Biomedical Information Extraction Pipelines for Public Health in the Age of Deep Learning

abstract: Unstructured texts containing biomedical information from sources such as electronic health records, scientific literature, discussion forums, and social media offer an opportunity to extract information for a wide range of applications in biomedical informatics. Building scalable and efficient pipelines for natural language processing and extraction of biomedical information plays an important role in the implementation and adoption of applications in areas such as public health. Advancements in machine learning and deep learning techniques have enabled rapid development of such pipelines. This dissertation presents entity extraction pipelines for two public health applications: virus phylogeography and pharmacovigilance. For virus phylogeography, geographical locations are extracted from biomedical scientific texts for metadata enrichment in the GenBank database containing 2.9 million virus nucleotide sequences. For pharmacovigilance, tools are developed to extract adverse drug reactions from social media posts to open avenues for post-market drug surveillance from non-traditional sources. Across these pipelines, high variance is observed in extraction performance among the entities of interest while using state-of-the-art neural network architectures. To explain the variation, linguistic measures are proposed to serve as indicators for entity extraction performance and to provide deeper insight into the domain complexity and the challenges associated with entity extraction. For both the phylogeography and pharmacovigilance pipelines presented in this work the annotated datasets and applications are open source and freely available to the public to foster further research in public health.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

Extracting Drug-Drug Interactions with Character-Level and Dependency-Based Embeddings

The DDI track of TAC-2018 challenge addresses the problem of an information retrieval of drug-drug interactions on structured product labeling documents with discontinuous and overlapping entities. In this paper, we present our participation for event extraction subtask (Task 1). We used a supervised long-short-term memory (LSTM) network with conditional random fields decoding (LSTM-CRF) approach with an automatic exploring of words and characters features. Additional dependency-based information was integrated into word embeddings to allow better word representation. Our system performed with above median score

A Survey of Document-Level Information Extraction

Document-level information extraction (IE) is a crucial task in natural language processing (NLP). This paper conducts a systematic review of recent document-level IE literature. In addition, we conduct a thorough error analysis with current state-of-the-art algorithms and identify their limitations as well as the remaining challenges for the task of document-level IE. According to our findings, labeling noises, entity coreference resolution, and lack of reasoning, severely affect the performance of document-level IE. The objective of this survey paper is to provide more insights and help NLP researchers to further enhance document-level IE performance

Automated Assessment of the Aftermath of Typhoons Using Social Media Texts

Disasters are one of the major threats to economics and human societies, causing substantial losses of human lives, properties and infrastructures. It has been our persistent endeavors to understand, prevent and reduce such disasters, and the popularization of social media is offering new opportunities to enhance disaster management in a crowd-sourcing approach. However, social media data is also characterized by its undue brevity, intense noise, and informality of language. The existing literature has not completely addressed these disadvantages, otherwise vast manual efforts are devoted to tackling these problems. The major focus of this research is on constructing a holistic framework to exploit social media data in typhoon damage assessment. The scope of this research covers data collection, relevance classification, location extraction and damage assessment while assorted approaches are utilized to overcome the disadvantages of social media data. Moreover, a semi-supervised or unsupervised approach is prioritized in forming the framework to minimize manual intervention. In data collection, query expansion strategy is adopted to optimize the search recall of typhoon-relevant information retrieval. Multiple filtering strategies are developed to screen the keywords and maintain the relevance to search topics in the keyword updates. A classifier based on a convolutional neural network is presented for relevance classification, with hashtags and word clusters as extra input channels to augment the information. In location extraction, a model is constructed by integrating Bidirectional Long Short-Time Memory and Conditional Random Fields. Feature noise correction layers and label smoothing are leveraged to handle the noisy training data. Finally, a multi-instance multi-label classifier identifies the damage relations in four categories, and the damage categories of a message are integrated with the damage descriptions score to obtain damage severity score for the message. A case study is conducted to verify the effectiveness of the framework. The outcomes indicate that the approaches and models developed in this study significantly improve in the classification of social media texts especially under the framework of semi-supervised or unsupervised learning. Moreover, the results of damage assessment from social media data are remarkably consistent with the official statistics, which demonstrates the practicality of the proposed damage scoring scheme

Identifying Locations of Violent Injuries in Las Vegas to Implement the Cardiff Violence Prevention Model

Public violence in the United States is a major health concern. Incidents involving violent crimes are often not reported to law enforcement. The Cardiff Model is a violence prevention program developed in the UK to identify and enable data sharing of violent injury locations between Emergency Rooms (ER) and local law enforcement to help identify areas for community improvements. The model is now in use in several major cities in the US to reduce violence. Las Vegas has seen an increase in public violence in recent years. As a result, researchers from the Southern Nevada Health District (SNHD) and University of Las Vegas (UNLV) believe the Cardiff Model is a viable solution to address this public health crisis. This research explores natural language processing and machine learning models to extract violent injury location information from ER records in preparation for introducing the Cardiff Violence Prevention Model in Clark County, Nevada