Enhancing clinical concept extraction with distributional semantics

AbstractExtracting concepts (such as drugs, symptoms, and diagnoses) from clinical narratives constitutes a basic enabling technology to unlock the knowledge within and support more advanced reasoning applications such as diagnosis explanation, disease progression modeling, and intelligent analysis of the effectiveness of treatment. The recent release of annotated training sets of de-identified clinical narratives has contributed to the development and refinement of concept extraction methods. However, as the annotation process is labor-intensive, training data are necessarily limited in the concepts and concept patterns covered, which impacts the performance of supervised machine learning applications trained with these data. This paper proposes an approach to minimize this limitation by combining supervised machine learning with empirical learning of semantic relatedness from the distribution of the relevant words in additional unannotated text.The approach uses a sequential discriminative classifier (Conditional Random Fields) to extract the mentions of medical problems, treatments and tests from clinical narratives. It takes advantage of all Medline abstracts indexed as being of the publication type “clinical trials” to estimate the relatedness between words in the i2b2/VA training and testing corpora. In addition to the traditional features such as dictionary matching, pattern matching and part-of-speech tags, we also used as a feature words that appear in similar contexts to the word in question (that is, words that have a similar vector representation measured with the commonly used cosine metric, where vector representations are derived using methods of distributional semantics). To the best of our knowledge, this is the first effort exploring the use of distributional semantics, the semantics derived empirically from unannotated text often using vector space models, for a sequence classification task such as concept extraction. Therefore, we first experimented with different sliding window models and found the model with parameters that led to best performance in a preliminary sequence labeling task.The evaluation of this approach, performed against the i2b2/VA concept extraction corpus, showed that incorporating features based on the distribution of words across a large unannotated corpus significantly aids concept extraction. Compared to a supervised-only approach as a baseline, the micro-averaged F-score for exact match increased from 80.3% to 82.3% and the micro-averaged F-score based on inexact match increased from 89.7% to 91.3%. These improvements are highly significant according to the bootstrap resampling method and also considering the performance of other systems. Thus, distributional semantic features significantly improve the performance of concept extraction from clinical narratives by taking advantage of word distribution information obtained from unannotated data

Modular Machine Learning Methods for Computer-Aided Diagnosis of Breast Cancer

The purpose of this study was to improve breast cancer diagnosis by reducing the number of benign biopsies performed. To this end, we investigated modular and ensemble systems of machine learning methods for computer-aided diagnosis (CAD) of breast cancer. A modular system partitions the input space into smaller domains, each of which is handled by a local model. An ensemble system uses multiple models for the same cases and combines the models\u27 predictions. Five supervised machine learning techniques (LDA, SVM, BP-ANN, CBR, CART) were trained to predict the biopsy outcome from mammographic findings (BIRADS™) and patient age based on a database of 2258 cases mixed from multiple institutions. The generalization of the models was tested on second set of 2177 cases. Clusters were identified in the database using a priori knowledge and unsupervised learning methods (agglomerative hierarchical clustering followed by K-Means, SOM, AutoClass). The performance of the global models over the clusters was examined and local models were trained for clusters. While some local models were superior to some global models, we were unable to build a modular CAD system that was better than the global BP-ANN model. The ensemble systems based on simplistic combination schemes did not result in significant improvements and more complicated combination schemes were found to be unduly optimistic. One of the most striking results of this dissertation was that CAD systems trained on a mixture of lesion types performed much better on masses than on calcifications. Our study of the institutional effects suggests that models built on cases mixed between institutions may overcome some of the weaknesses of models built on cases from a single institution. It was suggestive that each of the unsupervised methods identified a cluster of younger women with well-circumscribed or obscured, oval-shaped masses that accounted for the majority of the BP-ANN’s recommendations for follow up. From the cluster analysis and the CART models, we determined a simple diagnostic rule that performed comparably to the global BP-ANN. Approximately 98% sensitivity could be maintained while providing approximately 26% specificity. This should be compared to the clinical status quo of 100% sensitivity and 0% specificity on this database of indeterminate cases already referred to biopsy

Information Retrieval Systems Adapted to the Biomedical Domain

The terminology used in Biomedicine shows lexical peculiarities that have required the elaboration of terminological resources and information retrieval systems with specific functionalities. The main characteristics are the high rates of synonymy and homonymy, due to phenomena such as the proliferation of polysemic acronyms and their interaction with common language. Information retrieval systems in the biomedical domain use techniques oriented to the treatment of these lexical peculiarities. In this paper we review some of the techniques used in this domain, such as the application of Natural Language Processing (BioNLP), the incorporation of lexical-semantic resources, and the application of Named Entity Recognition (BioNER). Finally, we present the evaluation methods adopted to assess the suitability of these techniques for retrieving biomedical resources.Comment: 6 pages, 4 table

Ontology Enrichment from Free-text Clinical Documents: A Comparison of Alternative Approaches

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships, as well as difficulty in updating the ontology as domain knowledge changes. Methodologies developed in the fields of Natural Language Processing (NLP), Information Extraction (IE), Information Retrieval (IR), and Machine Learning (ML) provide techniques for automating the enrichment of ontology from free-text documents. In this dissertation, I extended these methodologies into biomedical ontology development. First, I reviewed existing methodologies and systems developed in the fields of NLP, IR, and IE, and discussed how existing methods can benefit the development of biomedical ontologies. This previously unconducted review was published in the Journal of Biomedical Informatics. Second, I compared the effectiveness of three methods from two different approaches, the symbolic (the Hearst method) and the statistical (the Church and Lin methods), using clinical free-text documents. Third, I developed a methodological framework for Ontology Learning (OL) evaluation and comparison. This framework permits evaluation of the two types of OL approaches that include three OL methods. The significance of this work is as follows: 1) The results from the comparative study showed the potential of these methods for biomedical ontology enrichment. For the two targeted domains (NCIT and RadLex), the Hearst method revealed an average of 21% and 11% new concept acceptance rates, respectively. The Lin method produced a 74% acceptance rate for NCIT; the Church method, 53%. As a result of this study (published in the Journal of Methods of Information in Medicine), many suggested candidates have been incorporated into the NCIT; 2) The evaluation framework is flexible and general enough that it can analyze the performance of ontology enrichment methods for many domains, thus expediting the process of automation and minimizing the likelihood that key concepts and relationships would be missed as domain knowledge evolves

An investigation into deviant morphology : issues in the implementation of a deep grammar for Indonesian

This thesis investigates deviant morphology in Indonesian for the implementation of a deep grammar. In particular we focus on the implementation of the verbal suffix -kan. This suffix has been described as having many functions, which alter the kinds of arguments and the number of arguments the verb takes (Dardjowidjojo 1971; Chung 1976; Arka 1993; Vamarasi 1999; Kroeger 2007; Son and Cole 2008). Deep grammars or precision grammars (Butt et al. 1999a; Butt et al. 2003; Bender et al. 2011) have been shown to be useful for natural language processing (NLP) tasks, such as machine translation and generation (Oepen et al. 2004; Cahill and Riester 2009; Graham 2011), and information extraction (MacKinlay et al. 2012), demonstrating the need for linguistically rich information to aid NLP tasks. Although these linguistically-motivated grammars are invaluable resources to the NLP community, the biggest drawback is the time required for the manual creation and curation of the lexicon. Our work aims to expedite this process by applying methods to assign syntactic information to kan-affixed verbs automatically. The method we employ exploits the hypothesis that semantic similarity is tightly connected with syntactic behaviour (Levin 1993). Our endeavour in automatically acquiring verbal information for an Indonesian deep grammar poses a number of lingustic challenges. First of all Indonesian verbs exhibit voice marking that is characteristic of the subgrouping of its language family. In order to be able to characterise verbal behaviour in Indonesian, we first need to devise a detailed analysis of voice for implementation. Another challenge we face is the claim that all open class words in Indonesian, at least as it is spoken in some varieties (Gil 1994; Gil 2010), cannot linguistically be analysed as being distinct from each other. That is, there is no distiction between nouns, verbs or adjectives in Indonesian, and all word from the open class categories should be analysed uniformly. This poses difficulties in implementing a grammar in a linguistically motivated way, as well discovering syntactic behaviour of verbs, if verbs cannot be distinguished from nouns. As part of our investigation we conduct experiments to verify the need to employ word class categories, and we find that indeed these are linguistically motivated labels in Indonesian. Through our investigation into deviant morphological behaviour, we gain a better characterisation of the morphosyntactic effects of -kan, and we discover that, although Indonesian has been labelled as a language with no open word class distinctions, word classes can be established as being linguistically-motivated

Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web

Ontology verbalization in agglutinating Bantu languages: a study of Runyankore and its generalizability

Natural Language Generation (NLG) systems have been developed to generate text in multiple domains, including personalized patient information. However, their application is limited in Africa because they generate text in English, yet indigenous languages are still predominantly spoken throughout the continent, especially in rural areas. The existing healthcare NLG systems cannot be reused for Bantu languages due to the complex grammatical structure, nor can the generated text be used in machine translation systems for Bantu languages because they are computationally under-resourced. This research aimed to verbalize ontologies in agglutinating Bantu languages. We had four research objectives: (1) noun pluralization and verb conjugation in Runyankore; (2) Runyankore verbalization patterns for the selected description logic constructors; (3) combining the pluralization, conjugation, and verbalization components to form a Runyankore grammar engine; and (4) generalizing the Runyankore and isiZulu approaches to ontology verbalization to other agglutinating Bantu languages. We used an approach that combines morphology with syntax and semantics to develop a noun pluralizer for Runyankore, and used Context-Free Grammars (CFGs) for verb conjugation. We developed verbalization algorithms for eight constructors in a description logic. We then combined these components into a grammar engine developed as a Protégé5X plugin. The investigation into generalizability used the bootstrap approach, and investigated bootstrapping for languages in the same language zone (intra-zone bootstrappability) and languages across language zones (inter-zone bootstrappability). We obtained verbalization patterns for Luganda and isiXhosa, in the same zones as Runyankore and isiZulu respectively, and chiShona, Kikuyu, and Kinyarwanda from different zones, and used the bootstrap metric that we developed to identify the most efficient source—target bootstrap pair. By regrouping Meinhof’s noun class system we were able to eliminate non-determinism during computation, and this led to the development of a generic noun pluralizer. We also showed that CFGs can conjugate verbs in the five additional languages. Finally, we proposed the architecture for an API that could be used to generate text in agglutinating Bantu languages. Our research provides a method for surface realization for an under-resourced and grammatically complex family of languages, Bantu languages. We leave the development of a complete NLG system based on the Runyankore grammar engine and of the API as areas for future work

Knowledge Modelling and Learning through Cognitive Networks

One of the most promising developments in modelling knowledge is cognitive network science, which aims to investigate cognitive phenomena driven by the networked, associative organization of knowledge. For example, investigating the structure of semantic memory via semantic networks has illuminated how memory recall patterns influence phenomena such as creativity, memory search, learning, and more generally, knowledge acquisition, exploration, and exploitation. In parallel, neural network models for artificial intelligence (AI) are also becoming more widespread as inferential models for understanding which features drive language-related phenomena such as meaning reconstruction, stance detection, and emotional profiling. Whereas cognitive networks map explicitly which entities engage in associative relationships, neural networks perform an implicit mapping of correlations in cognitive data as weights, obtained after training over labelled data and whose interpretation is not immediately evident to the experimenter. This book aims to bring together quantitative, innovative research that focuses on modelling knowledge through cognitive and neural networks to gain insight into mechanisms driving cognitive processes related to knowledge structuring, exploration, and learning. The book comprises a variety of publication types, including reviews and theoretical papers, empirical research, computational modelling, and big data analysis. All papers here share a commonality: they demonstrate how the application of network science and AI can extend and broaden cognitive science in ways that traditional approaches cannot

Semi-Supervised Named Entity Recognition:\ud Learning to Recognize 100 Entity Types with Little Supervision\ud

Named Entity Recognition (NER) aims to extract and to classify rigid designators in text such as proper names, biological species, and temporal expressions. There has been growing interest in this field of research since the early 1990s. In this thesis, we document a trend moving away from handcrafted rules, and towards machine learning approaches. Still, recent machine learning approaches have a problem with annotated data availability, which is a serious shortcoming in building and maintaining large-scale NER systems. \ud \ud In this thesis, we present an NER system built with very little supervision. Human supervision is indeed limited to listing a few examples of each named entity (NE) type. First, we introduce a proof-of-concept semi-supervised system that can recognize four NE types. Then, we expand its capacities by improving key technologies, and we apply the system to an entire hierarchy comprised of 100 NE types. \ud \ud Our work makes the following contributions: the creation of a proof-of-concept semi-supervised NER system; the demonstration of an innovative noise filtering technique for generating NE lists; the validation of a strategy for learning disambiguation rules using automatically identified, unambiguous NEs; and finally, the development of an acronym detection algorithm, thus solving a rare but very difficult problem in alias resolution. \ud \ud We believe semi-supervised learning techniques are about to break new ground in the machine learning community. In this thesis, we show that limited supervision can build complete NER systems. On standard evaluation corpora, we report performances that compare to baseline supervised systems in the task of annotating NEs in texts. \u