Exploiting semantics for improving clinical information retrieval

Clinical information retrieval (IR) presents several challenges including terminology mismatch and granularity mismatch. One of the main objectives in clinical IR is to fill the semantic gap among the queries and documents and going beyond keywords matching. To address these issues, in this study we attempt to use semantic information to improve the performance of clinical IR systems by representing queries in an expressive and meaningful context. In this study we propose query context modeling to improve the effectiveness of clinical IR systems. To model query contexts we propose two novel approaches to modeling medical query contexts. The first approach concerns modeling medical query contexts based on mining semantic-based AR for improving clinical text retrieval. The query context is derived from the rules that cover the query and then weighted according to their semantic relatedness to the query concepts. In our second approach we model a representative query context by developing query domain ontology. To develop query domain ontology we extract all the concepts that have semantic relationship with the query concept(s) in UMLS ontologies. Query context represents concepts extracted from query domain ontology and weighted according to their semantic relatedness to the query concept(s). The query context is then exploited in the patient records query expansion and re-ranking for improving clinical retrieval performance. We evaluate this approach on the TREC Medical Records dataset. Results show that our proposed approach significantly improves the retrieval performance compare to classic keyword-based IR model

A survey on the use of relevance feedback for information access systems

Users of online search engines often find it difficult to express their need for information in the form of a query. However, if the user can identify examples of the kind of documents they require then they can employ a technique known as relevance feedback. Relevance feedback covers a range of techniques intended to improve a user's query and facilitate retrieval of information relevant to a user's information need. In this paper we survey relevance feedback techniques. We study both automatic techniques, in which the system modifies the user's query, and interactive techniques, in which the user has control over query modification. We also consider specific interfaces to relevance feedback systems and characteristics of searchers that can affect the use and success of relevance feedback systems

A study of relevance feedback in vector space model

Information Retrieval is the science of searching for information or documents based on information need from a huge set of documents. It has been an active field of research since early 19th century and different models of retrieval came in to existence to cater the information need. This thesis starts with understanding some of the basic information retrieval models, followed by implementation of one of the most popular statistical retrieval model known as Vector Space Model. This model ranks the documents in the collection based on the similarity measure calculated between the query and the respective document. The user specifies the information need which is more commonly known as a query using the visual interface provided. The given query is then processed and the results are displayed to the user in a ranked order. We then focus on the Relevance feedback, a technique that modifies the user query based on the characteristics of the document collection to improve the results. In this thesis, we explore different types and models of relevance feedback that can be applied to Vector Space model and how they affect the performance of the model

Supporting Source Code Search with Context-Aware and Semantics-Driven Query Reformulation

Software bugs and failures cost trillions of dollars every year, and could even lead to deadly accidents (e.g., Therac-25 accident). During maintenance, software developers fix numerous bugs and implement hundreds of new features by making necessary changes to the existing software code. Once an issue report (e.g., bug report, change request) is assigned to a developer, she chooses a few important keywords from the report as a search query, and then attempts to find out the exact locations in the software code that need to be either repaired or enhanced. As a part of this maintenance, developers also often select ad hoc queries on the fly, and attempt to locate the reusable code from the Internet that could assist them either in bug fixing or in feature implementation. Unfortunately, even the experienced developers often fail to construct the right search queries. Even if the developers come up with a few ad hoc queries, most of them require frequent modifications which cost significant development time and efforts. Thus, construction of an appropriate query for localizing the software bugs, programming concepts or even the reusable code is a major challenge. In this thesis, we overcome this query construction challenge with six studies, and develop a novel, effective code search solution (BugDoctor) that assists the developers in localizing the software code of interest (e.g., bugs, concepts and reusable code) during software maintenance. In particular, we reformulate a given search query (1) by designing novel keyword selection algorithms (e.g., CodeRank) that outperform the traditional alternatives (e.g., TF-IDF), (2) by leveraging the bug report quality paradigm and source document structures which were previously overlooked and (3) by exploiting the crowd knowledge and word semantics derived from Stack Overflow Q&A site, which were previously untapped. Our experiment using 5000+ search queries (bug reports, change requests, and ad hoc queries) suggests that our proposed approach can improve the given queries significantly through automated query reformulations. Comparison with 10+ existing studies on bug localization, concept location and Internet-scale code search suggests that our approach can outperform the state-of-the-art approaches with a significant margin

Semantic concept extraction from electronic medical records for enhancing information retrieval performance

With the healthcare industry increasingly using EMRs, there emerges an opportunity for knowledge discovery within the healthcare domain that was not possible with paper-based medical records. One such opportunity is to discover UMLS concepts from EMRs. However, with opportunities come challenges that need to be addressed. Medical verbiage is very different from common English verbiage and it is reasonable to assume extracting any information from medical text requires different protocols than what is currently used in common English text. This thesis proposes two new semantic matching models: Term-Based Matching and CUI-Based Matching. These two models use specialized biomedical text mining tools that extract medical concepts from EMRs. Extensive experiments to rank the extracted concepts are conducted on the University of Pittsburgh BLULab NLP Repository for the TREC 2011 Medical Records track dataset that consists of 101,711 EMRs that contain concepts in 34 predefined topics. This thesis compares the proposed semantic matching models against the traditional weighting equations and information retrieval tools used in the academic world today

IfD - information for discrimination

The problem of term mismatch and ambiguity has long been serious and outstanding in IR. The problem can result in the system formulating an incomplete and imprecise query representation, leading to a failure of retrieval. Many query reformulation methods have been proposed to address the problem. These methods employ term classes which are considered as related to individual query terms. They are hindered by the computational cost of term classification, and by the fact that the terms in some class are generally related to some specific query term belonging to the class rather than relevant to the context of the query. In this thesis we propose a series of methods for automatic query reformulation (AQR). The methods constitute a formal model called IfD, standing for Information for Discrimination. In IfD, each discrimination measure is modelled as information contained in terms supporting one of two opposite hypotheses. The extent of association of terms with the query can thus be defined based directly on the discrimination. The strength of association of candidate terms with the query can then be computed, and good terms can be selected to enhance the query. Justifications for IfD are presented from several aspects: formal interpretations of infor­mation for discrimination are introduced to show its soundness; criteria are put forward to show its rationality; properties of discrimination measures are analysed to show its appro­priateness; examples are examined to show its usability; extension is discussed to show its potential; implementation is described to show its feasibility; comparisons with other methods are made to show its flexibility; improvements in retrieval performance are exhibited to show its powerful capability. Our conclusion is that the advantage and promise IfD should make it an indispensable methodology for AQR, which we believe can be an effective technique for improvement in retrieval performance

Re-ranking Real-time Web Tweets to Find Reliable and Influential Twitterers

Twitter is a powerful social media tool to share information on different topics around the world. Following different users/accounts is the most effective way to get information propagated in Twitter. Due to Twitter's limited searching and lack of navigation support, searching Twitter is not easy and requires effort to find reliable information. This thesis proposed a new methodology to rank tweets based on their authority with the goal of aiding users identifying influential Twitterers. This methodology, HIRKM rank, is influenced by PageRank, Alexa Rank, original tweet or a retweet and the use of hash tags to determine the authorisation of each tweet. This method is applied to rank TREC 2011 microblogging dataset which contains over 16 million tweets based on 50 predefined topics. The results are a list of tweets presented in a descending order based on their authorities which are relevant to the users search queries and will be evaluated using TREC’s official golden standard for the microblogging dataset

Improving Arabic Light Stemming in Information Retrieval Systems

Information retrieval refers to the retrieval of textual documents such as newsprint and magazine articles or Web documents. Due to extensive research in the IR field, there are many retrieval techniques that have been developed for Arabic language. The main objective of this research to improve Arabic information retrieval by enhancing light stemming and preprocessing stage and to contribute to the open source community, also establish a guideline for Arabic normalization and stop-word removal. To achieve these objectives, we create a GUI toolkit that implements preprocessing stage that is necessary for information retrieval. One of these steps is normalizing, which we improved and introduced a set of rules to be standardized and improved by other researchers. The next preprocessing step we improved is stop-word removal, we introduced two different stop-word lists, the first one is intensive stop-word list for reducing the size of the index and ambiguous words, and the other is light stop-word list for better results with recall in information retrieval applications. We improved light stemming by update a suffix rule, and introduce the use of Arabized words, 100 words manually collected, these words should not follow the stemming rules since they came to Arabic language from other languages, and show how this improve results compared to two popular stemming algorithms like Khoja and Larkey stemmers. The proposed toolkit was integrated into a popular IR platform known as Terrier IR platform. We implemented Arabic language support into the Terrier IR platform. We used TF-IDF scoring model from Terrier IR platform. We tested our results using OSAC datasets. We used java programming language and Terrier IR platform for the proposed systems. The infrastructure we used consisted of CORE I7 CPU ran speed at 3.4 GHZ and 8 GB RAM

A heuristic information retrieval study : an investigation of methods for enhanced searching of distributed data objects exploiting bidirectional relevance feedback

A thesis submitted for the degree of Doctor of Philosophy of the University of LutonThe primary aim of this research is to investigate methods of improving the effectiveness of current information retrieval systems. This aim can be achieved by accomplishing numerous supporting objectives. A foundational objective is to introduce a novel bidirectional, symmetrical fuzzy logic theory which may prove valuable to information retrieval, including internet searches of distributed data objects. A further objective is to design, implement and apply the novel theory to an experimental information retrieval system called ANACALYPSE, which automatically computes the relevance of a large number of unseen documents from expert relevance feedback on a small number of documents read. A further objective is to define a methodology used in this work as an experimental information retrieval framework consisting of multiple tables including various formulae which anow a plethora of syntheses of similarity functions, ternl weights, relative term frequencies, document weights, bidirectional relevance feedback and history adjusted term weights. The evaluation of bidirectional relevance feedback reveals a better correspondence between system ranking of documents and users' preferences than feedback free system ranking. The assessment of similarity functions reveals that the Cosine and Jaccard functions perform significantly better than the DotProduct and Overlap functions. The evaluation of history tracking of the documents visited from a root page reveals better system ranking of documents than tracking free information retrieval. The assessment of stemming reveals that system information retrieval performance remains unaffected, while stop word removal does not appear to be beneficial and can sometimes be harmful. The overall evaluation of the experimental information retrieval system in comparison to a leading edge commercial information retrieval system and also in comparison to the expert's golden standard of judged relevance according to established statistical correlation methods reveal enhanced system information retrieval effectiveness

Abduction, Explanation and Relevance Feedback

Selecting good query terms to represent an information need is difficult. The complexity of verbalising an information need can increase when the need is vague, when the document collection is unfamiliar or when the searcher is inexperienced with information retrieval (IR) systems. It is much easier, however, for a user to assess which documents contain relevant information. Relevance feedback (RF) techniques make use of this fact to automatically modify a query representation based on the documents a user considers relevant. RF has proved to be relatively successful at increasing the effectiveness of retrieval systems in certain types of search, and RF techniques have gradually appeared in operational systems and even some Web engines. However, the traditional approaches to RF do not consider the behavioural aspects of information seeking. The standard RF algorithms consider only what documents the user has marked as relevant; they do not consider how the user has assessed relevance. For RF to become an effective support to information seeking it is imperative to develop new models of RF that are capable of incorporating how users make relevance assessments. In this thesis I view RF as a process of explanation. A RF theory should provide an explanation of why a document is relevant to an information need. Such an explanation can be based on how information is used within documents. I use abductive inference to provide a framework for an explanation-based account of RF. Abductive inference is specifically designed as a technique for generating explanations of complex events, and has been widely used in a range of diagnostic systems. Such a framework is capable of producing a set of possible explanations for why a user marked a number of documents relevant at the current search iteration. The choice of which explanation to use is guided by information on how the user has interacted with the system---how many documents they have marked relevant, where in the document ranking the relevant documents occur and the relevance score given to a document by the user. This behavioural information is used to create explanations and to choose which type of explanation is required in the search. The explanation is then used as the basis of a modified query to be submitted to the system. I also investigate how the notion of explanation can be used at the interface to encourage more use of RF by searchers