognition and classification from web

Abstract

Global epidemic surveillance is an essential task for national biosecurity management and bioterrorism prevention. The main goal is to protect the public from major health threads. To perform this task effectively one requires reliable, timely and accurate medical information from a wide range of sources. Towards this goal, we present a framework for epidemiological analytics that can be used to extract and visualize infectious disease outbreaks from the variety of unstructured web sources automatically. More precisely, in this thesis, we consider several research tasks including document relevance classification, entity extraction and animal disease-related event recognition in the veterinary epidemiology domain. First, we crawl web sources and classify collected documents by topical relevance using supervised learning algorithms. Next, we propose a novel approach for automated ontology construction in the veterinary medicine domain. Our approach is based on semantic relationship discovery using syntactic patterns. We then apply our automatically-constructed ontology for the domain-specific entity extraction task. Moreover, we compare our ontology-based entity extraction results with an alternative sequence labeling approach. We introduce a sequence labeling method for the entity tagging that relies on syntactic feature extraction using a sliding window. Finally, we present our novel sentence-based event recognition approach that includes three main steps: entity extraction of animal diseases, species, locations, dates and the confirmation status n-grams; event-related sentence classification into two categories - suspected or confirmed; automated event tuple generation and aggregation. We show that our document relevance classification results as well as entity extraction and disease-related event recognition results are significantly better compared to the results reported by other animal disease surveillance systems.