Information Extraction System Research Articles

Koko

K oko is a declarative information extraction system that incorporates advances in natural language processing techniques in its extraction language. K oko 's extraction language supports simultaneous specification of conditions over the surface syntax and on the structure of the dependency parse tree of sentences, thereby allowing for more refined extractions. Furthermore, the K oko extraction language allows for aggregating evidence from an input document and supports conditions that are tolerant of linguistic variation of expressing concepts. In this demo, we outline the design of K oko , a system for extracting information and understanding the results of the extraction. K oko provides an interactive interface that allows participants to write queries, understand the input and results of the queries. In particular, the user can customize the input text, visualize the input text's dependency parse trees, and understand the correspondences between query components, dependency tree nodes, text tokens, and the computation and associated scores that led to an extraction.

A gene-phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach.

MotivationThe fundamental challenge of modern genetic analysis is to establish gene-phenotype correlations that are often found in the large-scale publications. Because lexical features of gene are relatively regular in text, the main challenge of these relation extraction is phenotype recognition. Due to phenotypic descriptions are often study- or author-specific, few lexicon can be used to effectively identify the entire phenotypic expressions in text, especially for plants.ResultsWe have proposed a pipeline for extracting phenotype, gene and their relations from biomedical literature. Combined with abbreviation revision and sentence template extraction, we improved the unsupervised word-embedding-to-sentence-embedding cascaded approach as representation learning to recognize the various broad phenotypic information in literature. In addition, the dictionary- and rule-based method was applied for gene recognition. Finally, we integrated one of famous information extraction system OLLIE to identify gene-phenotype relations. To demonstrate the applicability of the pipeline, we established two types of comparison experiment using model organism Arabidopsis thaliana. In the comparison of state-of-the-art baselines, our approach obtained the best performance (F1-Measure of 66.83%). We also applied the pipeline to 481 full-articles from TAIR gene-phenotype manual relationship dataset to prove the validity. The results showed that our proposed pipeline can cover 70.94% of the original dataset and add 373 new relations to expand it.Availability and implementationThe source code is available at http://www.wutbiolab.cn: 82/Gene-Phenotype-Relation-Extraction-Pipeline.zip.Supplementary information Supplementary data are available at Bioinformatics online.

Utility of social media and crowd-intelligence data for pharmacovigilance: a scoping review

BackgroundA scoping review to characterize the literature on the use of conversations in social media as a potential source of data for detecting adverse events (AEs) related to health products.MethodsOur specific research questions were (1) What social media listening platforms exist to detect adverse events related to health products, and what are their capabilities and characteristics? (2) What is the validity and reliability of data from social media for detecting these adverse events? MEDLINE, EMBASE, Cochrane Library, and relevant websites were searched from inception to May 2016. Any type of document (e.g., manuscripts, reports) that described the use of social media data for detecting health product AEs was included. Two reviewers independently screened citations and full-texts, and one reviewer and one verifier performed data abstraction. Descriptive synthesis was conducted.ResultsAfter screening 3631 citations and 321 full-texts, 70 unique documents with 7 companion reports available from 2001 to 2016 were included. Forty-six documents (66%) described an automated or semi-automated information extraction system to detect health product AEs from social media conversations (in the developmental phase). Seven pre-existing information extraction systems to mine social media data were identified in eight documents. Nineteen documents compared AEs reported in social media data with validated data and found consistent AE discovery in all except two documents. None of the documents reported the validity and reliability of the overall system, but some reported on the performance of individual steps in processing the data. The validity and reliability results were found for the following steps in the data processing pipeline: data de-identification (n = 1), concept identification (n = 3), concept normalization (n = 2), and relation extraction (n = 8). The methods varied widely, and some approaches yielded better results than others.ConclusionsOur results suggest that the use of social media conversations for pharmacovigilance is in its infancy. Although social media data has the potential to supplement data from regulatory agency databases; is able to capture less frequently reported AEs; and can identify AEs earlier than official alerts or regulatory changes, the utility and validity of the data source remains under-studied.Trial registrationOpen Science Framework (https://osf.io/kv9hu/).

Mars Target Encyclopedia: Rock and Soil Composition Extracted From the Literature

We have constructed an information extraction system called the Mars Target Encyclopedia that takes in planetary science publications and extracts scientific knowledge about target compositions. The extracted knowledge is stored in a searchable database that can greatly accelerate the ability of scientists to compare new discoveries with what is already known. To date, we have applied this system to ~6000 documents and achieved 41-56% precision in the extracted information.

Event Detection via Gated Multilingual Attention Mechanism

Identifying event instance in text plays a critical role in building NLP applications such as Information Extraction (IE) system. However, most existing methods for this task focus only on monolingual clues of a specific language and ignore the massive information provided by other languages. Data scarcity and monolingual ambiguity hinder the performance of these monolingual approaches. In this paper, we propose a novel multilingual approach---dubbed as Gated Multilingual Attention (GMLATT) framework---to address the two issues simultaneously. In specific, to alleviate data scarcity problem, we exploit the consistent information in multilingual data via context attention mechanism. Which takes advantage of the consistent evidence in multilingual data other than learning only from monolingual data. To deal with monolingual ambiguity problem, we propose gated cross-lingual attention to exploit the complement information conveyed by multilingual data, which is helpful for the disambiguation. The cross-lingual attention gate serves as a sentinel modelling the confidence of the clues provided by other languages and controls the information integration of various languages. We have conducted extensive experiments on the ACE 2005 benchmark. Experimental results show that our approach significantly outperforms state-of-the-art methods.

Content and Context: Two-Pronged Bootstrapped Learning for Regex-Formatted Entity Extraction

Regular expressions are an important building block of rule-based information extraction systems. Regexes can encode rules to recognize instances of simple entities which can then feed into the identification of more complex cross-entity relationships. Manually crafting a regex that recognizes all possible instances of an entity is difficult since an entity can manifest in a variety of different forms. Thus, the problem of automatically generalizing manually crafted seed regexes to improve the recall of IE systems has attracted research attention. In this paper, we propose a bootstrapped approach to improve the recall for extraction of regex-formatted entities, with the only source of supervision being the seed regex. Our approach starts from a manually authored high precision seed regex for the entity of interest, and uses the matches of the seed regex and the context around these matches to identify more instances of the entity. These are then used to identify a set of diverse, high recall regexes that are representative of this entity. Through an empirical evaluation over multiple real world document corpora, we illustrate the effectiveness of our approach.

Unsupervised Information Extraction from Behaviour Change Literature.

This paper describes our approach to construct a scalable system for unsupervised information extraction from the behaviour change intervention literature. Due to the many different types of attribute to be extracted, we adopt a passage retrieval based framework that provides the most likely value for an attribute. Our proposed method is capable of addressing variable length passage sizes and different validation criteria for the extracted values corresponding to each attribute to be found. We evaluate our approach by constructing a manually annotated ground-truth from a set of 50 research papers with reported studies on smoking cessation.

Learning From the Past: Uncovering Design Process Models Using an Enriched Process Mining

Design documents and design project footprints accumulated by corporate information technology systems have increasingly become valuable sources of evidence for design information and knowledge management. Identification and extraction of such embedded information and knowledge into a clear and usable format will greatly accelerate continuous learning from past design efforts for competitive product innovation and efficient design process management in future design projects. Most of the existing design information extraction systems focus on either organizing design documents for efficient retrieval or extracting relevant product information for product optimization. Different from traditional systems, this paper proposes a methodology of learning and extracting useful knowledge using past design project documents from design process perspective based on process mining techniques. Particularly different from conventional techniques that deal with timestamps or event logs only, a new process mining approach that is able to directly process textual data is proposed at the first stage of the proposed methodology. The outcome is a hierarchical process model that reveals the actual design process hidden behind a large amount of design documents and enables the connection of various design information from different perspectives. At the second stage, the discovered process model is analyzed to extract multifaceted knowledge patterns by applying a number of statistical analysis methods. The outcomes range from task dependency study from workflow analysis, identification of irregular task execution from performance analysis, cooperation pattern discovery from social net analysis to evaluation of personal contribution based on role analysis. Relying on the knowledge patterns extracted, lessons and best practices can be uncovered which offer great support to decision makers in managing any future design initiatives. The proposed methodology was tested using an email dataset from a university-hosted multiyear multidisciplinary design project.

Analytic survey of 57 cases of oral metastases.

Oral lesions have been reported among the first signs of an undiagnosed metastatic disease. Accurate diagnosis of an occult metastasis remains critical in determining the treatment course. Previous studies regarding oral metastatic tumors present varied data regarding the most frequent metastases to the oral cavity. These discrepancies echo the changes in incidence rates for certain malignancies over time and demonstrate the need for periodic updates in oral metastasis studies. Using Text Information Extraction System, a de-identified pathology database, we compiled 57 cases over a period of 19years using key terms to search for oral metastases. For both males and females, the most common primary sites were lung (21.1%), liver (12.3%), breast (10.5%), kidney (10.5%), and colorectal (8.8%). We found an equal number of lung and breast metastases in females and metastases from the liver to be the most prevalent for males. In most of our cases (54.9%), the patient had no history of the primary malignancy and the oral lesion preceded awareness of the widespread cancer. As a departure from many previous case series, we found lung and breast metastases to be equally numerous in women and liver as the most common oral metastasis in men. Also, we identified a tendency for the patient to present with a previous history in certain malignancies, such as breast cancer, whereas in other malignancies, such as renal cell carcinoma, our data demonstrated a propensity to present in the oral cavity without history of a primary tumor.

GerIE - An Open Information Extraction System for the German Language

GerIE - An Open Information Extraction System for the German Language

SemEHR: A general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research.

ObjectiveUnlocking the data contained within both structured and unstructured components of electronic health records (EHRs) has the potential to provide a step change in data available for secondary research use, generation of actionable medical insights, hospital management, and trial recruitment. To achieve this, we implemented SemEHR, an open source semantic search and analytics tool for EHRs.MethodsSemEHR implements a generic information extraction (IE) and retrieval infrastructure by identifying contextualized mentions of a wide range of biomedical concepts within EHRs. Natural language processing annotations are further assembled at the patient level and extended with EHR-specific knowledge to generate a timeline for each patient. The semantic data are serviced via ontology-based search and analytics interfaces.ResultsSemEHR has been deployed at a number of UK hospitals, including the Clinical Record Interactive Search, an anonymized replica of the EHR of the UK South London and Maudsley National Health Service Foundation Trust, one of Europe’s largest providers of mental health services. In 2 Clinical Record Interactive Search–based studies, SemEHR achieved 93% (hepatitis C) and 99% (HIV) F-measure results in identifying true positive patients. At King’s College Hospital in London, as part of the CogStack program (github.com/cogstack), SemEHR is being used to recruit patients into the UK Department of Health 100 000 Genomes Project (genomicsengland.co.uk). The validation study suggests that the tool can validate previously recruited cases and is very fast at searching phenotypes; time for recruitment criteria checking was reduced from days to minutes. Validated on open intensive care EHR data, Medical Information Mart for Intensive Care III, the vital signs extracted by SemEHR can achieve around 97% accuracy.ConclusionResults from the multiple case studies demonstrate SemEHR’s efficiency: weeks or months of work can be done within hours or minutes in some cases. SemEHR provides a more comprehensive view of patients, bringing in more and unexpected insight compared to study-oriented bespoke IE systems. SemEHR is open source, available at https://github.com/CogStack/SemEHR.

Learning Causality for Arabic - Proclitics

The use of prefixed particles is a prevalent linguistic form to express causation in Arabic Language. However, such particles are complicated and highly ambiguous as they imply different meanings according to their position in the text. This ambiguity emphasizes the high demand for a large-scale annotated corpus that contains instances of these particles. In this paper, we present the process of building our corpus, which includes a collection of annotated sentences each containing an instance of a candidate causal particle. We use the corpus to construct and optimize predictive models for the task of causation recognition. The performance of the best models is significantly better than the baselines. Arabic is a less–resourced language and we hope this work would help in building better Information Extraction systems.

Towards Knowledge Handling in Ontology-Based Information Extraction Systems

Ontologies proved to be efficient and powerful tools for gathering and sharing knowledge, providing explicit specifications of conceptualizations. However, the proper ontology construction processes and their updating of various data sources, require a huge effort and well-adjusted mechanisms to their extraction, positioning and sharing. In this context, the application of a proper Ontology-Based Information Extraction (OBIE) system may help in solving these problems. The paper is a successful attempt to purvey state-of-the-art of selected OBIE systems, followed by the process of taxonomy construction and aftermath knowledge systematization of particular OBIE approaches.

Integration of Cancer Registry Data into the Text Information Extraction System: Leveraging the Structured Data Import Tool

Introduction/Background: Cancer registries in the US collect timely and systematic data on new cancer cases, extent of disease, staging, biomarker status, treatment, survival, and mortality of cancer cases. Existing methodologies for accessing local cancer registry data for research are time-consuming and often rely on the manual merging of data by staff registrars. In addition, existing registries do not provide direct access to these data nor do they routinely provide linkage to discrete electronic health record (EHR) data, reports, or imaging data. Automation of such linkage can provide an impressive data resource and make valuable data available for translational cancer research. Methods: The UPMC Network Cancer Registry collects highly structured, longitudinal data on all reportable cancer patients, from the point of the diagnosis throughout treatment and follow-up/outcomes. Using commercial registry software, we collect data in compliance with standards governed by the North American Association of Central Cancer Registries. This standardization ensures that the data are highly structured with standard coding and collection methods, which support data exchange among central cancer registries and the Centers for Disease Control and Prevention. Results: At the UPMC Hillman Cancer Center and University of Pittsburgh, we explored the feasibility of linking this well-curated, structured cancer registry data with unstructured text (i.e., pathology and radiology reports), using the Text Information Extraction System (TIES). We used the TIES platform to integrate breast cancer cases from the UPMC Network Cancer Registry system and then combine these data with other EHR data as a pilot use case that can be replicated for other cancers. Conclusions: As a result of this integration, we now have a single searchable repository of information for breast cancer patients from the UPMC registry, combined with their pathology and radiology reports. The system that we developed is easily scalable to other health systems and cancer centers.

AUTOMATIC INFORMATION EXTRACTION FROM TEXT

We present a method for automatic extract the hyponym-hypernym relations from the text data. In previous years many researchers were worked on this system but they use some pre-encoded knowledge and patterns for implementing this type of system. But this not that much use when we think about extracting more relations or discovering any new pattern. This type of system discovered one more risk which is once we use the predefined pattern and if this pattern failed to produce new pattern then all most all operation will fail due to the previous wrong pattern. The researcher was used semi-supervised machine learning approach for introducing such kind of information extraction system but this paper focuses on converting the semi-supervised machine learning approach into unsupervised machine learning approach for fully automatic extracting information from text. This paper is trying to focus on these previous issues. The paper focuses on two main objectives. (i) Avoid pre-encoded pattern for more efficiency. (ii) Define a method for automatically extracting useful relationships from an unsupervised machine learning approach. We demonstrate a machine learning approach and, especially, at different levels and in different ways, can be used to create a practical IE system. We unsupervised machine learning approach gives the better result than semi-supervised machine learning approach in term of information extraction.

Supervised Learning and Knowledge-Based Approaches Applied to Biomedical Word Sense Disambiguation.

Word sense disambiguation (WSD) is an important step in biomedical text mining, which is responsible for assigning an unequivocal concept to an ambiguous term, improving the accuracy of biomedical information extraction systems. In this work we followed supervised and knowledge-based disambiguation approaches, with the best results obtained by supervised means. In the supervised method we used bag-of-words as local features, and word embeddings as global features. In the knowledge-based method we combined word embeddings, concept textual definitions extracted from the UMLS database, and concept association values calculated from the MeSH co-occurrence counts from MEDLINE articles. Also, in the knowledge-based method, we tested different word embedding averaging functions to calculate the surrounding context vectors, with the goal to give more importance to closest words of the ambiguous term. The MSH WSD dataset, the most common dataset used for evaluating biomedical concept disambiguation, was used to evaluate our methods. We obtained a top accuracy of 95.6 % by supervised means, while the best knowledge-based accuracy was 87.4 %. Our results show that word embedding models improved the disambiguation accuracy, proving to be a powerful resource in the WSD task.

USING MULTIPLE SEMANTIC MEASURES FOR COREFERENCE RESOLUTION IN ONTOLOGY POPULATION

The problem of populating an ontology consists in adding to it some new, domain-specific content from an input expressed, in particular, in a natural language. We focus on an important aspect in the ontology population process – finding and resolving coreferences, i.e., similar mentions of entities in the input text. Our contribution is a novel formal framework that extends the state-of-the-art approaches to coreference resolution by using multiple semantic similarity properties in the resolution process, i.e., we extend the list of the ontological properties used for coreference resolution with additional properties such as inverse, symmetry, intersection, union, etc. We use the proposed framework to improve our previously proposed algorithm for coreference resolution used in our general approach to text analysis and information extraction for populating subject domain ontologies. We describe a multi-agent implementation of our information extraction system and we show that using additional semantic similarity measures for evaluating coreferential candidates improves the quality of the coreference resolution process, especially for complex objects whose coreferencing has not been yet studied in detail.

The BigGrams: the semi-supervised information extraction system from HTML: an improvement in the wrapper induction

The aim of this study is to propose an information extraction system, called BigGrams, which is able to retrieve relevant and structural information (relevant phrases, keywords) from semi-structural web pages, i.e. HTML documents. For this purpose, a novel semi-supervised wrappers induction algorithm has been developed and embedded in the BigGrams system. The wrappers induction algorithm utilizes a formal concept analysis to induce information extraction patterns. Also, in this article, the author (1) presents the impact of the configuration of the information extraction system components on information extraction results and (2) tests the boosting mode of this system. Based on empirical research, the author established that the proposed taxonomy of seeds and the HTML tags level analysis, with appropriate pre-processing, improve information extraction results. Also, the boosting mode works well when certain requirements are met, i.e. when well-diversified input data are ensured.

Developing a cardiovascular disease risk factor annotated corpus of Chinese electronic medical records

BackgroundCardiovascular disease (CVD) has become the leading cause of death in China, and most of the cases can be prevented by controlling risk factors. The goal of this study was to build a corpus of CVD risk factor annotations based on Chinese electronic medical records (CEMRs). This corpus is intended to be used to develop a risk factor information extraction system that, in turn, can be applied as a foundation for the further study of the progress of risk factors and CVD.ResultsWe designed a light annotation task to capture CVD risk factors with indicators, temporal attributes and assertions that were explicitly or implicitly displayed in the records. The task included: 1) preparing data; 2) creating guidelines for capturing annotations (these were created with the help of clinicians); 3) proposing an annotation method including building the guidelines draft, training the annotators and updating the guidelines, and corpus construction. Meanwhile, we proposed some creative annotation guidelines: (1) the under-threshold medical examination values were annotated for our purpose of studying the progress of risk factors and CVD; (2) possible and negative risk factors were concerned for the same reason, and we created assertions for annotations; (3) we added four temporal attributes to CVD risk factors in CEMRs for constructing long term variations. Then, a risk factor annotated corpus based on de-identified discharge summaries and progress notes from 600 patients was developed. Built with the help of clinicians, this corpus has an inter-annotator agreement (IAA) F1-measure of 0.968, indicating a high reliability.ConclusionTo the best of our knowledge, this is the first annotated corpus concerning CVD risk factors in CEMRs and the guidelines for capturing CVD risk factor annotations from CEMRs were proposed. The obtained document-level annotations can be applied in future studies to monitor risk factors and CVD over the long term.

Ontology-based information extraction for juridical events with case studies in Brazilian legal realm

The number of available legal documents has presented an enormous growth in recent years, and the digital processing of such materials is prompting the necessity of systems that support the automatic relevant information extraction. This work presents a system for ontology-based information extraction from natural language texts, able to identify a set of legal events. The system is based on an innovative methodology based on domain ontology of legal events and a set of linguistic rules, integrated through inference mechanism, resulting in a flexible approach and scalable approach. A case study with the use of documents from the Superior Court in Brazil is related, with satisfactory results in precision and recall.