Use of Domain Knowledge in the Automatic Extraction of Structured Representations from Patient-Related Texts

2010 ◽  
pp. 14-27 ◽  
Author(s):  
Galia Angelova
Keyword(s):  
Domain Knowledge ◽  
Automatic Extraction ◽  
Structured Representations

Exploiting Latent Semantic Subspaces to Derive Associations for Specific Pharmaceutical Semantics

2020 ◽  
Vol 5 (4) ◽  
pp. 333-345
Author(s):  
Janus Wawrzinek ◽  
José María González Pinto ◽  
Oliver Wiehr ◽  
Wolf-Tilo Balke
Keyword(s):  
Domain Knowledge ◽  
State Of The Art ◽  
Drug Repositioning ◽  
Hypothesis Generation ◽  
Semantic Relations ◽  
Automatic Extraction ◽  
Biomedical Domain ◽  
Important Research ◽  
Disease Associations ◽  
Active Substances

Abstract State-of-the-art approaches in the field of neural embedding models (NEMs) enable progress in the automatic extraction and prediction of semantic relations between important entities like active substances, diseases, and genes. In particular, the prediction property is making them valuable for important research-related tasks such as hypothesis generation and drug repositioning. A core challenge in the biomedical domain is to have interpretable semantics from NEMs that can distinguish, for instance, between the following two situations: (a) drug x induces disease y and (b) drug x treats disease y. However, NEMs alone cannot distinguish between associations such as treats or induces. Is it possible to develop a model to learn a latent representation from the NEMs capable of such disambiguation? To what extent do we need domain knowledge to succeed in the task? In this paper, we answer both questions and show that our proposed approach not only succeeds in the disambiguation task but also advances current growing research efforts to find real predictions using a sophisticated retrospective analysis. Furthermore, we investigate which type of associations is generally better contextualized and therefore probably has a stronger influence in our disambiguation task. In this context, we present an approach to extract an interpretable latent semantic subspace from the original embedding space in which therapeutic drug–disease associations are more likely .

Automatic Extraction of Locations from News Articles Using Domain Knowledge

2020 ◽  
pp. 36-47
Author(s):  
Loitongbam Sanayai Meetei ◽  
Ringki Das ◽  
Thoudam Doren Singh ◽  
Sivaji Bandyopadhyay
Keyword(s):  
Domain Knowledge ◽  
Automatic Extraction

Extracting ontological knowledge from Java source code using Hidden Markov Models

2019 ◽  
Vol 9 (1) ◽  
pp. 181-199 ◽  
Author(s):  
Azanzi Jiomekong ◽  
Gaoussou Camara ◽  
Maurice Tchuente
Keyword(s):  
Hidden Markov Models ◽  
Domain Knowledge ◽  
Markov Models ◽  
Hidden Markov ◽  
Source Code ◽  
Epidemiological Surveillance ◽  
Automatic Extraction ◽  
Knowledge Sources ◽  
Terminology Extraction ◽  
Domain Experts

AbstractOntologies have become a key element since many decades in information systems such as in epidemiological surveillance domain. Building domain ontologies requires the access to domain knowledge owned by domain experts or contained in knowledge sources. However, domain experts are not always available for interviews. Therefore, there is a lot of value in using ontology learning which consists in automatic or semi-automatic extraction of ontological knowledge from structured or unstructured knowledge sources such as texts, databases, etc. Many techniques have been used but they all are limited in concepts, properties and terminology extraction leaving behind axioms and rules. Source code which naturally embed domain knowledge is rarely used. In this paper, we propose an approach based on Hidden Markov Models (HMMs) for concepts, properties, axioms and rules learning from Java source code. This approach is experimented with the source code of EPICAM, an epidemiological platform developed in Java and used in Cameroon for tuberculosis surveillance. Domain experts involved in the evaluation estimated that knowledge extracted was relevant to the domain. In addition, we performed an automatic evaluation of the relevance of the terms extracted to the medical domain by aligning them with ontologies hosted on Bioportal platform through the Ontology Recommender tool. The results were interesting since the terms extracted were covered at 82.9% by many biomedical ontologies such as NCIT, SNOWMEDCT and ONTOPARON.

Automated Assessment of Domain Knowledge With Online Knowledge Mapping

2006 ◽  
Author(s):  
Gregory K. W. K. Chung ◽  
Eva L. Baker ◽  
David G. Brill ◽  
Ravi Sinha ◽  
Farzad Saadat ◽  
...  
Keyword(s):  
Domain Knowledge ◽  
Knowledge Mapping ◽  
Automated Assessment

A Model for Structured Data Entry Based on Explicit Descriptional Knowledge

1994 ◽  
Vol 33 (05) ◽  
pp. 454-463 ◽  
Author(s):  
A. M. van Ginneken ◽  
J. van der Lei ◽  
J. H. van Bemmel ◽  
P. W. Moorman
Keyword(s):  
Domain Knowledge ◽  
Data Entry ◽  
Knowledge Bases ◽  
Structured Data ◽  
Research Quality ◽  
Free Text ◽  
Specific Knowledge ◽  
User Input ◽  
The One ◽  
Research Quality Assessment

Abstract:Clinical narratives in patient records are usually recorded in free text, limiting the use of this information for research, quality assessment, and decision support. This study focuses on the capture of clinical narratives in a structured format by supporting physicians with structured data entry (SDE). We analyzed and made explicit which requirements SDE should meet to be acceptable for the physician on the one hand, and generate unambiguous patient data on the other. Starting from these requirements, we found that in order to support SDE, the knowledge on which it is based needs to be made explicit: we refer to this knowledge as descriptional knowledge. We articulate the nature of this knowledge, and propose a model in which it can be formally represented. The model allows the construction of specific knowledge bases, each representing the knowledge needed to support SDE within a circumscribed domain. Data entry is made possible through a general entry program, of which the behavior is determined by a combination of user input and the content of the applicable domain knowledge base. We clarify how descriptional knowledge is represented, modeled, and used for data entry to achieve SDE, which meets the proposed requirements.

Classification of means and methods of the Web semantic retrieval

2017 ◽  
pp. 030-050
Author(s):  
J.V. Rogushina ◽  
Keyword(s):  
Search Engines ◽  
Domain Knowledge ◽  
Information Needs ◽  
Web Search ◽  
User Interaction ◽  
Query Languages ◽  
Semantic Search ◽  
Semantic Retrieval ◽  
The Web

Problems associated with the improve ment of information retrieval for open environment are considered and the need for it’s semantization is grounded. Thecurrent state and prospects of development of semantic search engines that are focused on the Web information resources processing are analysed, the criteria for the classification of such systems are reviewed. In this analysis the significant attention is paid to the semantic search use of ontologies that contain knowledge about the subject area and the search users. The sources of ontological knowledge and methods of their processing for the improvement of the search procedures are considered. Examples of semantic search systems that use structured query languages (eg, SPARQL), lists of keywords and queries in natural language are proposed. Such criteria for the classification of semantic search engines like architecture, coupling, transparency, user context, modification requests, ontology structure, etc. are considered. Different ways of support of semantic and otology based modification of user queries that improve the completeness and accuracy of the search are analyzed. On base of analysis of the properties of existing semantic search engines in terms of these criteria, the areas for further improvement of these systems are selected: the development of metasearch systems, semantic modification of user requests, the determination of an user-acceptable transparency level of the search procedures, flexibility of domain knowledge management tools, increasing productivity and scalability. In addition, the development of means of semantic Web search needs in use of some external knowledge base which contains knowledge about the domain of user information needs, and in providing the users with the ability to independent selection of knowledge that is used in the search process. There is necessary to take into account the history of user interaction with the retrieval system and the search context for personalization of the query results and their ordering in accordance with the user information needs. All these aspects were taken into account in the design and implementation of semantic search engine "MAIPS" that is based on an ontological model of users and resources cooperation into the Web.

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