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Using openEHR Archetypes for Automated Extraction of Numerical Information from Clinical Narratives
(2019)
Up to 80% of medical information is documented by unstructured data such as clinical reports written in natural language. Such data is called unstructured because the information it contains cannot be retrieved automatically as straightforward as from structured data. However, we assume that the use of this flexible kind of documentation will remain a substantial part of a patient’s medical record, so that clinical information systems have to deal appropriately with this type of information description. On the other hand, there are efforts to achieve semantic interoperability between clinical application systems through information modelling concepts like HL7 FHIR or openEHR. Considering this, we propose an approach to transform unstructured documented information into openEHR archetypes. Furthermore, we aim to support the field of clinical text mining by recognizing and publishing the connections between openEHR archetypes and heterogeneous phrasings. We have evaluated our method by extracting the values to three openEHR archetypes from unstructured documents in English and German language.
In der vorliegenden Masterarbeit geht es um die automatische Annotation von Bildern mithilfe der Kategoriesystematik der Wikipedia. Die Annotation soll anhand der Bildbeschriftungen und ihren Textreferenzen erfolgen. Hierbei wird für vorhandene Bilder eine passende Kategorie vorgeschlagen. Es handelt sich bei den Bildern um Abbildungen aus naturwissenschaftlichen Artikeln, die in Open Access Journals veröffentlicht wurden. Ziel der Arbeit ist es, ein konzeptionelles Verfahren zu erarbeiten, dieses anhand einer ausgewählten Anzahl von Bildern durchzuführen und zu evaluieren. Die Abbildungen sollen für weitere Forschungsarbeiten und für die Projekte der Wikimedia Foundation zur Verfügung stehen. Das Annotationsverfahren findet im Projekt NOA - Nachnutzung von Open Access Abbildungen Verwendung.
Regional knowledge map is a tool recently demanded by some actors in an institutional level to help regional policy and innovation in a territory. Besides, knowledge maps facilitate the interaction between the actors of a territory and the collective learning. This paper reports the work in progress of a research project which objective is to define a methodology to efficiently design territorial knowledge maps, by extracting information of big volumes of data contained in diverse sources of information related to a region. Knowledge maps facilitate management of the intellectual capital in organisations. This paper investigates the value to apply this tool to a territorial region to manage the structures, infrastructures and the resources to enable regional innovation and regional development. Their design involves the identification of information sources that are required to find which knowledge is located in a territory, which actors are involved in innovation, and which is the context to develop this innovation (structures, infrastructures, resources and social capital). This paper summarizes the theoretical background and framework for the design of a methodology for the construction of knowledge maps, and gives an overview of the main challenges for the design of regional knowledge maps.
Legal documents often have a complex layout with many different headings, headers and footers, side notes, etc. For the further processing, it is important to extract these individual components correctly from a legally binding document, for example a signed PDF. A common approach to do so is to classify each (text) region of a page using its geometric and textual features. This approach works well, when the training and test data have a similar structure and when the documents of a collection to be analyzed have a rather uniform layout. We show that the use of global page properties can improve the accuracy of text element classification: we first classify each page into one of three layout types. After that, we can train a classifier for each of the three page types and thereby improve the accuracy on a manually annotated collection of 70 legal documents consisting of 20,938 text elements. When we split by page type, we achieve an improvement from 0.95 to 0.98 for single-column pages with left marginalia and from 0.95 to 0.96 for double-column pages. We developed our own feature-based method for page layout detection, which we benchmark against a standard implementation of a CNN image classifier. The approach presented here is based on corpus of freely available German contracts and general terms and conditions.
Both the corpus and all manual annotations are made freely available. The method is language agnostic.
Generalisierte Rechtsdokumente, bei denen für die individuellen Ausprägungen eines Vertrages die Positionen im Text bekannt sind, können eingesetzt werden, um erstens das Genehmigungsverfahren von Neuverträgen automatisiert zu unterstützen und zweitens als Vertragsgenerator neue Rechtsdokumente vorausgewählt zur Verfügung zu stellen. In diesem Beitrag wird, mithilfe von bekannten juristischen Texten gezeigt, wie formelhafte Textabschnitte identifiziert und häufige individuelle Ausprägungen klassifiziert werden können, um als Musterabschnitte eingesetzt zu werden. Es werden Einsatzbereiche vorgestellt und vorhandenes Potential für Legal Tech-Anwendungen aufgezeigt.
Regional Innovation Systems describe the relations between actors, structures and infrastructures in a region in order to stimulate innovation and regional development. For these systems the collection and organization of information is crucial. In the present paper we investigate the possibilities to extract information from websites of companies. First we describe regional innovation systems and the information types that are necessary to create them. Then we discuss the possibilities of text mining and keyword extraction techniques to extract this information from company websites. Finally, we describe a small scale experiment in which keywords related to economic sectors and commodities are extracted from the websites of over 200 companies. This experiment shows what the main challenges are for information extraction from websites for regional innovation systems.
Das Thema dieser Bachelorarbeit ist die automatische Generierung von Notationen der Dewey-Dezimalklassifikation für Metadaten. Die Metadaten sind im Dublin-Core-Format und stammen vom Server für wissenschaftliche Schriften der Hochschule Hannover. Zu Beginn erfolgt eine allgemeine Einführung über die Methoden und Hauptanwendungsbereiche des automatischen Klassifizierens. Danach werden die Dewey-Dezimalklassifikation und der Prozess der Metadatengewinnung beschrieben. Der theoretische Teil endet mit der Beschreibung von zwei Projekten. In dem ersten Projekt wurde ebenfalls versucht Metadaten mit Notationen der Dewey-Dezimalklassifikation anzureichern. Das Ergebnis des zweiten Projekts ist eine Konkordanz zwischen der Schlagwortnormdatei und der Dewey-Dezimalklassifikation. Diese Konkordanz wurde im praktischen Teil dieser Arbeit dazu benutzt um automatisch Notationen der Dewey-Dezimalklassifikation zu vergeben.
Automatic classification of scientific records using the German Subject Heading Authority File (SWD)
(2012)
The following paper deals with an automatic text classification method which does not require training documents. For this method the German Subject Heading Authority File (SWD), provided by the linked data service of the German National Library is used. Recently the SWD was enriched with notations of the Dewey Decimal Classification (DDC). In consequence it became possible to utilize the subject headings as textual representations for the notations of the DDC. Basically, we we derive the classification of a text from the classification of the words in the text given by the thesaurus. The method was tested by classifying 3826 OAI-Records from 7 different repositories. Mean reciprocal rank and recall were chosen as evaluation measure. Direct comparison to a machine learning method has shown that this method is definitely competitive. Thus we can conclude that the enriched version of the SWD provides high quality information with a broad coverage for classification of German scientific articles.
Purpose: Radiology reports mostly contain free-text, which makes it challenging to obtain structured data. Natural language processing (NLP) techniques transform free-text reports into machine-readable document vectors that are important for creating reliable, scalable methods for data analysis. The aim of this study is to classify unstructured radiograph reports according to fractures of the distal fibula and to find the best text mining method.
Materials & Methods: We established a novel German language report dataset: a designated search engine was used to identify radiographs of the ankle and the reports were manually labeled according to fractures of the distal fibula. This data was used to establish a machine learning pipeline, which implemented the text representation methods bag-of-words (BOW), term frequency-inverse document frequency (TF-IDF), principal component analysis (PCA), non-negative matrix factorization (NMF), latent Dirichlet allocation (LDA), and document embedding (doc2vec). The extracted document vectors were used to train neural networks (NN), support vector machines (SVM), and logistic regression (LR) to recognize distal fibula fractures. The results were compared via cross-tabulations of the accuracy (acc) and area under the curve (AUC).
Results: In total, 3268 radiograph reports were included, of which 1076 described a fracture of the distal fibula. Comparison of the text representation methods showed that BOW achieved the best results (AUC = 0.98; acc = 0.97), followed by TF-IDF (AUC = 0.97; acc = 0.96), NMF (AUC = 0.93; acc = 0.92), PCA (AUC = 0.92; acc = 0.9), LDA (AUC = 0.91; acc = 0.89) and doc2vec (AUC = 0.9; acc = 0.88). When comparing the different classifiers, NN (AUC = 0,91) proved to be superior to SVM (AUC = 0,87) and LR (AUC = 0,85).
Conclusion: An automated classification of unstructured reports of radiographs of the ankle can reliably detect findings of fractures of the distal fibula. A particularly suitable feature extraction method is the BOW model.
Key Points:
- The aim was to classify unstructured radiograph reports according to distal fibula fractures.
- Our automated classification system can reliably detect fractures of the distal fibula.
- A particularly suitable feature extraction method is the BOW model.