Improving ranking for systematic reviews using query adaptation

Identifying relevant studies for inclusion in systematic reviews requires significant effort from human experts who manually screen large numbers of studies. The problem is made more difficult by the growing volume of medical literature and Information Retrieval techniques have proved to be useful to reduce workload. Reviewers are often interested in particular types of evidence such as Diagnostic Test Accuracy studies. This paper explores the use of query adaption to identify particular types of evidence and thereby reduce the workload placed on reviewers. A simple retrieval system that ranks studies using TF.IDF weighted cosine similarity was implemented. The Log-Likelihood, ChiSquared and Odds-Ratio lexical statistics and relevance feedback were used to generate sets of terms that indicate evidence relevant to Diagnostic Test Accuracy reviews. Experiments using a set of 80 systematic reviews from the CLEF2017 and CLEF2018 eHealth tasks demonstrate that the approach improves retrieval performance

Cross-domain sentiment classification using a sentiment sensitive thesaurus

Automatic classification of sentiment is important for numerous applications such as opinion mining, opinion summarization, contextual advertising, and market analysis. However, sentiment is expressed differently in different domains, and annotating corpora for every possible domain of interest is costly. Applying a sentiment classifier trained using labeled data for a particular domain to classify sentiment of user reviews on a different domain often results in poor performance. We propose a method to overcome this problem in cross-domain sentiment classification. First, we create a sentiment sensitive distributional thesaurus using labeled data for the source domains and unlabeled data for both source and target domains. Sentiment sensitivity is achieved in the thesaurus by incorporating document level sentiment labels in the context vectors used as the basis for measuring the distributional similarity between words. Next, we use the created thesaurus to expand feature vectors during train and test times in a binary classifier. The proposed method significantly outperforms numerous baselines and returns results that are comparable with previously proposed cross-domain sentiment classification methods. We conduct an extensive empirical analysis of the proposed method on single and multi-source domain adaptation, unsupervised and supervised domain adaptation, and numerous similarity measures for creating the sentiment sensitive thesaurus

Doctor of Philosophy

dissertationMedical knowledge learned in medical school can become quickly outdated given the tremendous growth of the biomedical literature. It is the responsibility of medical practitioners to continuously update their knowledge with recent, best available clinical evidence to make informed decisions about patient care. However, clinicians often have little time to spend on reading the primary literature even within their narrow specialty. As a result, they often rely on systematic evidence reviews developed by medical experts to fulfill their information needs. At the present, systematic reviews of clinical research are manually created and updated, which is expensive, slow, and unable to keep up with the rapidly growing pace of medical literature. This dissertation research aims to enhance the traditional systematic review development process using computer-aided solutions. The first study investigates query expansion and scientific quality ranking approaches to enhance literature search on clinical guideline topics. The study showed that unsupervised methods can improve retrieval performance of a popular biomedical search engine (PubMed). The proposed methods improve the comprehensiveness of literature search and increase the ratio of finding relevant studies with reduced screening effort. The second and third studies aim to enhance the traditional manual data extraction process. The second study developed a framework to extract and classify texts from PDF reports. This study demonstrated that a rule-based multipass sieve approach is more effective than a machine-learning approach in categorizing document-level structures and iv that classifying and filtering publication metadata and semistructured texts enhances the performance of an information extraction system. The proposed method could serve as a document processing step in any text mining research on PDF documents. The third study proposed a solution for the computer-aided data extraction by recommending relevant sentences and key phrases extracted from publication reports. This study demonstrated that using a machine-learning classifier to prioritize sentences for specific data elements performs equally or better than an abstract screening approach, and might save time and reduce errors in the full-text screening process. In summary, this dissertation showed that there are promising opportunities for technology enhancement to assist in the development of systematic reviews. In this modern age when computing resources are getting cheaper and more powerful, the failure to apply computer technologies to assist and optimize the manual processes is a lost opportunity to improve the timeliness of systematic reviews. This research provides methodologies and tests hypotheses, which can serve as the basis for further large-scale software engineering projects aimed at fully realizing the prospect of computer-aided systematic reviews

Generating Natural Language Queries for More Effective Systematic Review Screening Prioritisation

Screening prioritisation in medical systematic reviews aims to rank the set of documents retrieved by complex Boolean queries. The goal is to prioritise the most important documents so that subsequent review steps can be carried out more efficiently and effectively. The current state of the art uses the final title of the review to rank documents using BERT-based neural neural rankers. However, the final title is only formulated at the end of the review process, which makes this approach impractical as it relies on ex post facto information. At the time of screening, only a rough working title is available, with which the BERT-based ranker achieves is significantly worse than the final title. In this paper, we explore alternative sources of queries for screening prioritisation, such as the Boolean query used to retrieve the set of documents to be screened, and queries generated by instruction-based generative large language models such as ChatGPT and Alpaca. Our best approach is not only practical based on the information available at screening time, but is similar in effectiveness with the final title.Comment: Preprints for Accepted paper in SIGIR-AP-202

Identifying Relevant Evidence for Systematic Reviews and Review Updates

Systematic reviews identify, assess and synthesise the evidence available to answer complex research questions. They are essential in healthcare, where the volume of evidence in scientific research publications is vast and cannot feasibly be identified or analysed by individual clinicians or decision makers. However, the process of creating a systematic review is time consuming and expensive. The pace of scientific publication in medicine and related fields also means that evidence bases are continually changing and review conclusions can quickly become out of date. Therefore, developing methods to support the creating and updating of reviews is essential to reduce the workload required and thereby ensure that reviews remain up to date. This research aims to support systematic reviews, thus improving healthcare through natural language processing and information retrieval techniques. More specifically, this thesis aims to support the process of identifying relevant evidence for systematic reviews and review updates to reduce the workload required from researchers. This research proposes methods to improve studies ranking for systematic reviews. In addition, this thesis describes a dataset of systematic review updates in the field of medicine created using 25 Cochrane reviews. Moreover, this thesis develops an algorithm to automatically refine the Boolean query to improve the identification of relevant studies for review updates. The research demonstrates that automating the process of identifying relevant evidence can reduce the workload of conducting and updating systematic reviews

Access to recorded interviews: A research agenda

Recorded interviews form a rich basis for scholarly inquiry. Examples include oral histories, community memory projects, and interviews conducted for broadcast media. Emerging technologies offer the potential to radically transform the way in which recorded interviews are made accessible, but this vision will demand substantial investments from a broad range of research communities. This article reviews the present state of practice for making recorded interviews available and the state-of-the-art for key component technologies. A large number of important research issues are identified, and from that set of issues, a coherent research agenda is proposed