A framework for enhancing the query and medical record representations for patient search

Electronic medical records (EMRs) are digital documents stored by medical institutions that detail the observed symptoms, the conducted diagnostic tests, the identified diagnoses and the prescribed treatments. These EMRs are being increasingly used worldwide to improve healthcare services. For example, when a doctor compiles the possible treatments for a patient showing some particular symptoms, it is advantageous to consult the information about patients who were previously treated for those same symptoms. However, finding patients with particular medical conditions is challenging, due to the implicit knowledge inherent within the patients' medical records and queries - such knowledge may be known by medical practitioners, but may be hidden from an information retrieval (IR) system. For instance, the mention of a treatment such as a drug may indicate to a practitioner that a particular diagnosis has been made for the patient, but this diagnosis may not be explicitly mentioned in the patient's medical records. Moreover, the use of negated language (e.g.\ `without', `no') to describe a medical condition of a patient (e.g.\ the patient has no fever) may cause a search system to erroneously retrieve that patient for a query when searching for patients with that medical condition (e.g.\ find patients with fever). This thesis focuses on enhancing the search of EMRs, with the aim of identifying patients with medical histories relevant to the medical conditions stated in a text query. During retrieval, a healthcare practitioner indicates a number of inclusion criteria describing the medical conditions of the patients of interest. To attain effective retrieval performance, we hypothesise that, in a patient search system, both the information needs and patients' histories should be represented based upon \emph{the medical decision process}. In particular, this thesis argues that since the medical decision process typically encompasses four aspects (symptom, diagnostic test, diagnosis and treatment), a patient search system should take into account these aspects and apply inferences to recover the possible implicit knowledge. We postulate that considering these aspects and their derived implicit knowledge at three different levels of the retrieval process (namely, sentence, medical record and inter-record levels) enhances the retrieval performance. Indeed, we propose a novel framework that can gain insights from EMRs and queries, by modelling and reasoning upon information during retrieval in terms of the four aforementioned aspects at the three levels of the retrieval process, and can use these insights to enhance patient search. Firstly, at the sentence level, we extract the medical conditions in the medical records and queries. In particular, we propose to represent only the medical conditions related to the four medical aspects in order to improve the accuracy of our search system. In addition, we identify the context (negative/positive) of terms, which leads to an accurate representation of the medical conditions both in the EMRs and queries. In particular, we aim to prevent patients whose EMRs state the medical conditions in the contexts different from the query from being ranked highly. For example, preventing patients whose EMRs state ``no history of dementia'' from being retrieved for a query searching for patients with dementia. Secondly, at the medical record level, using external knowledge-based resources (e.g.\ ontologies and health-related websites), we leverage the relationships between medical terms to infer the wider medical history of the patient in terms of the four medical aspects. In particular, we estimate the relevance of a patient to the query by exploiting association rules that we extract from the semantic relationships between medical terms using the four aspects of the medical process. For example, patients with a medical history involving a \emph{CABG surgery} (treatment) can be inferred as relevant to a query searching for a patient suffering from \emph{heart disease} (diagnosis), since a CABG surgery is a treatment of heart disease. Thirdly, at the inter-record level, we enhance the retrieval of patients in two different manners. First, we exploit knowledge about how the four medical aspects are handled by different hospital departments to gain a better understanding about the appropriateness of EMRs created by different departments for a given query. We propose to aggregate EMRs at the department level (i.e.\ inter-record level) to extract implicit knowledge (i.e.\ the expertise of each department) and model this department's expertise, while ranking patients. For instance, patients having EMRs from the cardiology department are likely to be relevant to a query searching for patients who suffered from a heart attack. Second, as a medical query typically contains several medical conditions that the relevant patients should satisfy, we propose to explicitly model the relevance towards multiple query medical conditions in the EMRs related to a particular patient during retrieval. In particular, we rank highly those patients that match all the stated medical conditions in the query by adapting coverage-based diversification approaches originally proposed for the web search domain. Finally, we examine the combination of our aforementioned approaches that exploit the implicit knowledge at the three levels of the retrieval process to further improve the retrieval performance by adapting techniques from the fields of data fusion and machine learning. In particular, data fusion techniques, such as CombSUM and CombMNZ, are used to combine the relevance scores computed by the different approaches of the proposed framework. On the other hand, we deploy state-of-the-art learning to rank approaches (e.g.\ LambdaMART and AdaRank) to learn from a set of training data an effective combination of the relevance scores computed by the approaches of the framework. In addition, we introduce a novel selective ranking approach that uses a classifier to effectively apply one of the approaches of the framework on a per-query basis. This thesis draws insights from a thorough evaluation and analysis of the proposed framework using a standard test collection provided by the TREC Medical Records track. The experimental results show the effectiveness of the framework. In particular, the results demonstrate the importance of dealing with the implicit knowledge in patient search by focusing on the medical decision criteria aspects at the three levels of the retrieval process

A Relation Extraction Approach for Clinical Decision Support

In this paper, we investigate how semantic relations between concepts extracted from medical documents can be employed to improve the retrieval of medical literature. Semantic relations explicitly represent relatedness between concepts and carry high informative power that can be leveraged to improve the effectiveness of retrieval functionalities of clinical decision support systems. We present preliminary results and show how relations are able to provide a sizable increase of the precision for several topics, albeit having no impact on others. We then discuss some future directions to minimize the impact of negative results while maximizing the impact of good results.Comment: 4 pages, 1 figure, DTMBio-KMH 2018, in conjunction with ACM 27th Conference on Information and Knowledge Management (CIKM), October 22-26 2018, Lingotto, Turin, Ital

DCU@TRECMed 2012: Using ad-hoc baselines for domain-specific retrieval

This paper describes the first participation of DCU in the TREC Medical Records Track (TRECMed). We performed some initial experiments on the 2011 TRECMed data based on the BM25 retrieval model. Surprisingly, we found that the standard BM25 model with default parameters, performs comparable to the best automatic runs submitted to TRECMed 2011 and would have resulted in rank four out of 29 participating groups. We expected that some form of domain adaptation would increase performance. However, results on the 2011 data proved otherwise: concept-based query expansion decreased performance, and filtering and reranking by term proximity also decreased performance slightly. We submitted four runs based on the BM25 retrieval model to TRECMed 2012 using standard BM25, standard query expansion, result filtering, and concept-based query expansion. Official results for 2012 confirm that domain-specific knowledge does not increase performance compared to the BM25 baseline as applied by us

Ontology-Based MEDLINE Document Classification

An increasing and overwhelming amount of biomedical information is available in the research literature mainly in the form of free-text. Biologists need tools that automate their information search and deal with the high volume and ambiguity of free-text. Ontologies can help automatic information processing by providing standard concepts and information about the relationships between concepts. The Medical Subject Headings (MeSH) ontology is already available and used by MEDLINE indexers to annotate the conceptual content of biomedical articles. This paper presents a domain-independent method that uses the MeSH ontology inter-concept relationships to extend the existing MeSH-based representation of MEDLINE documents. The extension method is evaluated within a document triage task organized by the Genomics track of the 2005 Text REtrieval Conference (TREC). Our method for extending the representation of documents leads to an improvement of 17% over a non-extended baseline in terms of normalized utility, the metric defined for the task. The SVMlight software is used to classify documents

On the Use of XML in Medical Imaging Web-Based Applications

The rapid growth of digital technology in medical fields over recent years has increased the need for applications able to manage patient medical records, imaging data, and chart information. Web-based applications are implemented with the purpose to link digital databases, storage and transmission protocols, management of large volumes of data and security concepts, allowing the possibility to read, analyze, and even diagnose remotely from the medical center where the information was acquired. The objective of this paper is to analyze the use of the Extensible Markup Language (XML) language in web-based applications that aid in diagnosis or treatment of patients, considering how this protocol allows indexing and exchanging the huge amount of information associated with each medical case. The purpose of this paper is to point out the main advantages and drawbacks of the XML technology in order to provide key ideas for future web-based applicationsPeer ReviewedPostprint (author's final draft

DutchHatTrick: semantic query modeling, ConText, section detection, and match score maximization

This report discusses the collaborative work of the ErasmusMC, University of Twente, and the University of Amsterdam on the TREC 2011 Medical track. Here, the task is to retrieve patient visits from the University of Pittsburgh NLP Repository for 35 topics. The repository consists of 101,711 patient reports, and a patient visit was recorded in one or more reports

CAMMD: Context Aware Mobile Medical Devices

Telemedicine applications on a medical practitioners mobile device should be context-aware. This can vastly improve the effectiveness of mobile applications and is a step towards realising the vision of a ubiquitous telemedicine environment. The nomadic nature of a medical practitioner emphasises location, activity and time as key context-aware elements. An intelligent middleware is needed to effectively interpret and exploit these contextual elements. This paper proposes an agent-based architectural solution called Context-Aware Mobile Medical Devices (CAMMD). This framework can proactively communicate patient records to a portable device based upon the active context of its medical practitioner. An expert system is utilised to cross-reference the context-aware data of location and time against a practitioners work schedule. This proactive distribution of medical data enhances the usability and portability of mobile medical devices. The proposed methodology alleviates constraints on memory storage and enhances user interaction with the handheld device. The framework also improves utilisation of network bandwidth resources. An experimental prototype is presented highlighting the potential of this approach