Text Analysis System Research Articles

Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium.

To develop scalable informatics infrastructure for normalization of both structured and unstructured electronic health record (EHR) data into a unified, concept-based model for high-throughput phenotype extraction. Software tools and applications were developed to extract information from EHRs. Representative and convenience samples of both structured and unstructured data from two EHR systems-Mayo Clinic and Intermountain Healthcare-were used for development and validation. Extracted information was standardized and normalized to meaningful use (MU) conformant terminology and value set standards using Clinical Element Models (CEMs). These resources were used to demonstrate semi-automatic execution of MU clinical-quality measures modeled using the Quality Data Model (QDM) and an open-source rules engine. Using CEMs and open-source natural language processing and terminology services engines-namely, Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) and Common Terminology Services (CTS2)-we developed a data-normalization platform that ensures data security, end-to-end connectivity, and reliable data flow within and across institutions. We demonstrated the applicability of this platform by executing a QDM-based MU quality measure that determines the percentage of patients between 18 and 75 years with diabetes whose most recent low-density lipoprotein cholesterol test result during the measurement year was <100 mg/dL on a randomly selected cohort of 273 Mayo Clinic patients. The platform identified 21 and 18 patients for the denominator and numerator of the quality measure, respectively. Validation results indicate that all identified patients meet the QDM-based criteria. End-to-end automated systems for extracting clinical information from diverse EHR systems require extensive use of standardized vocabularies and terminologies, as well as robust information models for storing, discovering, and processing that information. This study demonstrates the application of modular and open-source resources for enabling secondary use of EHR data through normalization into standards-based, comparable, and consistent format for high-throughput phenotyping to identify patient cohorts.

An Interactive System for Visual Analytics of Dynamic Topic Models

The vast amount and rapid growth of data on the Web and in document repositories make knowledge extraction and trend analysis a challenging task. A well-proven approach for the unsupervised analysis of large text corpora is dynamic topic modeling. While there is a solid body of research on fundamentals and applications of this technique, visual-interactive analysis systems for allowing end-users to perform analysis tasks using topic models are still rare. In this paper, we present D-VITA, an interactive text analysis system that exploits dynamic topic modeling to detect the latent topic structure and dynamics in a collection of documents. D-VITA supports end-users in understanding and exploiting the topic modeling results by providing interactive visualizations of the topic evolution in document collections and by browsing documents based on keyword search and similarity of their topic distributions. The system was evaluated by a scientific community that used D-VITA for trend analysis in their data sources. The results indicate high usability of D-VITA and its usefulness for productive analysis tasks.

Time Trends in Printed News Coverage of Female Subjects, 1880–2008

Former studies have suggested that female subjects are substantially underrepresented in most media. However, no study has systematically investigated historical trends in women's coverage over the last century. We use data collected by the Lydia text analysis system to assess the development in the coverage of female subjects in 13 daily newspapers, dating back to 1880. Our trend analysis shows that female subjects' representation has remained relatively low throughout modern history. Following a temporary rise during the 1930s, it declined until the 1960s, and then showed a modest uptake in recent decades. The data further demonstrate that no newspaper section comes even close to equality between male and female names.

Knowledge-based biomedical word sense disambiguation: an evaluation and application to clinical document classification

Word sense disambiguation (WSD) methods automatically assign an unambiguous concept to an ambiguous term based on context, and are important to many text-processing tasks. In this study we developed and evaluated a knowledge-based WSD method that uses semantic similarity measures derived from the Unified Medical Language System (UMLS) and evaluated the contribution of WSD to clinical text classification. We evaluated our system on biomedical WSD datasets and determined the contribution of our WSD system to clinical document classification on the 2007 Computational Medicine Challenge corpus. Our system compared favorably with other knowledge-based methods. Machine learning classifiers trained on disambiguated concepts significantly outperformed those trained using all concepts. We developed a WSD system that achieves high disambiguation accuracy on standard biomedical WSD datasets and showed that our WSD system improves clinical document classification. We integrated our WSD system with MetaMap and the clinical Text Analysis and Knowledge Extraction System, two popular biomedical natural language processing systems. All codes required to reproduce our results and all tools developed as part of this study are released as open source, available under http://code.google.com/p/ytex.

Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records.

ObjectiveWe aimed to mine the data in the Electronic Medical Record to automatically discover patients' Rheumatoid Arthritis disease activity at discrete rheumatology clinic visits. We cast the problem as a document classification task where the feature space includes concepts from the clinical narrative and lab values as stored in the Electronic Medical Record.Materials and MethodsThe Training Set consisted of 2792 clinical notes and associated lab values. Test Set 1 included 1749 clinical notes and associated lab values. Test Set 2 included 344 clinical notes for which there were no associated lab values. The Apache clinical Text Analysis and Knowledge Extraction System was used to analyze the text and transform it into informative features to be combined with relevant lab values.ResultsExperiments over a range of machine learning algorithms and features were conducted. The best performing combination was linear kernel Support Vector Machines with Unified Medical Language System Concept Unique Identifier features with feature selection and lab values. The Area Under the Receiver Operating Characteristic Curve (AUC) is 0.831 (σ = 0.0317), statistically significant as compared to two baselines (AUC = 0.758, σ = 0.0291). Algorithms demonstrated superior performance on cases clinically defined as extreme categories of disease activity (Remission and High) compared to those defined as intermediate categories (Moderate and Low) and included laboratory data on inflammatory markers.ConclusionAutomatic Rheumatoid Arthritis disease activity discovery from Electronic Medical Record data is a learnable task approximating human performance. As a result, this approach might have several research applications, such as the identification of patients for genome-wide pharmacogenetic studies that require large sample sizes with precise definitions of disease activity and response to therapies.

Navigating an imagined Middle&amp;ndash;earth: Finding and analyzing text&amp;ndash;based and film&amp;ndash;based mental images of Middle&amp;ndash;earth through TheOneRing.net online fan community

The proliferation of social media brings new opportunities to discover the ways in which we receive, process, and disseminate information — even information that seems confined to our imaginations. Mental imagery — those images we create in our imaginations as we read a text or watch a film — is not well understood. Netlytic, a Web-based system for automated text analysis, permitted the capture and analysis of online discussions relating to mental images of J.R.R. Tolkien’s and Peter Jackson’s The Lord of the Rings as text and as film adaptation, giving insight to our understanding of mental imagery as a form of human cognition and information processing. Furthermore, this study serves as a starting point for further development of academic research using Web-based text analysis systems and online communities.

Getting More Out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics

This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/outcome models in the UK's largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors' own group) who work in text processing for biomedicine and other areas. GATE is available online <1> under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis.

A common type system for clinical natural language processing

BackgroundOne challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information in clinical text to a standard representation that is comparable and interoperable. Information may be processed and shared when a type system specifies the allowable data structures. Therefore, we aim to define a common type system for clinical NLP that enables interoperability between structured and unstructured data generated in different clinical settings.ResultsWe describe a common type system for clinical NLP that has an end target of deep semantics based on Clinical Element Models (CEMs), thus interoperating with structured data and accommodating diverse NLP approaches. The type system has been implemented in UIMA (Unstructured Information Management Architecture) and is fully functional in a popular open-source clinical NLP system, cTAKES (clinical Text Analysis and Knowledge Extraction System) versions 2.0 and later.ConclusionsWe have created a type system that targets deep semantics, thereby allowing for NLP systems to encapsulate knowledge from text and share it alongside heterogenous clinical data sources. Rather than surface semantics that are typically the end product of NLP algorithms, CEM-based semantics explicitly build in deep clinical semantics as the point of interoperability with more structured data types.

Methods for dictionary generation

A classification of lexicographic resources is proposed to support automatic textanalysis systems. Four types of dictionaries are distinguished and described, namely, terminological, terminological-statistical, thesauri, and ontologies. Methods for dictionary generation are divided into static and dynamic, as well as linear and stepwise. Methods for weighting terms are divided into intertextual and intratextual. The features of the TF*IDF algorithm are considered in detail. Two techniques for dictionary generation are described.

Argo: an integrative, interactive, text mining-based workbench supporting curation

Curation of biomedical literature is often supported by the automatic analysis of textual content that generally involves a sequence of individual processing components. Text mining (TM) has been used to enhance the process of manual biocuration, but has been focused on specific databases and tasks rather than an environment integrating TM tools into the curation pipeline, catering for a variety of tasks, types of information and applications. Processing components usually come from different sources and often lack interoperability. The well established Unstructured Information Management Architecture is a framework that addresses interoperability by defining common data structures and interfaces. However, most of the efforts are targeted towards software developers and are not suitable for curators, or are otherwise inconvenient to use on a higher level of abstraction. To overcome these issues we introduce Argo, an interoperable, integrative, interactive and collaborative system for text analysis with a convenient graphic user interface to ease the development of processing workflows and boost productivity in labour-intensive manual curation. Robust, scalable text analytics follow a modular approach, adopting component modules for distinct levels of text analysis. The user interface is available entirely through a web browser that saves the user from going through often complicated and platform-dependent installation procedures. Argo comes with a predefined set of processing components commonly used in text analysis, while giving the users the ability to deposit their own components. The system accommodates various areas and levels of user expertise, from TM and computational linguistics to ontology-based curation. One of the key functionalities of Argo is its ability to seamlessly incorporate user-interactive components, such as manual annotation editors, into otherwise completely automatic pipelines. As a use case, we demonstrate the functionality of an in-built manual annotation editor that is well suited for in-text corpus annotation tasks.Database URL: http://www.nactem.ac.uk/Argo

A system for coreference resolution for the clinical narrative

To research computational methods for coreference resolution in the clinical narrative and build a system implementing the best methods. The Ontology Development and Information Extraction corpus annotated for coreference relations consists of 7214 coreferential markables, forming 5992 pairs and 1304 chains. We trained classifiers with semantic, syntactic, and surface features pruned by feature selection. For the three system components--for the resolution of relative pronouns, personal pronouns, and noun phrases--we experimented with support vector machines with linear and radial basis function (RBF) kernels, decision trees, and perceptrons. Evaluation of algorithms and varied feature sets was performed using standard metrics. The best performing combination is support vector machines with an RBF kernel and all features (MUC score=0.352, B(3)=0.690, CEAF=0.486, BLANC=0.596) outperforming a traditional decision tree baseline. The application showed good performance similar to performance on general English text. The main error source was sentence distances exceeding a window of 10 sentences between markables. A possible solution to this problem is hinted at by the fact that coreferent markables sometimes occurred in predictable (although distant) note sections. Another system limitation is failure to fully utilize synonymy and ontological knowledge. Future work will investigate additional ways to incorporate syntactic features into the coreference problem. We investigated computational methods for coreference resolution in the clinical narrative. The best methods are released as modules of the open source Clinical Text Analysis and Knowledge Extraction System and Ontology Development and Information Extraction platforms.

Automated discovery of drug treatment patterns for endocrine therapy of breast cancer within an electronic medical record

To develop an algorithm for the discovery of drug treatment patterns for endocrine breast cancer therapy within an electronic medical record and to test the hypothesis that information extracted using it is comparable to the information found by traditional methods. The electronic medical charts of 1507 patients diagnosed with histologically confirmed primary invasive breast cancer. The automatic drug treatment classification tool consisted of components for: (1) extraction of drug treatment-relevant information from clinical narratives using natural language processing (clinical Text Analysis and Knowledge Extraction System); (2) extraction of drug treatment data from an electronic prescribing system; (3) merging information to create a patient treatment timeline; and (4) final classification logic. Agreement between results from the algorithm and from a nurse abstractor is measured for categories: (0) no tamoxifen or aromatase inhibitor (AI) treatment; (1) tamoxifen only; (2) AI only; (3) tamoxifen before AI; (4) AI before tamoxifen; (5) multiple AIs and tamoxifen cycles in no specific order; and (6) no specific treatment dates. Specificity (all categories): 96.14%-100%; sensitivity (categories (0)-(4)): 90.27%-99.83%; sensitivity (categories (5)-(6)): 0-23.53%; positive predictive values: 80%-97.38%; negative predictive values: 96.91%-99.93%. Our approach illustrates a secondary use of the electronic medical record. The main challenge is event temporality. We present an algorithm for automated treatment classification within an electronic medical record to combine information extracted through natural language processing with that extracted from structured databases. The algorithm has high specificity for all categories, high sensitivity for five categories, and low sensitivity for two categories.

The Yale cTAKES extensions for document classification: architecture and application.

Open-source clinical natural-language-processing (NLP) systems have lowered the barrier to the development of effective clinical document classification systems. Clinical natural-language-processing systems annotate the syntax and semantics of clinical text; however, feature extraction and representation for document classification pose technical challenges. The authors developed extensions to the clinical Text Analysis and Knowledge Extraction System (cTAKES) that simplify feature extraction, experimentation with various feature representations, and the development of both rule and machine-learning based document classifiers. The authors describe and evaluate their system, the Yale cTAKES Extensions (YTEX), on the classification of radiology reports that contain findings suggestive of hepatic decompensation. The F(1)-Score of the system for the retrieval of abdominal radiology reports was 96%, and was 79%, 91%, and 95% for the presence of liver masses, ascites, and varices, respectively. The authors released YTEX as open source, available at http://code.google.com/p/ytex.

An evaluation of text analysis technologies

A performance evaluation of 15 text-analysis systems was recently conducted to realistically assess the state of the art for detailed information extraction from unconstrained continuous text. Reports associated with terrorism were chosen as the target domain, and all systems were tested on a collection of previously unseen texts released by a government agency. Based on multiple strategies for computing each metric, the competing systems were evaluated for recall, precision, and overgeneration. The results support the claim that systems incorporating natural language-processing techniques are more effective than systems based on stochastic techniques alone. A wide range of language-processing strategies was employed by the top-scoring systems, indicating that many natural language-processing techniques provide a viable foundation for sophisticated text analysis. Further evaluation is needed to produce a more detailed assessment of the relative merits of specific technologies and establish true performance limits for automated information extraction.

GENERATING AUTOMATED TEXT COMPLEXITY CLASSIFICATIONS THAT ARE ALIGNED WITH TARGETED TEXT COMPLEXITY STANDARDS

ABSTRACTThe Common Core Standards call for students to be exposed to a much greater level of text complexity than has been the norm in schools for the past forty years. Textbook publishers, teachers, and assessment developers are being asked to refocus materials and methods to ensure that students are challenged to read texts at steadily increasing complexity levels as they progress through school so that all students remain on track to achieve college and career readiness by the end of 12th grade. Although automated text analysis tools have been proposed as one method for helping educators achieve this goal, research suggests that existing tools are subject to three limitations: inadequate construct coverage; overly narrow criterion variables; and inappropriate treatment of genre effects. Modeling approaches developed to address these limitations are described. Recommended approaches are incorporated into a new text analysis system called SourceRater. Validity analyses implemented on an independent sample of texts suggest that, compared to existing approaches, SourceRater's estimates of text complexity are more reflective of the complexity classifications given in the new Standards. Implications for the development of learning progressions designed to help educators organize curriculum, instruction and assessment in reading are discussed.

Using Computational Techniques to Fill the Gap between Qualitative Data Analysis and Text Analytics

The recent mass digitization of text data has led to a need to efficiently and effectively deal with the mountain of textual data that is generated. Digitized text is increasingly in the form of digitized data flows (Brent, 2008). Digitized data flows are non-static streams of generated content – including twitter, electronic news, etc. An oft-cited statistic is that currently 85% of all business data is in the form of text (cited in Hotho, Nürnberger &amp; Paass, 2005). This mountain of data leads us to the question whether the labor-intensive traditional qualitative data analysis techniques are best suited for this large amount of data. Other techniques for dealing with large amounts of data may also be found wanting because those techniques remove the researcher from an immersion in the data. Both dealing with large amounts of data and allowing immersion in data are clearly desired features of any text analysis system.

Trading Strategies to Exploit Blog and News Sentiment

We use quantitative media (blogs, and news as a comparison) data generated by a large-scale natural language processing (NLP) text analysis system to perform a comprehensive and comparative study on how company related news variables anticipates or reflects the company's stock trading volumes and financial returns. Building on our findings, we give a sentiment-based market-neutral trading strategy which gives consistently favorable returns with low volatility over a long period. Our results are significant in confirming the performance of general blog and news sentiment analysis methods over broad domains and sources. Moreover, several remarkable differences between news and blogs are also identified.

CyberGate: A Design Framework and System for Text Analysis of Computer-Mediated Communication

Content analysis of computer-mediated communication (CMC) is important for evaluating the effectiveness of electronic communication in various organizational settings. CMC text analysis relies on systems capable of providing suitable navigation and knowledge discovery functionalities. However, existing CMC systems focus on structural features, with little support for features derived from message text. This deficiency is attributable to the informational richness and representational complexities associated with CMC text. In order to address this shortcoming, we propose a design framework for CMC text analysis systems. Grounded in systemic functional linguistic theory, the proposed framework advocates the development of systems capable of representing the rich array of information types inherent in CMC text. It also provides guidelines regarding the choice of features, feature selection, and visualization techniques that CMC text analysis systems should employ. The CyberGate system was developed as an instantiation of the design framework. CyberGate incorporates a rich feature set and complementary feature selection and visualization methods, including the writeprints and ink blots techniques. An application example was used to illustrate the system's ability to discern important patterns in CMC text. Furthermore, results from numerous experiments conducted in comparison with benchmark methods confirmed the viability of CyberGate's features and techniques. The results revealed that the CyberGate system and its underlying design framework can dramatically improve CMC text analysis capabilities over those provided by existing systems.

TOWARDS A SYSTEMATIC EVALUATION OF PROTEIN MUTATION EXTRACTION SYSTEMS

The development of text analysis systems targeting the extraction of information about mutations from research publications is an emergent topic in biomedical research. Current systems differ in both scope and approach, thus preventing a meaningful comparison of their performance and therefore possible synergies. To overcome this evaluation bottleneck, we developed a comprehensive framework for the systematic analysis of mutation extraction systems, precisely defining tasks and corresponding evaluation metrics, that will allow a comparison of existing and future applications.

Text analytics for life science using the Unstructured Information Management Architecture

Biomedical text plays a fundamental role in knowledge discovery in life science, in both basic research (in the field of bioinformatics) and in industry sectors devoted to improving medical practice, drug development, and health care (such as medical informatics, clinical genomics, and other sectors). Several groups in the IBM Research Division are collaborating on the development of a prototype system for text analysis, search, and text-mining methods to support problem solving in life science. The system is called (Biological Text Knowledge Services), and it integrates research technologies from multiple IBM Research labs. BioTeKS is also the first major application of the UIMA (Unstructured Information Management Architecture) initiative also emerging from IBM Research. BioTeKS is intended to analyze biomedical text such as MEDLINETM abstracts, medical records, and patents; text is analyzed by automatically identifying terms or names corresponding to key biomedical entities (e.g., genes, proteins, compounds, or drugs) and concepts or facts related to them. In this paper, we describe the value of text analysis in biomedical research, the development of the BioTeKS system, and applications which demonstrate its functions.