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Clinical Decision Support (CDS) can be regarded as an information retrieval (IR) task, where medical records are used to retrieve the full-text biomedical articles to satisfy the information needs from physicians, aiming at better medical solutions. Recent attempts have introduced the advances of deep learning by employing neural IR methods for CDS, where, however, only the document-query relationship...
In molecular biology, phenotypes are often described using complex semantics and diverse biomedical expressions, thereby facilitating the development of named entity recognition (NER). Here, we propose a novel approach of recognizing plant phenotypes by cascading word embedding to sentence embedding with a class label enhancement. We utilized a word embedding method to find high-frequency phenotypes...
Biomedical semantic indexing refers to annotating biomedical citations with Medical Subject Headings, which is crucial for texting mining, information retrieval and other researches in the field of bioinformatics. The traditional methods ignore the relations among labels and need complicated feature engineering. In this paper, we present a novel model with a deep serial multi-task learning structure,...
In this paper, we propose a modeling and validation method for the communicating embedded systems. The approach consists of three steps. The first one introduces a SysML semi-formal representation of connected systems by extending the UML meta-model with a connectivity profile. The second step performs an automatic transformation from the semi-formal modeling represented in SysML, towards a formal...
SysML is a prominent standard serving model-based system design for systems-of-systems (SoS). It facilitates the description of complex system design, as a hierarchy of interacting system components, while at the same time enables the independent description of each component behaviour. However, in order for the system designer to decide whether a SoS architecture is efficient, non-functional properties,...
Enterprises are increasingly being exposed to a number of changes stemming from the overall business environment and their collaborative network of users and partners. Current techniques and models created by using standard frameworks such as Enterprise Architecture are not able to cover relevant design aspects required for service interactions, thus new design elements and aspects stemming from new...
Traditionally, product configuration and production configuration processes are executed separately by different stakeholders in different phases of the product life cycle. With increasing demand for individualized products, the need for flexible production processes, modular factories and intelligent production infrastructures is also increasing. Therefore, the production environment must be continuously...
The Unified Modeling Language (UML) is a modeling language standardized by the OMG. The goal of UML is to supply software engineers, software developers, and system architects with tools for analysis, design, and implementation of software-based systems as well as for modeling business and similar processes. However, UML semantics is not formally defined. On the other hand, Colored Petri nets models...
This article describes an approach for the instantiation of Information and Communication Technology (ICT) system models suitable for distributed multi-domain system models executed by smart grid co-simulation environments. The main focus of the work concentrates on presenting and applying a transformation process that enables to transform electrical grid descriptions into correlating network description...
The document indexing is a fairly sensitive phase in the information retrieval. However, terms presented in a document are not sufficient to completely represent it. Then, the exploitation of the implicit information, through external resources, is necessary for better indexing. For this purpose, a new indexing model for biomedical documents based on description logics has been proposed to generate...
Model comparison is an important challenge in model-driven engineering, with many application areas such as model versioning and domain model recovery. There are numerous techniques that address this challenge in the literature, ranging from graph-based to linguistic ones. Most of these involve pairwise comparison, which might work, e.g. for model versioning with a small number of models to consider...
Virtual worlds and avatar-based interactive computer games are a hype among consumers and researchers for many years now. In recent years, such games on mobile devices also became increasingly important. However, most virtual worlds require the use of proprietary clients and authoring environments and lack portability, which limits their usefulness for targeting wider audiences like e.g. in consumer...
This paper presents a novel methodology for deriving Conceptual Data Models in the scope of Model-based Systems Engineering. Based on an assessment of currently employed methodologies, substantial limitations of the state of the art are identified. Consequently, a new methodology, overcoming present shortcomings, is elaborated, containing detailed and prescriptive guidelines for deriving conceptual...
Privacy is a major quality attribute of any software. Since personal data of users are collected, stored, processed, and transferred by the applications they use, they need to be assured that proper data protection is in place. Since privacy principles should be taken into account and incorporated into application design, this paper aims to promote privacy by design and presents a development of privacy...
The adoption of model based systems engineering takes models and puts them front and center to support all systems engineering activities. The majority of the models are static models describing some aspects concerning the structure of the system. This paper addresses the question of what makes a good model. The paper discusses modeling languages and how quality is defined and measured in software...
The transcription factor NF-κB is a biological component that is central to the regulation of genes involved in the innate immune system. Dysregulation of the pathway is known to be involved in a large number of inflammatory diseases. Although considerable research has been performed since its discovery in 1986, we are still not in a position to control the signalling pathway, and thus limit the effects...
Modeling languages, just as all software artifacts, evolve. This poses the risk that legacy models of a company get lost, when they become incompatible with the new language version. To address this risk, a multitude of approaches for metamodel-model co-evolution were proposed in the last 10 years. However, the high number of solutions makes it difficult for practitioners to choose an appropriate...
A key open question in the area of software modeling is which costs and benefits it brings to software development and maintenance. For answering this question, better empirical studies into software modeling are needed. In this paper I focus on what I believe are the pitfalls in- and prospects for such types of studies. This paper is an abstract for an invited keynote at the Modeling in Software...
The Unified Modeling Language (UML) is widely taught in academia and has good acceptance in industry. However, there is not an ample dataset of UML diagrams publicly available. Our aim is to offer a dataset of UML files, together with meta-data of the software projects where the UML files belong to. Therefore, we have systematically mined over 12 million GitHub projects to find UML files in them....
When designing cloud applications many decisions must be made like the selection of the right set of software components. Often, there are several third-party implementations on the market from which software architects have the choice between several solutions that are functionally very similar. Even though they are comparable in functionality, the solutions differ in their quality attributes, and...
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