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Title: Semantic text classification for cancer text mining
Author: Baker, Simon
Awarding Body: University of Cambridge
Current Institution: University of Cambridge
Date of Award: 2018
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Cancer researchers and oncologists benefit greatly from text mining major knowledge sources in biomedicine such as PubMed. Fundamentally, text mining depends on accurate text classification. In conventional natural language processing (NLP), this requires experts to annotate scientific text, which is costly and time consuming, resulting in small labelled datasets. This leads to extensive feature engineering and handcrafting in order to fully utilise small labelled datasets, which is again time consuming, and not portable between tasks and domains. In this work, we explore emerging neural network methods to reduce the burden of feature engineering while outperforming the accuracy of conventional pipeline NLP techniques. We focus specifically on the cancer domain in terms of applications, where we introduce two NLP classification tasks and datasets: the first task is that of semantic text classification according to the Hallmarks of Cancer (HoC), which enables text mining of scientific literature assisted by a taxonomy that explains the processes by which cancer starts and spreads in the body. The second task is that of the exposure routes of chemicals into the body that may lead to exposure to carcinogens. We present several novel contributions. We introduce two new semantic classification tasks (the hallmarks, and exposure routes) at both sentence and document levels along with accompanying datasets, and implement and investigate a conventional pipeline NLP classification approach for both tasks, performing both intrinsic and extrinsic evaluation. We propose a new approach to classification using multilevel embeddings and apply this approach to several tasks; we subsequently apply deep learning methods to the task of hallmark classification and evaluate its outcome. Utilising our text classification methods, we develop and two novel text mining tools targeting real-world cancer researchers. The first tool is a cancer hallmark text mining tool that identifies association between a search query and cancer hallmarks; the second tool is a new literature-based discovery (LBD) system designed for the cancer domain. We evaluate both tools with end users (cancer researchers) and find they demonstrate good accuracy and promising potential for cancer research.
Supervisor: Korhonen, Anna Sponsor: Commonwealth Scholarship ; Cambridge Trust
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
Keywords: Cancer ; Text Mining ; Machine Learning ; Classification ; Literature-based Discovery ; Hallmarks of Cancer ; Deep Learning ; Artificial Intelligence